Starting phenix.real_space_refine on Sun Jul 5 11:22:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.cif Found real_map, /net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7qur_14152/07_2026/7qur_14152.cif" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.135 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians I 9 10.91 5 S 120 5.16 5 C 17094 2.51 5 N 4386 2.21 5 O 5565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 27174 Number of models: 1 Model: "" Number of chains: 21 Chain: "A" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "B" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "C" Number of atoms: 8611 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 Conformer: "B" Number of residues, atoms: 1101, 8594 Classifications: {'peptide': 1101} Link IDs: {'PTRANS': 49, 'TRANS': 1051} Chain breaks: 2 bond proxies already assigned to first conformer: 8772 Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 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 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 chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 chiralities: 2 Chain: "M" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "N" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "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 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 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 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 chiralities: 12 Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "B" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 93 Classifications: {'water': 93} Link IDs: {None: 92} Chain: "C" Number of atoms: 96 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 96 Classifications: {'water': 96} Link IDs: {None: 95} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N ATYR A 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR A 505 " occ=0.50 residue: pdb=" N ATYR B 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR B 505 " occ=0.50 residue: pdb=" N ATYR C 505 " occ=0.50 ... (22 atoms not shown) pdb=" OH BTYR C 505 " occ=0.50 Time building chain proxies: 10.01, per 1000 atoms: 0.37 Number of scatterers: 27174 At special positions: 0 Unit cell: (141.04, 156.62, 167.28, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) I 9 52.95 S 120 16.00 O 5565 8.00 N 4386 7.00 C 17094 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=42, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.04 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.02 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 743 " - pdb=" SG CYS A 749 " distance=2.03 Simple disulfide: pdb=" SG CYS A 840 " - pdb=" SG CYS A 851 " distance=2.03 Simple disulfide: pdb=" SG CYS A1032 " - pdb=" SG CYS A1043 " distance=2.03 Simple disulfide: pdb=" SG CYS A1082 " - pdb=" SG CYS A1126 " distance=2.03 Simple disulfide: pdb=" SG CYS B 15 " - pdb=" SG CYS B 136 " distance=2.03 Simple disulfide: pdb=" SG CYS B 131 " - pdb=" SG CYS B 166 " distance=2.04 Simple disulfide: pdb=" SG CYS B 291 " - pdb=" SG CYS B 301 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.04 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 538 " - pdb=" SG CYS B 590 " distance=2.03 Simple disulfide: pdb=" SG CYS B 617 " - pdb=" SG CYS B 649 " distance=2.03 Simple disulfide: pdb=" SG CYS B 662 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 743 " - pdb=" SG CYS B 749 " distance=2.03 Simple disulfide: pdb=" SG CYS B 840 " - pdb=" SG CYS B 851 " distance=2.03 Simple disulfide: pdb=" SG CYS B1032 " - pdb=" SG CYS B1043 " distance=2.03 Simple disulfide: pdb=" SG CYS B1082 " - pdb=" SG CYS B1126 " distance=2.03 Simple disulfide: pdb=" SG CYS C 15 " - pdb=" SG CYS C 136 " distance=2.03 Simple disulfide: pdb=" SG CYS C 131 " - pdb=" SG CYS C 166 " distance=2.04 Simple disulfide: pdb=" SG CYS C 291 " - pdb=" SG CYS C 301 " distance=2.03 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 538 " - pdb=" SG CYS C 590 " distance=2.03 Simple disulfide: pdb=" SG CYS C 617 " - pdb=" SG CYS C 649 " distance=2.02 Simple disulfide: pdb=" SG CYS C 662 " - pdb=" SG CYS C 671 " distance=2.03 Simple disulfide: pdb=" SG CYS C 743 " - pdb=" SG CYS C 749 " distance=2.03 Simple disulfide: pdb=" SG CYS C 840 " - pdb=" SG CYS C 851 " distance=2.03 Simple disulfide: pdb=" SG CYS C1032 " - pdb=" SG CYS C1043 " distance=2.03 Simple disulfide: pdb=" SG CYS C1082 " - pdb=" SG CYS C1126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-3 " NAG G 1 " - " FUC G 2 " ~> Even though FUC is an alpha isomer, a beta linkage is required... " NAG K 1 " - " FUC K 2 " " NAG O 1 " - " FUC O 2 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG K 1 " - " NAG K 3 " " NAG L 1 " - " NAG L 2 " " NAG M 1 " - " NAG M 2 " " NAG N 1 " - " NAG N 2 " " NAG O 1 " - " NAG O 3 " BETA1-6 " NAG G 1 " - " FUC G 4 " " NAG K 1 " - " FUC K 4 " " NAG O 1 " - " FUC O 4 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 122 " " NAG A1303 " - " ASN A 282 " " NAG A1304 " - " ASN A 331 " " NAG A1305 " - " ASN A 343 " " NAG A1306 " - " ASN A 616 " " NAG A1307 " - " ASN A 149 " " NAG A1308 " - " ASN A 709 " " NAG A1309 " - " ASN A1074 " " NAG A1310 " - " ASN A1098 " " NAG A1311 " - " ASN A1134 " " NAG A1312 " - " ASN A 17 " " NAG B1301 " - " ASN B 61 " " NAG B1302 " - " ASN B 122 " " NAG B1303 " - " ASN B 282 " " NAG B1304 " - " ASN B 331 " " NAG B1305 " - " ASN B 343 " " NAG B1306 " - " ASN B 616 " " NAG B1307 " - " ASN B 149 " " NAG B1308 " - " ASN B 709 " " NAG B1309 " - " ASN B1074 " " NAG B1310 " - " ASN B1098 " " NAG B1311 " - " ASN B1134 " " NAG B1312 " - " ASN B 17 " " NAG C1302 " - " ASN C 61 " " NAG C1303 " - " ASN C 122 " " NAG C1304 " - " ASN C 282 " " NAG C1305 " - " ASN C 331 " " NAG C1306 " - " ASN C 343 " " NAG C1307 " - " ASN C 616 " " NAG C1308 " - " ASN C 149 " " NAG C1309 " - " ASN C 709 " " NAG C1310 " - " ASN C1074 " " NAG C1311 " - " ASN C1098 " " NAG C1312 " - " ASN C1134 " " NAG C1313 " - " ASN C 17 " " NAG D 1 " - " ASN A 234 " " NAG E 1 " - " ASN A 717 " " NAG F 1 " - " ASN A 801 " " NAG G 1 " - " ASN A 165 " " NAG H 1 " - " ASN B 234 " " NAG I 1 " - " ASN B 717 " " NAG J 1 " - " ASN B 801 " " NAG K 1 " - " ASN B 165 " " NAG L 1 " - " ASN C 234 " " NAG M 1 " - " ASN C 717 " " NAG N 1 " - " ASN C 801 " " NAG O 1 " - " ASN C 165 " Time building additional restraints: 2.56 Conformation dependent library (CDL) restraints added in 2.3 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: 1.15 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 370 removed outlier: 3.963A pdb=" N ASN A 370 " --> pdb=" O VAL A 367 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.471A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER A 443 " --> pdb=" O ASN A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'A' and resid 737 through 744 Processing helix chain 'A' and resid 746 through 754 Processing helix chain 'A' and resid 757 through 783 removed outlier: 3.552A pdb=" N THR A 761 " --> pdb=" O GLY A 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP A 775 " --> pdb=" O ALA A 771 " (cutoff:3.500A) Processing helix chain 'A' and resid 816 through 825 Processing helix chain 'A' and resid 836 through 841 Processing helix chain 'A' and resid 843 through 848 removed outlier: 3.606A pdb=" N ARG A 847 " --> pdb=" O ASP A 843 " (cutoff:3.500A) Processing helix chain 'A' and resid 848 through 856 Processing helix chain 'A' and resid 866 through 885 Processing helix chain 'A' and resid 886 through 891 Processing helix chain 'A' and resid 897 through 909 Processing helix chain 'A' and resid 912 through 919 removed outlier: 4.001A pdb=" N LEU A 916 " --> pdb=" O THR A 912 " (cutoff:3.500A) Processing helix chain 'A' and resid 919 through 940 Processing helix chain 'A' and resid 945 through 965 removed outlier: 3.552A pdb=" N GLN A 949 " --> pdb=" O LEU A 945 " (cutoff:3.500A) Processing helix chain 'A' and resid 966 through 968 No H-bonds generated for 'chain 'A' and resid 966 through 968' Processing helix chain 'A' and resid 976 through 984 Processing helix chain 'A' and resid 985 through 1033 removed outlier: 4.016A pdb=" N VAL A 991 " --> pdb=" O VAL A 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN A 992 " --> pdb=" O GLU A 988 " (cutoff:3.500A) Processing helix chain 'B' and resid 294 through 304 Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 3.963A pdb=" N ASN B 370 " --> pdb=" O VAL B 367 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 389 removed outlier: 4.471A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'B' and resid 737 through 744 Processing helix chain 'B' and resid 746 through 754 Processing helix chain 