Starting phenix.real_space_refine on Fri Feb 6 17:25:08 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9w76_65718/02_2026/9w76_65718.cif Found real_map, /net/cci-nas-00/data/ceres_data/9w76_65718/02_2026/9w76_65718.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9w76_65718/02_2026/9w76_65718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9w76_65718/02_2026/9w76_65718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9w76_65718/02_2026/9w76_65718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9w76_65718/02_2026/9w76_65718.map" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 117 5.16 5 C 16632 2.51 5 N 4284 2.21 5 O 5199 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 34 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 26232 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 8399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8399 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 43, 'TRANS': 1033} Chain breaks: 1 Chain: "B" Number of atoms: 8399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8399 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 43, 'TRANS': 1033} Chain breaks: 1 Chain: "C" Number of atoms: 8399 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1077, 8399 Classifications: {'peptide': 1077} Link IDs: {'PTRANS': 43, 'TRANS': 1033} Chain breaks: 1 Chain: "D" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "G" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "I" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "J" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 50 Unusual residues: {'BMA': 1, 'MAN': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLA': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "B" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLA': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Chain: "C" Number of atoms: 239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 239 Unusual residues: {'BLA': 1, 'NAG': 14} Classifications: {'undetermined': 15} Link IDs: {None: 14} Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 14 Time building chain proxies: 6.53, per 1000 atoms: 0.25 Number of scatterers: 26232 At special positions: 0 Unit cell: (136.71, 130.2, 164.61, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 117 16.00 O 5199 8.00 N 4284 7.00 C 16632 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=39, symmetry=0 Simple disulfide: pdb=" SG CYS A 122 " - pdb=" SG CYS A 146 " distance=2.04 Simple disulfide: pdb=" SG CYS A 265 " - pdb=" SG CYS A 275 " distance=2.03 Simple disulfide: pdb=" SG CYS A 310 " - pdb=" SG CYS A 335 " distance=2.04 Simple disulfide: pdb=" SG CYS A 353 " - pdb=" SG CYS A 406 " distance=2.03 Simple disulfide: pdb=" SG CYS A 365 " - pdb=" SG CYS A 490 " distance=2.03 Simple disulfide: pdb=" SG CYS A 503 " - pdb=" SG CYS A 555 " distance=2.03 Simple disulfide: pdb=" SG CYS A 582 " - pdb=" SG CYS A 614 " distance=2.03 Simple disulfide: pdb=" SG CYS A 627 " - pdb=" SG CYS A 636 " distance=2.03 Simple disulfide: pdb=" SG CYS A 700 " - pdb=" SG CYS A 722 " distance=2.02 Simple disulfide: pdb=" SG CYS A 705 " - pdb=" SG CYS A 711 " distance=2.03 Simple disulfide: pdb=" SG CYS A 802 " - pdb=" SG CYS A 813 " distance=2.03 Simple disulfide: pdb=" SG CYS A 994 " - pdb=" SG CYS A1005 " distance=2.02 Simple disulfide: pdb=" SG CYS A1044 " - pdb=" SG CYS A1088 " distance=2.03 Simple disulfide: pdb=" SG CYS B 122 " - pdb=" SG CYS B 146 " distance=2.03 Simple disulfide: pdb=" SG CYS B 265 " - pdb=" SG CYS B 275 " distance=2.03 Simple disulfide: pdb=" SG CYS B 310 " - pdb=" SG CYS B 335 " distance=2.04 Simple disulfide: pdb=" SG CYS B 353 " - pdb=" SG CYS B 406 " distance=2.03 Simple disulfide: pdb=" SG CYS B 365 " - pdb=" SG CYS B 490 " distance=2.03 Simple disulfide: pdb=" SG CYS B 503 " - pdb=" SG CYS B 555 " distance=2.03 Simple disulfide: pdb=" SG CYS B 582 " - pdb=" SG CYS B 614 " distance=2.03 Simple disulfide: pdb=" SG CYS B 627 " - pdb=" SG CYS B 636 " distance=2.03 Simple disulfide: pdb=" SG CYS B 700 " - pdb=" SG CYS B 722 " distance=2.02 Simple disulfide: pdb=" SG CYS B 705 " - pdb=" SG CYS B 711 " distance=2.03 Simple disulfide: pdb=" SG CYS B 802 " - pdb=" SG CYS B 813 " distance=2.03 Simple disulfide: pdb=" SG CYS B 994 " - pdb=" SG CYS B1005 " distance=2.02 Simple disulfide: pdb=" SG CYS B1044 " - pdb=" SG CYS B1088 " distance=2.03 Simple disulfide: pdb=" SG CYS C 122 " - pdb=" SG CYS C 146 " distance=2.03 Simple disulfide: pdb=" SG CYS C 265 " - pdb=" SG CYS C 275 " distance=2.03 Simple disulfide: pdb=" SG CYS C 310 " - pdb=" SG