'B' and resid 757 through 783 removed outlier: 3.553A pdb=" N THR B 761 " --> pdb=" O GLY B 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP B 775 " --> pdb=" O ALA B 771 " (cutoff:3.500A) Processing helix chain 'B' and resid 816 through 825 Processing helix chain 'B' and resid 836 through 841 Processing helix chain 'B' and resid 843 through 848 removed outlier: 3.606A pdb=" N ARG B 847 " --> pdb=" O ASP B 843 " (cutoff:3.500A) Processing helix chain 'B' and resid 848 through 856 Processing helix chain 'B' and resid 866 through 885 Processing helix chain 'B' and resid 886 through 891 Processing helix chain 'B' and resid 897 through 909 Processing helix chain 'B' and resid 912 through 919 removed outlier: 4.001A pdb=" N LEU B 916 " --> pdb=" O THR B 912 " (cutoff:3.500A) Processing helix chain 'B' and resid 919 through 940 Processing helix chain 'B' and resid 945 through 965 removed outlier: 3.551A pdb=" N GLN B 949 " --> pdb=" O LEU B 945 " (cutoff:3.500A) Processing helix chain 'B' and resid 966 through 968 No H-bonds generated for 'chain 'B' and resid 966 through 968' Processing helix chain 'B' and resid 976 through 984 Processing helix chain 'B' and resid 985 through 1033 removed outlier: 4.015A pdb=" N VAL B 991 " --> pdb=" O VAL B 987 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLN B 992 " --> pdb=" O GLU B 988 " (cutoff:3.500A) Processing helix chain 'C' and resid 294 through 304 Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 364 through 370 removed outlier: 3.964A pdb=" N ASN C 370 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 4.472A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 438 through 443 removed outlier: 3.532A pdb=" N SER C 443 " --> pdb=" O ASN C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 502 through 505 Processing helix chain 'C' and resid 737 through 744 Processing helix chain 'C' and resid 746 through 754 Processing helix chain 'C' and resid 757 through 783 removed outlier: 3.553A pdb=" N THR C 761 " --> pdb=" O GLY C 757 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASP C 775 " --> pdb=" O ALA C 771 " (cutoff:3.500A) Processing helix chain 'C' and resid 816 through 825 Processing helix chain 'C' and resid 836 through 841 Processing helix chain 'C' and resid 843 through 848 removed outlier: 3.607A pdb=" N ARG C 847 " --> pdb=" O ASP C 843 " (cutoff:3.500A) Processing helix chain 'C' and resid 848 through 856 Processing helix chain 'C' and resid 866 through 885 Processing helix chain 'C' and resid 886 through 891 Processing helix chain 'C' and resid 897 through 909 Processing helix chain 'C' and resid 912 through 919 removed outlier: 4.002A pdb=" N LEU C 916 " --> pdb=" O THR C 912 " (cutoff:3.500A) Processing helix chain 'C' and resid 919 through 940 Processing helix chain 'C' and resid 945 through 965 removed outlier: 3.551A pdb=" N GLN C 949 " --> pdb=" O LEU C 945 " (cutoff:3.500A) Processing helix chain 'C' and resid 966 through 968 No H-bonds generated for 'chain 'C' and resid 966 through 968' Processing helix chain 'C' and resid 976 through 984 Processing helix chain 'C' and resid 985 through 1033 removed outlier: 4.017A pdb=" N VAL C 991 " --> pdb=" O VAL C 987 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N GLN C 992 " --> pdb=" O GLU C 988 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.927A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N THR A 76 " --> pdb=" O VAL A 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 27 through 31 removed outlier: 3.927A pdb=" N ALA A 27 " --> pdb=" O TRP A 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.991A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 83 through 85 removed outlier: 6.439A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 83 through 85 removed outlier: 12.804A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL A 126 " --> pdb=" O GLU A 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU A 169 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE A 128 " --> pdb=" O THR A 167 " (cutoff:3.500A) removed outlier: 8.599A pdb=" N THR A 167 " --> pdb=" O ILE A 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL A 130 " --> pdb=" O ASN A 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN A 165 " --> pdb=" O VAL A 130 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N GLU A 132 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA A 163 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN A 134 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL A 159 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP A 138 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE A 157 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE A 140 " --> pdb=" O SER A 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER A 155 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY A 142 " --> pdb=" O MET A 153 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N MET A 153 " --> pdb=" O GLY A 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR A 144 " --> pdb=" O SER A 151 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N SER A 151 " --> pdb=" O TYR A 144 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL A 595 " --> pdb=" O THR A 315 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 6.856A pdb=" N PHE A 565 " --> pdb=" O PHE B 43 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AB3, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA A 672 " --> pdb=" O PRO A 665 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 701 through 703 removed outlier: 6.184A pdb=" N ALA A 701 " --> pdb=" O ILE B 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'A' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR A1076 " --> pdb=" O SER A1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA A1078 " --> pdb=" O PHE A1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE A1095 " --> pdb=" O ALA A1078 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 718 through 728 removed outlier: 7.050A pdb=" N GLY A1059 " --> pdb=" O SER A1055 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER A1055 " --> pdb=" O GLY A1059 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A1061 " --> pdb=" O PRO A1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU A1063 " --> pdb=" O SER A1051 " (cutoff:3.500A) removed outlier: 4.292A pdb=" N SER A1051 " --> pdb=" O LEU A1063 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N VAL A1065 " --> pdb=" O LEU A1049 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS A 733 " --> pdb=" O LEU A 861 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 787 through 789 Processing sheet with id=AB9, first strand: chain 'A' and resid 1121 through 1122 Processing sheet with id=AC1, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR B 76 " --> pdb=" O VAL B 70 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA B 27 " --> pdb=" O TRP B 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN B 61 " --> pdb=" O TYR B 269 " (cutoff:3.500A) removed outlier: 5.768A pdb=" N TYR B 269 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N SER B 205 " --> pdb=" O PRO B 225 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 47 through 55 removed outlier: 3.991A pdb=" N ASP B 287 " --> pdb=" O LYS B 278 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 83 through 85 removed outlier: 6.439A pdb=" N ALA B 243 " --> pdb=" O ILE B 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE B 101 " --> pdb=" O ALA B 243 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG B 102 " --> pdb=" O ASN B 121 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 83 through 85 removed outlier: 12.805A pdb=" N PHE B 238 " --> pdb=" O PHE B 135 " (cutoff:3.500A) removed outlier: 12.504A pdb=" N ASN B 137 " --> pdb=" O PHE B 238 " (cutoff:3.500A) removed outlier: 9.496A pdb=" N THR B 240 " --> pdb=" O ASN B 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU B 242 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 11.165A pdb=" N VAL B 126 " --> pdb=" O GLU B 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU B 169 " --> pdb=" O VAL B 126 " (cutoff:3.500A) removed outlier: 11.149A pdb=" N ILE B 128 " --> pdb=" O THR B 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR B 167 " --> pdb=" O ILE B 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL B 130 " --> pdb=" O ASN B 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN B 165 " --> pdb=" O VAL B 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU B 132 " --> pdb=" O ALA B 163 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N ALA B 163 " --> pdb=" O GLU B 132 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N GLN B 134 " --> pdb=" O SER B 161 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL B 159 " --> pdb=" O CYS B 136 " (cutoff:3.500A) removed outlier: 11.013A pdb=" N ASP B 138 " --> pdb=" O PHE B 157 " (cutoff:3.500A) removed outlier: 9.415A pdb=" N PHE B 157 " --> pdb=" O ASP B 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE B 140 " --> pdb=" O SER B 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER B 155 " --> pdb=" O PHE B 140 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N GLY B 142 " --> pdb=" O MET B 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET B 153 " --> pdb=" O GLY B 142 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N TYR B 144 " --> pdb=" O SER B 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER B 151 " --> pdb=" O TYR B 144 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL B 595 " --> pdb=" O THR B 315 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU B 324 " --> pdb=" O CYS B 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP B 574 " --> pdb=" O ILE B 587 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AD2, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AD3, first strand: chain 'B' and resid 654 through 655 removed outlier: 6.099A pdb=" N GLU B 654 " --> pdb=" O ALA B 694 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR B 696 " --> pdb=" O GLU B 654 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ALA B 672 " --> pdb=" O PRO B 665 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'B' and resid 701 through 703 removed outlier: 6.389A pdb=" N ALA B 701 " --> pdb=" O ILE C 788 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD4 Processing sheet with id=AD5, first strand: chain 'B' and resid 711 through 715 removed outlier: 3.920A pdb=" N THR B1076 " --> pdb=" O SER B1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA B1078 " --> pdb=" O PHE B1095 " (cutoff:3.500A) removed outlier: 4.524A pdb=" N PHE B1095 " --> pdb=" O ALA B1078 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'B' and resid 718 through 728 removed outlier: 7.050A pdb=" N GLY B1059 " --> pdb=" O SER B1055 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N SER B1055 " --> pdb=" O GLY B1059 " (cutoff:3.500A) removed outlier: 6.617A pdb=" N VAL B1061 " --> pdb=" O PRO B1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU B1063 " --> pdb=" O SER B1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER B1051 " --> pdb=" O LEU B1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL B1065 " --> pdb=" O LEU B1049 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'B' and resid 733 through 736 removed outlier: 4.202A pdb=" N LYS B 733 " --> pdb=" O LEU B 861 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'B' and resid 1121 through 1122 Processing sheet with id=AD9, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N THR C 76 " --> pdb=" O VAL C 70 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 27 through 31 removed outlier: 3.928A pdb=" N ALA C 27 " --> pdb=" O TRP C 64 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N ASN C 61 " --> pdb=" O TYR C 269 " (cutoff:3.500A) removed outlier: 5.769A pdb=" N TYR C 269 " --> pdb=" O ASN C 61 " (cutoff:3.500A) removed outlier: 5.714A pdb=" N SER C 205 " --> pdb=" O PRO C 225 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 47 through 55 removed outlier: 3.990A pdb=" N ASP C 287 " --> pdb=" O LYS C 278 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 83 through 85 removed outlier: 6.438A pdb=" N ALA C 243 " --> pdb=" O ILE C 101 " (cutoff:3.500A) removed outlier: 6.051A pdb=" N ILE C 101 " --> pdb=" O ALA C 243 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N ARG C 102 " --> pdb=" O ASN C 121 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 83 through 85 removed outlier: 12.804A pdb=" N PHE C 238 " --> pdb=" O PHE C 135 " (cutoff:3.500A) removed outlier: 12.503A pdb=" N ASN C 137 " --> pdb=" O PHE C 238 " (cutoff:3.500A) removed outlier: 9.497A pdb=" N THR C 240 " --> pdb=" O ASN C 137 " (cutoff:3.500A) removed outlier: 4.991A pdb=" N LEU C 242 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 11.166A pdb=" N VAL C 126 " --> pdb=" O GLU C 169 " (cutoff:3.500A) removed outlier: 9.756A pdb=" N GLU C 169 " --> pdb=" O VAL C 126 " (cutoff:3.500A) removed outlier: 11.148A pdb=" N ILE C 128 " --> pdb=" O THR C 167 " (cutoff:3.500A) removed outlier: 8.598A pdb=" N THR C 167 " --> pdb=" O ILE C 128 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N VAL C 130 " --> pdb=" O ASN C 165 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ASN C 165 " --> pdb=" O VAL C 130 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N GLU C 132 " --> pdb=" O ALA C 163 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N ALA C 163 " --> pdb=" O GLU C 132 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLN C 134 " --> pdb=" O SER C 161 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL C 159 " --> pdb=" O CYS C 136 " (cutoff:3.500A) removed outlier: 11.014A pdb=" N ASP C 138 " --> pdb=" O PHE C 157 " (cutoff:3.500A) removed outlier: 9.416A pdb=" N PHE C 157 " --> pdb=" O ASP C 138 " (cutoff:3.500A) removed outlier: 11.096A pdb=" N PHE C 140 " --> pdb=" O SER C 155 " (cutoff:3.500A) removed outlier: 9.263A pdb=" N SER C 155 " --> pdb=" O PHE C 140 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N GLY C 142 " --> pdb=" O MET C 153 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET C 153 " --> pdb=" O GLY C 142 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N TYR C 144 " --> pdb=" O SER C 151 " (cutoff:3.500A) removed outlier: 6.454A pdb=" N SER C 151 " --> pdb=" O TYR C 144 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 311 through 315 removed outlier: 4.642A pdb=" N VAL C 595 " --> pdb=" O THR C 315 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 324 through 328 removed outlier: 4.338A pdb=" N GLU C 324 " --> pdb=" O CYS C 538 " (cutoff:3.500A) removed outlier: 5.282A pdb=" N ASP C 574 " --> pdb=" O ILE C 587 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 354 through 358 removed outlier: 4.068A pdb=" N VAL C 395 " --> pdb=" O ILE C 358 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.476A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AF1, first strand: chain 'C' and resid 473 through 474 Processing sheet with id=AF2, first strand: chain 'C' and resid 654 through 655 removed outlier: 6.100A pdb=" N GLU C 654 " --> pdb=" O ALA C 694 " (cutoff:3.500A) removed outlier: 8.311A pdb=" N THR C 696 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N ALA C 672 " --> pdb=" O PRO C 665 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'C' and resid 711 through 715 removed outlier: 3.919A pdb=" N THR C1076 " --> pdb=" O SER C1097 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ALA C1078 " --> pdb=" O PHE C1095 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N PHE C1095 " --> pdb=" O ALA C1078 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'C' and resid 718 through 728 removed outlier: 7.049A pdb=" N GLY C1059 " --> pdb=" O SER C1055 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N SER C1055 " --> pdb=" O GLY C1059 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N VAL C1061 " --> pdb=" O PRO C1053 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LEU C1063 " --> pdb=" O SER C1051 " (cutoff:3.500A) removed outlier: 4.291A pdb=" N SER C1051 " --> pdb=" O LEU C1063 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL C1065 " --> pdb=" O LEU C1049 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'C' and resid 733 through 736 removed outlier: 4.203A pdb=" N LYS C 733 " --> pdb=" O LEU C 861 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'C' and resid 1121 through 1122 1118 hydrogen bonds defined for protein. 3009 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 7.26 Time building geometry restraints manager: 3.26 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: 14037 17.75 - 35.49: 1275 35.49 - 53.24: 348 53.24 - 70.99: 99 70.99 - 88.74: 30 Dihedral angle restraints: 15789 sinusoidal: 6159 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 15786 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: 0.04 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: 3.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 33.940 Find NCS groups from input model: 0.620 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:6.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8714 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 : 15.806 88.735 9489 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.90 % Favored : 96.01 % Rotamer: Outliers : 1.01 % Allowed : 15.27 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.13 (0.14), residues: 3297 helix: 1.63 (0.20), residues: 705 sheet: 0.34 (0.19), residues: 738 loop : -0.97 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 847 TYR 0.015 0.001 TYR B 265 PHE 0.013 0.001 PHE B 192 TRP 0.015 0.001 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00489 / 0.24 (27492) covalent geometry : angle 0.67520 / 0.31 (37407) SS BOND : bond 0.00314 / 0.20 ( 42) SS BOND : angle 1.03121 / 0.68 ( 84) hydrogen bonds : bond 0.12023 / 8.09 ( 1091) hydrogen bonds : angle 6.97285 / 4.98 ( 3009) link_BETA1-3 : bond 0.02017 / 1.01 ( 3) link_BETA1-3 : angle 3.68648 / 2.19 ( 9) link_BETA1-4 : bond 0.00420 / 0.24 ( 12) link_BETA1-4 : angle 3.78609 / 2.26 ( 36) link_BETA1-6 : bond 0.00483 / 0.24 ( 3) link_BETA1-6 : angle 1.26308 / 0.76 ( 9) link_NAG-ASN : bond 0.00475 / 0.37 ( 48) link_NAG-ASN : angle 4.29093 / 2.94 ( 144) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 265 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 236 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASP cc_start: 0.7472 (t0) cc_final: 0.7098 (p0) REVERT: A 904 TYR cc_start: 0.7216 (t80) cc_final: 0.6937 (t80) REVERT: A 957 GLN cc_start: 0.8053 (tt0) cc_final: 0.7435 (tm-30) REVERT: A 986 LYS cc_start: 0.8182 (tttp) cc_final: 0.7821 (ttpt) REVERT: B 986 LYS cc_start: 0.8218 (tttp) cc_final: 0.7875 (ttpt) REVERT: B 1113 GLN cc_start: 0.8367 (mm-40) cc_final: 0.8140 (mm110) REVERT: C 118 LEU cc_start: 0.8972 (OUTLIER) cc_final: 0.8567 (tp) REVERT: C 281 GLU cc_start: 0.8526 (pm20) cc_final: 0.8311 (pm20) outliers start: 29 outliers final: 18 residues processed: 256 average time/residue: 0.6111 time to fit residues: 185.6448 Evaluate side-chains 223 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 204 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 210 ILE Chi-restraints excluded: chain A residue 323 THR Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1101 HIS Chi-restraints excluded: chain B residue 242 LEU Chi-restraints excluded: chain B residue 638 THR Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1101 HIS Chi-restraints excluded: chain C residue 118 LEU Chi-restraints excluded: chain C residue 210 ILE Chi-restraints excluded: chain C residue 242 LEU Chi-restraints excluded: chain C residue 323 THR Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1101 HIS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 197 optimal weight: 5.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 0.6980 chunk 248 optimal weight: 2.9990 chunk 207 optimal weight: 2.9990 chunk 155 optimal weight: 0.3980 chunk 244 optimal weight: 5.9990 chunk 183 optimal weight: 0.8980 chunk 298 optimal weight: 2.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 314 GLN A 613 GLN A 804 GLN A 957 GLN B 314 GLN B 613 GLN B1054 GLN C 334 ASN C 804 GLN C 957 GLN C1113 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.137398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.096709 restraints weight = 35672.399| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.50 r_work: 0.3039 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2901 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2901 r_free = 0.2901 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 5 (7 function evaluations) r_final: 0.2901 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8376 moved from start: 0.1008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 27600 Z= 0.186 Angle : 0.644 13.417 37689 Z= 0.322 Chirality : 0.047 0.405 4416 Planarity : 0.005 0.073 4752 Dihedral : 7.097 63.916 3657 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.77 % Favored : 96.04 % Rotamer: Outliers : 1.88 % Allowed : 14.23 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.12 (0.14), residues: 3297 helix: 1.74 (0.19), residues: 690 sheet: 0.40 (0.18), residues: 777 loop : -1.05 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG B 847 TYR 0.026 0.002 TYR A1067 PHE 0.016 0.002 PHE C 133 TRP 0.025 0.002 TRP C 886 HIS 0.004 0.001 HIS C 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00432 / 0.19 (27492) covalent geometry : angle 0.59797 / 0.31 (37407) SS BOND : bond 0.00453 / 0.30 ( 42) SS BOND : angle 1.43614 / 0.95 ( 84) hydrogen bonds : bond 0.04838 / 3.27 ( 1091) hydrogen bonds : angle 5.94945 / 4.25 ( 3009) link_BETA1-3 : bond 0.01769 / 0.89 ( 3) link_BETA1-3 : angle 3.92024 / 2.30 ( 9) link_BETA1-4 : bond 0.00210 / 0.12 ( 12) link_BETA1-4 : angle 3.16455 / 1.90 ( 36) link_BETA1-6 : bond 0.00319 / 0.16 ( 3) link_BETA1-6 : angle 1.39838 / 0.83 ( 9) link_NAG-ASN : bond 0.00448 / 0.33 ( 48) link_NAG-ASN : angle 3.27428 / 2.26 ( 144) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 218 time to evaluate : 1.043 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 796 ASP cc_start: 0.7275 (t0) cc_final: 0.6407 (p0) REVERT: A 834 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6748 (mt) REVERT: A 841 LEU cc_start: 0.7314 (tp) cc_final: 0.7076 (tm) REVERT: A 964 LYS cc_start: 0.8267 (OUTLIER) cc_final: 0.7954 (mtpt) REVERT: A 986 LYS cc_start: 0.7864 (tttp) cc_final: 0.7370 (ttpt) REVERT: A 1092 GLU cc_start: 0.6955 (OUTLIER) cc_final: 0.6370 (mm-30) REVERT: B 197 ILE cc_start: 0.8577 (OUTLIER) cc_final: 0.8321 (mm) REVERT: B 834 ILE cc_start: 0.7358 (OUTLIER) cc_final: 0.6802 (mt) REVERT: B 1092 GLU cc_start: 0.7000 (OUTLIER) cc_final: 0.6555 (mm-30) REVERT: C 281 GLU cc_start: 0.8556 (pm20) cc_final: 0.8152 (pm20) REVERT: C 616 ASN cc_start: 0.7889 (OUTLIER) cc_final: 0.7686 (m-40) REVERT: C 654 GLU cc_start: 0.7559 (tt0) cc_final: 0.7103 (mt-10) REVERT: C 1092 GLU cc_start: 0.6906 (OUTLIER) cc_final: 0.6368 (mm-30) outliers start: 54 outliers final: 18 residues processed: 257 average time/residue: 0.6084 time to fit residues: 185.8475 Evaluate side-chains 240 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 214 time to evaluate : 0.862 ------------------------------------------------------------------------------- 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 346 ARG 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 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 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 197 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 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 146 optimal weight: 0.0060 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 4.9990 chunk 258 optimal weight: 5.9990 chunk 179 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 119 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 265 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 217 optimal weight: 0.6980 overall best weight: 1.7400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN B 804 GLN C 804 GLN C 957 GLN C1125 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.136091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3190 r_free = 0.3190 target = 0.096388 restraints weight = 28501.451| |-----------------------------------------------------------------------------| r_work (start): 0.3172 rms_B_bonded: 2.25 r_work: 0.3039 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2906 rms_B_bonded: 4.07 restraints_weight: 0.2500 r_work (final): 0.2906 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2902 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2902 r_free = 0.2902 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2902 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 27600 Z= 0.191 Angle : 0.644 14.229 37689 Z= 0.322 Chirality : 0.047 0.411 4416 Planarity : 0.004 0.068 4752 Dihedral : 6.481 58.367 3636 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 3.43 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.05 % Favored : 95.77 % Rotamer: Outliers : 1.95 % Allowed : 14.34 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3297 helix: 1.65 (0.19), residues: 690 sheet: 0.43 (0.18), residues: 777 loop : -1.06 (0.14), residues: 1830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B1039 TYR 0.023 0.002 TYR C1067 PHE 0.016 0.002 PHE C 133 TRP 0.021 0.002 TRP C 886 HIS 0.003 0.001 HIS C1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.19 (27492) covalent geometry : angle 0.59889 / 0.31 (37407) SS BOND : bond 0.00421 / 0.29 ( 42) SS BOND : angle 1.42984 / 0.95 ( 84) hydrogen bonds : bond 0.04909 / 3.31 ( 1091) hydrogen bonds : angle 5.93115 / 4.23 ( 3009) link_BETA1-3 : bond 0.01626 / 0.81 ( 3) link_BETA1-3 : angle 3.32218 / 1.95 ( 9) link_BETA1-4 : bond 0.00290 / 0.16 ( 12) link_BETA1-4 : angle 3.46037 / 2.06 ( 36) link_BETA1-6 : bond 0.00250 / 0.12 ( 3) link_BETA1-6 : angle 1.32288 / 0.81 ( 9) link_NAG-ASN : bond 0.00426 / 0.32 ( 48) link_NAG-ASN : angle 3.21014 / 2.22 ( 144) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 230 time to evaluate : 1.092 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 616 ASN cc_start: 0.8103 (OUTLIER) cc_final: 0.7884 (m-40) REVERT: A 780 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: A 796 ASP cc_start: 0.7219 (t0) cc_final: 0.6350 (p0) REVERT: A 834 ILE cc_start: 0.7452 (OUTLIER) cc_final: 0.6912 (mt) REVERT: A 904 TYR cc_start: 0.6987 (t80) cc_final: 0.6502 (t80) REVERT: A 964 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.7977 (mtpt) REVERT: A 986 LYS cc_start: 0.7897 (tttp) cc_final: 0.7401 (ttpt) REVERT: A 1092 GLU cc_start: 0.7044 (OUTLIER) cc_final: 0.6587 (mm-30) REVERT: B 197 ILE cc_start: 0.8573 (OUTLIER) cc_final: 0.8325 (mm) REVERT: B 755 GLN cc_start: 0.6566 (OUTLIER) cc_final: 0.5142 (mp10) REVERT: B 796 ASP cc_start: 0.7222 (t0) cc_final: 0.6088 (p0) REVERT: B 834 ILE cc_start: 0.7456 (OUTLIER) cc_final: 0.6947 (mt) REVERT: B 1092 GLU cc_start: 0.7113 (OUTLIER) cc_final: 0.6720 (mm-30) REVERT: C 104 TRP cc_start: 0.9141 (OUTLIER) cc_final: 0.8506 (m-90) REVERT: C 281 GLU cc_start: 0.8570 (pm20) cc_final: 0.8142 (pm20) REVERT: C 654 GLU cc_start: 0.7544 (tt0) cc_final: 0.7095 (mt-10) REVERT: C 776 LYS cc_start: 0.8020 (OUTLIER) cc_final: 0.7328 (ttmt) REVERT: C 834 ILE cc_start: 0.7428 (OUTLIER) cc_final: 0.6911 (mt) REVERT: C 1092 GLU cc_start: 0.6916 (OUTLIER) cc_final: 0.6537 (mm-30) outliers start: 56 outliers final: 17 residues processed: 263 average time/residue: 0.6019 time to fit residues: 188.1404 Evaluate side-chains 253 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 223 time to evaluate : 1.158 ------------------------------------------------------------------------------- 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 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 645 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 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 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 292 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 211 optimal weight: 1.9990 chunk 276 optimal weight: 4.9990 chunk 237 optimal weight: 0.7980 chunk 178 optimal weight: 2.9990 chunk 208 optimal weight: 0.9980 chunk 131 optimal weight: 5.9990 chunk 325 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 156 optimal weight: 10.0000 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A1125 ASN 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 = 0.3733 r_free = 0.3733 target = 0.137198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.098538 restraints weight = 28762.579| |-----------------------------------------------------------------------------| r_work (start): 0.3232 rms_B_bonded: 2.14 r_work: 0.3098 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2966 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2966 r_free = 0.2966 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 = 0.2966 r_free = 0.2966 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2966 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8591 moved from start: 0.1392 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= 0.138 Angle : 0.593 11.289 37689 Z= 0.297 Chirality : 0.046 0.533 4416 Planarity : 0.004 0.063 4752 Dihedral : 6.038 57.967 3636 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 1.67 % Allowed : 14.68 % Favored : 83.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.11 (0.14), residues: 3297 helix: 1.74 (0.19), residues: 690 sheet: 0.47 (0.18), residues: 771 loop : -1.07 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 847 TYR 0.019 0.001 TYR A1067 PHE 0.014 0.001 PHE A 817 TRP 0.022 0.002 TRP C 886 HIS 0.003 0.001 HIS B1101 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.14 (27492) covalent geometry : angle 0.55333 / 0.29 (37407) SS BOND : bond 0.00333 / 0.22 ( 42) SS BOND : angle 1.23475 / 0.83 ( 84) hydrogen bonds : bond 0.04318 / 2.90 ( 1091) hydrogen bonds : angle 5.75134 / 4.10 ( 3009) link_BETA1-3 : bond 0.01709 / 0.86 ( 3) link_BETA1-3 : angle 3.37710 / 1.98 ( 9) link_BETA1-4 : bond 0.00324 / 0.18 ( 12) link_BETA1-4 : angle 3.24411 / 1.93 ( 36) link_BETA1-6 : bond 0.00277 / 0.14 ( 3) link_BETA1-6 : angle 1.25061 / 0.77 ( 9) link_NAG-ASN : bond 0.00558 / 0.44 ( 48) link_NAG-ASN : angle 2.86553 / 1.99 ( 144) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 234 time to evaluate : 1.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8298 (OUTLIER) cc_final: 0.8092 (mtp85) REVERT: A 780 GLU cc_start: 0.8459 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: A 796 ASP cc_start: 0.7281 (t0) cc_final: 0.6398 (p0) REVERT: A 834 ILE cc_start: 0.7557 (OUTLIER) cc_final: 0.7000 (mt) REVERT: A 904 TYR cc_start: 0.7229 (t80) cc_final: 0.6656 (t80) REVERT: A 964 LYS cc_start: 0.8510 (OUTLIER) cc_final: 0.8203 (mtpt) REVERT: A 986 LYS cc_start: 0.8070 (tttp) cc_final: 0.7585 (ttpt) REVERT: A 1092 GLU cc_start: 0.7023 (OUTLIER) cc_final: 0.6637 (mm-30) REVERT: B 15 CYS cc_start: 0.7179 (m) cc_final: 0.6893 (m) REVERT: B 177 MET cc_start: 0.7757 (tmm) cc_final: 0.7307 (ttt) REVERT: B 755 GLN cc_start: 0.6785 (OUTLIER) cc_final: 0.5261 (mp10) REVERT: B 796 ASP cc_start: 0.7198 (t0) cc_final: 0.6071 (p0) REVERT: B 834 ILE cc_start: 0.7638 (OUTLIER) cc_final: 0.7100 (mt) REVERT: B 964 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.8183 (mtpt) REVERT: B 1092 GLU cc_start: 0.7040 (OUTLIER) cc_final: 0.6746 (mt-10) REVERT: C 15 CYS cc_start: 0.7024 (m) cc_final: 0.6694 (m) REVERT: C 104 TRP cc_start: 0.9272 (OUTLIER) cc_final: 0.8646 (m-90) REVERT: C 190 ARG cc_start: 0.8244 (tpp-160) cc_final: 0.7816 (tpt170) REVERT: C 281 GLU cc_start: 0.8682 (pm20) cc_final: 0.8296 (pm20) REVERT: C 616 ASN cc_start: 0.8030 (OUTLIER) cc_final: 0.7796 (m110) REVERT: C 654 GLU cc_start: 0.7789 (tt0) cc_final: 0.7339 (mt-10) REVERT: C 776 LYS cc_start: 0.8382 (OUTLIER) cc_final: 0.7686 (ttmt) REVERT: C 834 ILE cc_start: 0.7561 (OUTLIER) cc_final: 0.7036 (mt) REVERT: C 1092 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6556 (mm-30) outliers start: 48 outliers final: 20 residues processed: 262 average time/residue: 0.5363 time to fit residues: 167.3658 Evaluate side-chains 257 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 223 time to evaluate : 0.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 242 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 616 ASN Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 645 THR Chi-restraints excluded: chain B residue 727 LEU Chi-restraints excluded: chain B residue 740 MET Chi-restraints excluded: chain B residue 755 GLN Chi-restraints excluded: chain B residue 834 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 197 ILE Chi-restraints excluded: chain C residue 616 ASN Chi-restraints excluded: chain C residue 638 THR Chi-restraints excluded: chain C residue 645 THR Chi-restraints excluded: chain C residue 740 MET Chi-restraints excluded: chain C residue 776 LYS Chi-restraints excluded: chain C residue 834 ILE Chi-restraints excluded: chain C residue 1010 GLN Chi-restraints excluded: chain C residue 1092 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 30 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 162 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 325 optimal weight: 2.9990 chunk 11 optimal weight: 2.9990 chunk 203 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 804 GLN B 955 ASN C 804 GLN C 957 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.134459 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.094926 restraints weight = 32091.363| |-----------------------------------------------------------------------------| r_work (start): 0.3177 rms_B_bonded: 2.24 r_work: 0.3040 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2903 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2908 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2908 r_free = 0.2908 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2908 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 27600 Z= 0.229 Angle : 0.672 13.698 37689 Z= 0.336 Chirality : 0.048 0.431 4416 Planarity : 0.005 0.062 4752 Dihedral : 6.386 57.999 3636 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.23 % Favored : 95.59 % Rotamer: Outliers : 1.88 % Allowed : 14.86 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.20 (0.14), residues: 3297 helix: 1.56 (0.19), residues: 690 sheet: 0.51 (0.18), residues: 771 loop : -1.12 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 403 TYR 0.024 0.002 TYR B1067 PHE 0.014 0.002 PHE C1121 TRP 0.027 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00541 / 0.23 (27492) covalent geometry : angle 0.62802 / 0.33 (37407) SS BOND : bond 0.00573 / 0.38 ( 42) SS BOND : angle 1.79201 / 1.19 ( 84) hydrogen bonds : bond 0.05058 / 3.41 ( 1091) hydrogen bonds : angle 5.94407 / 4.23 ( 3009) link_BETA1-3 : bond 0.01562 / 0.78 ( 3) link_BETA1-3 : angle 3.38645 / 1.99 ( 9) link_BETA1-4 : bond 0.00281 / 0.16 ( 12) link_BETA1-4 : angle 3.57593 / 2.13 ( 36) link_BETA1-6 : bond 0.00198 / 0.10 ( 3) link_BETA1-6 : angle 1.43940 / 0.87 ( 9) link_NAG-ASN : bond 0.00641 / 0.49 ( 48) link_NAG-ASN : angle 3.14963 / 2.19 ( 144) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 231 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 190 ARG cc_start: 0.8379 (OUTLIER) cc_final: 0.8166 (mtp85) REVERT: A 780 GLU cc_start: 0.8517 (OUTLIER) cc_final: 0.8085 (mt-10) REVERT: A 796 ASP cc_start: 0.7428 (t0) cc_final: 0.6507 (p0) REVERT: A 834 ILE cc_start: 0.7666 (OUTLIER) cc_final: 0.7111 (mt) REVERT: A 904 TYR cc_start: 0.7313 (t80) cc_final: 0.6726 (t80) REVERT: A 964 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8234 (mtpt) REVERT: A 986 LYS cc_start: 0.8104 (tttp) cc_final: 0.7601 (ttpt) REVERT: A 1092 GLU cc_start: 0.7109 (OUTLIER) cc_final: 0.6674 (mt-10) REVERT: B 15 CYS cc_start: 0.7284 (m) cc_final: 0.7022 (m) REVERT: B 197 ILE cc_start: 0.8808 (OUTLIER) cc_final: 0.8527 (mm) REVERT: B 755 GLN cc_start: 0.6789 (OUTLIER) cc_final: 0.5333 (mp10) REVERT: B 796 ASP cc_start: 0.7303 (t0) cc_final: 0.6257 (p0) REVERT: B 834 ILE cc_start: 0.7709 (OUTLIER) cc_final: 0.7171 (mt) REVERT: B 964 LYS cc_start: 0.8458 (OUTLIER) cc_final: 0.8228 (mtpt) REVERT: B 1092 GLU cc_start: 0.7072 (OUTLIER) cc_final: 0.6843 (mt-10) REVERT: C 15 CYS cc_start: 0.7039 (m) cc_final: 0.6754 (m) REVERT: C 104 TRP cc_start: 0.9295 (OUTLIER) cc_final: 0.8705 (m-90) REVERT: C 190 ARG cc_start: 0.8305 (tpp-160) cc_final: 0.7852 (tpt170) REVERT: C 616 ASN cc_start: 0.8154 (OUTLIER) cc_final: 0.7919 (m110) REVERT: C 654 GLU cc_start: 0.7793 (tt0) cc_final: 0.7352 (mt-10) REVERT: C 776 LYS cc_start: 0.8397 (OUTLIER) cc_final: 0.7736 (ttmt) REVERT: C 834 ILE cc_start: 0.7600 (OUTLIER) cc_final: 0.7080 (mt) outliers start: 54 outliers final: 24 residues processed: 265 average time/residue: 0.5734 time to fit residues: 181.4538 Evaluate side-chains 261 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 223 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 483 VAL Chi-restraints excluded: chain A residue 645 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 964 LYS Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP Chi-restraints excluded: chain B residue 62 VAL 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 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 62 VAL Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER Chi-restraints excluded: chain C residue 177 MET 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 230 optimal weight: 5.9990 chunk 168 optimal weight: 0.9990 chunk 314 optimal weight: 0.9980 chunk 317 optimal weight: 1.9990 chunk 311 optimal weight: 4.9990 chunk 131 optimal weight: 1.9990 chunk 154 optimal weight: 0.9980 chunk 49 optimal weight: 0.9980 chunk 253 optimal weight: 0.7980 chunk 123 optimal weight: 0.4980 chunk 271 optimal weight: 0.0980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 804 GLN C 314 GLN C 613 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 = 0.3741 r_free = 0.3741 target = 0.137954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.099717 restraints weight = 26770.932| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.06 r_work: 0.3117 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.2980 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2988 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2988 r_free = 0.2988 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2988 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 27600 Z= 0.121 Angle : 0.584 13.742 37689 Z= 0.290 Chirality : 0.045 0.426 4416 Planarity : 0.004 0.058 4752 Dihedral : 5.818 57.730 3635 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.38 % Favored : 96.44 % Rotamer: Outliers : 1.39 % Allowed : 15.52 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.14), residues: 3297 helix: 1.76 (0.19), residues: 690 sheet: 0.42 (0.18), residues: 762 loop : -1.08 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 847 TYR 0.018 0.001 TYR A1067 PHE 0.013 0.001 PHE B1121 TRP 0.025 0.001 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00268 / 0.12 (27492) covalent geometry : angle 0.54068 / 0.28 (37407) SS BOND : bond 0.00369 / 0.25 ( 42) SS BOND : angle 1.42977 / 0.95 ( 84) hydrogen bonds : bond 0.04082 / 2.74 ( 1091) hydrogen bonds : angle 5.65998 / 4.03 ( 3009) link_BETA1-3 : bond 0.01652 / 0.82 ( 3) link_BETA1-3 : angle 3.20095 / 1.89 ( 9) link_BETA1-4 : bond 0.00384 / 0.22 ( 12) link_BETA1-4 : angle 3.19119 / 1.90 ( 36) link_BETA1-6 : bond 0.00326 / 0.16 ( 3) link_BETA1-6 : angle 1.17712 / 0.70 ( 9) link_NAG-ASN : bond 0.00516 / 0.40 ( 48) link_NAG-ASN : angle 2.95563 / 2.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 266 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 227 time to evaluate : 1.168 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8019 (mt-10) REVERT: A 796 ASP cc_start: 0.7356 (t0) cc_final: 0.6380 (p0) REVERT: A 834 ILE cc_start: 0.7594 (OUTLIER) cc_final: 0.7032 (mt) REVERT: A 904 TYR cc_start: 0.7244 (t80) cc_final: 0.6661 (t80) REVERT: A 1092 GLU cc_start: 0.6991 (OUTLIER) cc_final: 0.6646 (mt-10) REVERT: B 755 GLN cc_start: 0.6792 (OUTLIER) cc_final: 0.5279 (mp10) REVERT: B 796 ASP cc_start: 0.7188 (t0) cc_final: 0.6028 (p0) REVERT: B 834 ILE cc_start: 0.7651 (OUTLIER) cc_final: 0.7098 (mt) REVERT: B 964 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8083 (mtpt) REVERT: C 15 CYS cc_start: 0.6986 (m) cc_final: 0.6700 (m) REVERT: C 104 TRP cc_start: 0.9250 (OUTLIER) cc_final: 0.8625 (m-90) REVERT: C 281 GLU cc_start: 0.8681 (pm20) cc_final: 0.8306 (pm20) REVERT: C 654 GLU cc_start: 0.7812 (tt0) cc_final: 0.7338 (mt-10) REVERT: C 776 LYS cc_start: 0.8377 (OUTLIER) cc_final: 0.7688 (ttmt) REVERT: C 834 ILE cc_start: 0.7547 (OUTLIER) cc_final: 0.7023 (mt) outliers start: 39 outliers final: 17 residues processed: 251 average time/residue: 0.6018 time to fit residues: 180.2027 Evaluate side-chains 250 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 224 time to evaluate : 1.095 ------------------------------------------------------------------------------- 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 210 ILE Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 242 LEU Chi-restraints excluded: chain A residue 483 VAL Chi-restraints excluded: chain A residue 638 THR Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU Chi-restraints excluded: chain A residue 834 ILE Chi-restraints excluded: chain A residue 1010 GLN Chi-restraints excluded: chain A residue 1092 GLU Chi-restraints excluded: chain A residue 1127 ASP 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 330 random chunks: chunk 191 optimal weight: 3.9990 chunk 80 optimal weight: 5.9990 chunk 164 optimal weight: 4.9990 chunk 267 optimal weight: 0.0970 chunk 87 optimal weight: 6.9990 chunk 18 optimal weight: 3.9990 chunk 174 optimal weight: 4.9990 chunk 124 optimal weight: 2.9990 chunk 281 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 overall best weight: 2.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3679 r_free = 0.3679 target = 0.134511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3163 r_free = 0.3163 target = 0.094558 restraints weight = 32518.425| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.36 r_work: 0.3007 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.1696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 27600 Z= 0.247 Angle : 0.679 14.041 37689 Z= 0.340 Chirality : 0.050 0.627 4416 Planarity : 0.005 0.059 4752 Dihedral : 6.298 57.832 3633 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.93 % Favored : 95.89 % Rotamer: Outliers : 1.74 % Allowed : 15.00 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.14), residues: 3297 helix: 1.60 (0.19), residues: 690 sheet: 0.50 (0.18), residues: 771 loop : -1.12 (0.14), residues: 1836 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 403 TYR 0.024 0.002 TYR B1067 PHE 0.015 0.002 PHE C1121 TRP 0.037 0.003 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00584 / 0.25 (27492) covalent geometry : angle 0.63489 / 0.33 (37407) SS BOND : bond 0.00594 / 0.40 ( 42) SS BOND : angle 1.79809 / 1.19 ( 84) hydrogen bonds : bond 0.05084 / 3.43 ( 1091) hydrogen bonds : angle 5.91570 / 4.21 ( 3009) link_BETA1-3 : bond 0.01460 / 0.73 ( 3) link_BETA1-3 : angle 3.32736 / 1.95 ( 9) link_BETA1-4 : bond 0.00232 / 0.13 ( 12) link_BETA1-4 : angle 3.62144 / 2.15 ( 36) link_BETA1-6 : bond 0.00148 / 0.07 ( 3) link_BETA1-6 : angle 1.37864 / 0.84 ( 9) link_NAG-ASN : bond 0.00789 / 0.61 ( 48) link_NAG-ASN : angle 3.18484 / 2.18 ( 144) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 230 time to evaluate : 1.058 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8311 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: A 796 ASP cc_start: 0.7293 (t0) cc_final: 0.6173 (p0) REVERT: A 834 ILE cc_start: 0.7482 (OUTLIER) cc_final: 0.6908 (mt) REVERT: A 964 LYS cc_start: 0.8244 (OUTLIER) cc_final: 0.7975 (mtpt) REVERT: A 986 LYS cc_start: 0.7871 (tttp) cc_final: 0.7348 (ttpt) REVERT: A 1092 GLU cc_start: 0.7047 (OUTLIER) cc_final: 0.6644 (mt-10) REVERT: B 177 MET cc_start: 0.7450 (OUTLIER) cc_final: 0.5983 (tmm) REVERT: B 755 GLN cc_start: 0.6582 (OUTLIER) cc_final: 0.5158 (mp10) REVERT: B 796 ASP cc_start: 0.7178 (t0) cc_final: 0.6045 (p0) REVERT: B 834 ILE cc_start: 0.7471 (OUTLIER) cc_final: 0.6927 (mt) REVERT: B 964 LYS cc_start: 0.8102 (OUTLIER) cc_final: 0.7880 (mtpt) REVERT: C 15 CYS cc_start: 0.6874 (m) cc_final: 0.6611 (m) REVERT: C 104 TRP cc_start: 0.9115 (OUTLIER) cc_final: 0.8519 (m-90) REVERT: C 281 GLU cc_start: 0.8549 (pm20) cc_final: 0.8100 (pm20) REVERT: C 654 GLU cc_start: 0.7574 (tt0) cc_final: 0.7092 (mt-10) REVERT: C 776 LYS cc_start: 0.7971 (OUTLIER) cc_final: 0.7275 (ttmt) REVERT: C 834 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.6895 (mt) outliers start: 49 outliers final: 23 residues processed: 261 average time/residue: 0.5924 time to fit residues: 183.6946 Evaluate side-chains 260 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 226 time to evaluate : 1.033 ------------------------------------------------------------------------------- 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 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 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 177 MET 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 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 844 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 305 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 155 optimal weight: 0.4980 chunk 221 optimal weight: 1.9990 chunk 89 optimal weight: 0.6980 chunk 139 optimal weight: 0.9990 chunk 292 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 122 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 chunk 242 optimal weight: 3.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 804 GLN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.097863 restraints weight = 30792.554| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.19 r_work: 0.3084 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2946 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.2946 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2954 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2954 r_free = 0.2954 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2954 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8594 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 27600 Z= 0.136 Angle : 0.599 14.026 37689 Z= 0.298 Chirality : 0.047 0.576 4416 Planarity : 0.004 0.056 4752 Dihedral : 5.890 57.689 3633 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.50 % Favored : 96.32 % Rotamer: Outliers : 1.32 % Allowed : 15.45 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3297 helix: 1.71 (0.19), residues: 690 sheet: 0.33 (0.18), residues: 789 loop : -1.07 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.018 0.001 TYR B1067 PHE 0.013 0.001 PHE B1121 TRP 0.037 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.13 (27492) covalent geometry : angle 0.55650 / 0.29 (37407) SS BOND : bond 0.00396 / 0.26 ( 42) SS BOND : angle 1.35994 / 0.90 ( 84) hydrogen bonds : bond 0.04255 / 2.86 ( 1091) hydrogen bonds : angle 5.70061 / 4.06 ( 3009) link_BETA1-3 : bond 0.01652 / 0.83 ( 3) link_BETA1-3 : angle 3.20805 / 1.88 ( 9) link_BETA1-4 : bond 0.00339 / 0.19 ( 12) link_BETA1-4 : angle 3.35730 / 1.99 ( 36) link_BETA1-6 : bond 0.00262 / 0.13 ( 3) link_BETA1-6 : angle 1.21959 / 0.74 ( 9) link_NAG-ASN : bond 0.00641 / 0.50 ( 48) link_NAG-ASN : angle 2.99361 / 2.05 ( 144) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.057 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8074 (mt-10) REVERT: A 796 ASP cc_start: 0.7352 (t0) cc_final: 0.6249 (p0) REVERT: A 834 ILE cc_start: 0.7649 (OUTLIER) cc_final: 0.7062 (mt) REVERT: A 904 TYR cc_start: 0.7077 (t80) cc_final: 0.6633 (t80) REVERT: A 964 LYS cc_start: 0.8518 (OUTLIER) cc_final: 0.8231 (mtpt) REVERT: A 986 LYS cc_start: 0.8048 (tttp) cc_final: 0.7554 (ttpt) REVERT: A 1092 GLU cc_start: 0.6979 (OUTLIER) cc_final: 0.6622 (mt-10) REVERT: B 755 GLN cc_start: 0.6749 (OUTLIER) cc_final: 0.5259 (mp10) REVERT: B 796 ASP cc_start: 0.7237 (t0) cc_final: 0.6102 (p0) REVERT: B 834 ILE cc_start: 0.7644 (OUTLIER) cc_final: 0.7077 (mt) REVERT: B 964 LYS cc_start: 0.8323 (OUTLIER) cc_final: 0.8065 (mtpt) REVERT: C 15 CYS cc_start: 0.7009 (m) cc_final: 0.6726 (m) REVERT: C 104 TRP cc_start: 0.9269 (OUTLIER) cc_final: 0.8667 (m-90) REVERT: C 281 GLU cc_start: 0.8699 (pm20) cc_final: 0.8313 (pm20) REVERT: C 654 GLU cc_start: 0.7835 (tt0) cc_final: 0.7360 (mt-10) REVERT: C 776 LYS cc_start: 0.8394 (OUTLIER) cc_final: 0.7706 (ttmt) REVERT: C 834 ILE cc_start: 0.7576 (OUTLIER) cc_final: 0.7076 (mt) outliers start: 37 outliers final: 18 residues processed: 248 average time/residue: 0.6106 time to fit residues: 180.0785 Evaluate side-chains 249 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 221 time to evaluate : 1.031 ------------------------------------------------------------------------------- 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 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 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 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 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 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 297 optimal weight: 0.9980 chunk 265 optimal weight: 2.9990 chunk 230 optimal weight: 0.9990 chunk 176 optimal weight: 4.9990 chunk 65 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 324 optimal weight: 6.9990 chunk 207 optimal weight: 2.9990 chunk 40 optimal weight: 4.9990 chunk 172 optimal weight: 1.9990 chunk 312 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 GLN ** A1101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 935 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 = 0.3693 r_free = 0.3693 target = 0.135658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.096211 restraints weight = 28733.245| |-----------------------------------------------------------------------------| r_work (start): 0.3171 rms_B_bonded: 2.22 r_work: 0.3032 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2892 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2899 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2899 r_free = 0.2899 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2899 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 27600 Z= 0.198 Angle : 0.647 14.663 37689 Z= 0.322 Chirality : 0.049 0.552 4416 Planarity : 0.004 0.057 4752 Dihedral : 6.110 57.706 3633 Min Nonbonded Distance : 2.405 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.81 % Favored : 96.01 % Rotamer: Outliers : 1.50 % Allowed : 15.24 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.17 (0.14), residues: 3297 helix: 1.64 (0.19), residues: 690 sheet: 0.42 (0.18), residues: 804 loop : -1.10 (0.14), residues: 1803 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 403 TYR 0.022 0.002 TYR B1067 PHE 0.013 0.002 PHE C1121 TRP 0.039 0.002 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00463 / 0.20 (27492) covalent geometry : angle 0.60204 / 0.31 (37407) SS BOND : bond 0.00493 / 0.33 ( 42) SS BOND : angle 1.59531 / 1.06 ( 84) hydrogen bonds : bond 0.04761 / 3.21 ( 1091) hydrogen bonds : angle 5.81718 / 4.14 ( 3009) link_BETA1-3 : bond 0.01575 / 0.79 ( 3) link_BETA1-3 : angle 3.29341 / 1.93 ( 9) link_BETA1-4 : bond 0.00266 / 0.15 ( 12) link_BETA1-4 : angle 3.54432 / 2.10 ( 36) link_BETA1-6 : bond 0.00163 / 0.08 ( 3) link_BETA1-6 : angle 1.33575 / 0.81 ( 9) link_NAG-ASN : bond 0.00697 / 0.54 ( 48) link_NAG-ASN : angle 3.14811 / 2.14 ( 144) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 227 time to evaluate : 1.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7901 (mt-10) REVERT: A 796 ASP cc_start: 0.7240 (t0) cc_final: 0.6091 (p0) REVERT: A 834 ILE cc_start: 0.7425 (OUTLIER) cc_final: 0.6840 (mt) REVERT: A 904 TYR cc_start: 0.6774 (t80) cc_final: 0.6358 (t80) REVERT: A 964 LYS cc_start: 0.8215 (OUTLIER) cc_final: 0.7951 (mtpt) REVERT: A 986 LYS cc_start: 0.7844 (tttp) cc_final: 0.7321 (ttpt) REVERT: A 1092 GLU cc_start: 0.6962 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: B 177 MET cc_start: 0.7491 (tmm) cc_final: 0.7169 (ttt) REVERT: B 755 GLN cc_start: 0.6547 (OUTLIER) cc_final: 0.5084 (mp10) REVERT: B 796 ASP cc_start: 0.7175 (t0) cc_final: 0.6032 (p0) REVERT: B 834 ILE cc_start: 0.7414 (OUTLIER) cc_final: 0.6845 (mt) REVERT: B 964 LYS cc_start: 0.8060 (OUTLIER) cc_final: 0.7843 (mtpt) REVERT: C 15 CYS cc_start: 0.6852 (m) cc_final: 0.6588 (m) REVERT: C 104 TRP cc_start: 0.9112 (OUTLIER) cc_final: 0.8513 (m-90) REVERT: C 654 GLU cc_start: 0.7576 (tt0) cc_final: 0.7110 (mt-10) REVERT: C 776 LYS cc_start: 0.7962 (OUTLIER) cc_final: 0.7263 (ttmt) REVERT: C 834 ILE cc_start: 0.7398 (OUTLIER) cc_final: 0.6903 (mt) outliers start: 41 outliers final: 20 residues processed: 253 average time/residue: 0.5910 time to fit residues: 178.1082 Evaluate side-chains 257 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 227 time to evaluate : 1.064 ------------------------------------------------------------------------------- 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 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 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 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 834 ILE Chi-restraints excluded: chain B residue 844 ILE Chi-restraints excluded: chain B residue 964 LYS Chi-restraints excluded: chain B residue 1010 GLN Chi-restraints excluded: chain B residue 1092 GLU Chi-restraints excluded: chain C residue 63 THR Chi-restraints excluded: chain C residue 104 TRP Chi-restraints excluded: chain C residue 161 SER 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 2 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 204 optimal weight: 0.7980 chunk 329 optimal weight: 2.9990 chunk 79 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 166 optimal weight: 4.9990 chunk 321 optimal weight: 0.9980 chunk 235 optimal weight: 0.9980 chunk 307 optimal weight: 0.6980 chunk 144 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 935 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 = 0.3732 r_free = 0.3732 target = 0.137245 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.099001 restraints weight = 27291.890| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 2.06 r_work: 0.3106 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2967 rms_B_bonded: 3.88 restraints_weight: 0.2500 r_work (final): 0.2967 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2976 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2976 r_free = 0.2976 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2976 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8537 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 27600 Z= 0.132 Angle : 0.592 14.662 37689 Z= 0.294 Chirality : 0.046 0.522 4416 Planarity : 0.004 0.057 4752 Dihedral : 5.781 57.521 3633 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.18 % Allowed : 3.47 % Favored : 96.35 % Rotamer: Outliers : 1.36 % Allowed : 15.38 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.14), residues: 3297 helix: 1.75 (0.19), residues: 690 sheet: 0.32 (0.18), residues: 789 loop : -1.07 (0.14), residues: 1818 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 190 TYR 0.018 0.001 TYR B1067 PHE 0.012 0.001 PHE B1121 TRP 0.038 0.002 TRP B 886 HIS 0.003 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (27492) covalent geometry : angle 0.54942 / 0.28 (37407) SS BOND : bond 0.00379 / 0.25 ( 42) SS BOND : angle 1.30195 / 0.86 ( 84) hydrogen bonds : bond 0.04166 / 2.80 ( 1091) hydrogen bonds : angle 5.63908 / 4.02 ( 3009) link_BETA1-3 : bond 0.01702 / 0.85 ( 3) link_BETA1-3 : angle 3.17124 / 1.86 ( 9) link_BETA1-4 : bond 0.00343 / 0.20 ( 12) link_BETA1-4 : angle 3.32771 / 1.98 ( 36) link_BETA1-6 : bond 0.00256 / 0.13 ( 3) link_BETA1-6 : angle 1.21046 / 0.74 ( 9) link_NAG-ASN : bond 0.00670 / 0.53 ( 48) link_NAG-ASN : angle 2.98261 / 2.03 ( 144) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6594 Ramachandran restraints generated. 3297 Oldfield, 0 Emsley, 3297 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 263 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 226 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 780 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7997 (mt-10) REVERT: A 796 ASP cc_start: 0.7260 (t0) cc_final: 0.6192 (p0) REVERT: A 904 TYR cc_start: 0.7002 (t80) cc_final: 0.6612 (t80) REVERT: A 964 LYS cc_start: 0.8442 (OUTLIER) cc_final: 0.8143 (mtpt) REVERT: A 1092 GLU cc_start: 0.6938 (OUTLIER) cc_final: 0.6643 (mt-10) REVERT: B 177 MET cc_start: 0.7716 (tmm) cc_final: 0.7273 (ttt) REVERT: B 755 GLN cc_start: 0.6708 (OUTLIER) cc_final: 0.5216 (mp10) REVERT: B 796 ASP cc_start: 0.7195 (t0) cc_final: 0.6131 (p0) REVERT: B 834 ILE cc_start: 0.7573 (OUTLIER) cc_final: 0.6949 (mt) REVERT: B 964 LYS cc_start: 0.8243 (OUTLIER) cc_final: 0.7984 (mtpt) REVERT: C 15 CYS cc_start: 0.6977 (m) cc_final: 0.6694 (m) REVERT: C 104 TRP cc_start: 0.9242 (OUTLIER) cc_final: 0.8666 (m-90) REVERT: C 190 ARG cc_start: 0.8255 (tpp-160) cc_final: 0.8005 (tpt170) REVERT: C 281 GLU cc_start: 0.8653 (pm20) cc_final: 0.8254 (pm20) REVERT: C 654 GLU cc_start: 0.7746 (tt0) cc_final: 0.7256 (mt-10) REVERT: C 776 LYS cc_start: 0.8312 (OUTLIER) cc_final: 0.7612 (ttmt) REVERT: C 834 ILE cc_start: 0.7533 (OUTLIER) cc_final: 0.7040 (mt) outliers start: 37 outliers final: 20 residues processed: 250 average time/residue: 0.5909 time to fit residues: 175.4583 Evaluate side-chains 253 residues out of total 2862 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 224 time to evaluate : 0.918 ------------------------------------------------------------------------------- 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 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 727 LEU Chi-restraints excluded: chain A residue 740 MET Chi-restraints excluded: chain A residue 780 GLU 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 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 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 161 SER 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 118 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 137 optimal weight: 9.9990 chunk 226 optimal weight: 2.9990 chunk 253 optimal weight: 0.9980 chunk 144 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 95 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 197 optimal weight: 5.9990 chunk 103 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 804 GLN C 957 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.134215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3196 r_free = 0.3196 target = 0.095437 restraints weight = 28175.509| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.10 r_work: 0.3058 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2930 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2930 r_free = 0.2930 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2930 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8687 moved from start: 0.1842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 27600 Z= 0.263 Angle : 0.704 13.595 37689 Z= 0.351 Chirality : 0.052 0.698 4416 Planarity : 0.005 0.058 4752 Dihedral : 6.356 57.783 3633 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.71 Ramachandran Plot: Outliers : 0.18 % Allowed : 4.14 % Favored : 95.68 % Rotamer: Outliers : 1.25 % Allowed : 15.52 % Favored : 83.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.27 (0.14), residues: 3297 helix: 1.51 (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 ARG 0.005 0.001 ARG C 403 TYR 0.025 0.002 TYR C1067 PHE 0.016 0.002 PHE C1121 TRP 0.052 0.003 TRP B 886 HIS 0.004 0.001 HIS A 66 Details of bonding type rmsd/Z covalent geometry : bond 0.00623 / 0.26 (27492) covalent geometry : angle 0.65781 / 0.34 (37407) SS BOND : bond 0.00608 / 0.42 ( 42) SS BOND : angle 1.78191 / 1.18 ( 84) hydrogen bonds : bond 0.05238 / 3.53 ( 1091) hydrogen bonds : angle 5.96210 / 4.25 ( 3009) link_BETA1-3 : bond 0.01460 / 0.73 ( 3) link_BETA1-3 : angle 3.31538 / 1.94 ( 9) link_BETA1-4 : bond 0.00204 / 0.11 ( 12) link_BETA1-4 : angle 3.76579 / 2.23 ( 36) link_BETA1-6 : bond 0.00089 / 0.04 ( 3) link_BETA1-6 : angle 1.42641 / 0.86 ( 9) link_NAG-ASN : bond 0.00722 / 0.55 ( 48) link_NAG-ASN : angle 3.31649 / 2.23 ( 144) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14320.16 seconds wall clock time: 243 minutes 28.89 seconds (14608.89 seconds total)