CYS C 335 " distance=2.03 Simple disulfide: pdb=" SG CYS C 353 " - pdb=" SG CYS C 406 " distance=2.03 Simple disulfide: pdb=" SG CYS C 365 " - pdb=" SG CYS C 490 " distance=2.03 Simple disulfide: pdb=" SG CYS C 503 " - pdb=" SG CYS C 555 " distance=2.03 Simple disulfide: pdb=" SG CYS C 582 " - pdb=" SG CYS C 614 " distance=2.03 Simple disulfide: pdb=" SG CYS C 627 " - pdb=" SG CYS C 636 " distance=2.03 Simple disulfide: pdb=" SG CYS C 700 " - pdb=" SG CYS C 722 " distance=2.02 Simple disulfide: pdb=" SG CYS C 705 " - pdb=" SG CYS C 711 " distance=2.03 Simple disulfide: pdb=" SG CYS C 802 " - pdb=" SG CYS C 813 " distance=2.03 Simple disulfide: pdb=" SG CYS C 994 " - pdb=" SG CYS C1005 " distance=2.02 Simple disulfide: pdb=" SG CYS C1044 " - pdb=" SG CYS C1088 " 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 ALPHA1-3 " BMA D 3 " - " MAN D 4 " " BMA G 3 " - " MAN G 4 " " BMA J 3 " - " MAN J 4 " BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " " NAG E 1 " - " NAG E 2 " " NAG F 1 " - " NAG F 2 " " NAG G 1 " - " NAG G 2 " " NAG G 2 " - " BMA G 3 " " NAG H 1 " - " NAG H 2 " " NAG I 1 " - " NAG I 2 " " NAG J 1 " - " NAG J 2 " " NAG J 2 " - " BMA J 3 " " NAG K 1 " - " NAG K 2 " " NAG L 1 " - " NAG L 2 " NAG-ASN " NAG A1301 " - " ASN A 59 " " NAG A1302 " - " ASN A 305 " " NAG A1303 " - " ASN A 581 " " NAG A1304 " - " ASN A 622 " " NAG A1305 " - " ASN A 671 " " NAG A1306 " - " ASN A1036 " " NAG A1307 " - " ASN A1060 " " NAG A1308 " - " ASN A 145 " " NAG A1309 " - " ASN A 256 " " NAG A1311 " - " ASN A 149 " " NAG A1312 " - " ASN A 317 " " NAG A1313 " - " ASN A 103 " " NAG A1314 " - " ASN A 17 " " NAG A1315 " - " ASN A 679 " " NAG B1301 " - " ASN B 59 " " NAG B1302 " - " ASN B 305 " " NAG B1303 " - " ASN B 581 " " NAG B1304 " - " ASN B 622 " " NAG B1305 " - " ASN B 671 " " NAG B1306 " - " ASN B1036 " " NAG B1307 " - " ASN B1060 " " NAG B1308 " - " ASN B 145 " " NAG B1309 " - " ASN B 256 " " NAG B1311 " - " ASN B 149 " " NAG B1312 " - " ASN B 317 " " NAG B1313 " - " ASN B 103 " " NAG B1314 " - " ASN B 17 " " NAG B1315 " - " ASN B 679 " " NAG C1301 " - " ASN C 59 " " NAG C1302 " - " ASN C 305 " " NAG C1303 " - " ASN C 581 " " NAG C1304 " - " ASN C 622 " " NAG C1305 " - " ASN C 671 " " NAG C1306 " - " ASN C1036 " " NAG C1307 " - " ASN C1060 " " NAG C1308 " - " ASN C 145 " " NAG C1309 " - " ASN C 256 " " NAG C1311 " - " ASN C 149 " " NAG C1312 " - " ASN C 317 " " NAG C1313 " - " ASN C 103 " " NAG C1314 " - " ASN C 17 " " NAG C1315 " - " ASN C 679 " " NAG D 1 " - " ASN A 218 " " NAG E 1 " - " ASN A 344 " " NAG F 1 " - " ASN A 763 " " NAG G 1 " - " ASN B 218 " " NAG H 1 " - " ASN B 344 " " NAG I 1 " - " ASN B 763 " " NAG J 1 " - " ASN C 218 " " NAG K 1 " - " ASN C 344 " " NAG L 1 " - " ASN C 763 " Time building additional restraints: 2.35 Conformation dependent library (CDL) restraints added in 1.1 seconds 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6060 Finding SS restraints... Secondary structure from input PDB file: 75 helices and 43 sheets defined 26.2% alpha, 24.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.20 Creating SS restraints... Processing helix chain 'A' and resid 268 through 277 Processing helix chain 'A' and resid 311 through 317 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.972A pdb=" N ASN A 344 " --> pdb=" O VAL A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 357 through 363 removed outlier: 4.565A pdb=" N ASN A 362 " --> pdb=" O THR A 359 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 384 removed outlier: 3.763A pdb=" N VAL A 381 " --> pdb=" O GLY A 378 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ARG A 382 " --> pdb=" O ASP A 379 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 412 through 417 removed outlier: 3.583A pdb=" N ASP A 416 " --> pdb=" O SER A 412 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N ALA A 417 " --> pdb=" O ARG A 413 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 412 through 417' Processing helix chain 'A' and resid 581 through 583 No H-bonds generated for 'chain 'A' and resid 581 through 583' Processing helix chain 'A' and resid 584 through 590 Processing helix chain 'A' and resid 591 through 594 Processing helix chain 'A' and resid 595 through 601 removed outlier: 4.086A pdb=" N TYR A 601 " --> pdb=" O SER A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 699 through 705 Processing helix chain 'A' and resid 708 through 716 Processing helix chain 'A' and resid 717 through 719 No H-bonds generated for 'chain 'A' and resid 717 through 719' Processing helix chain 'A' and resid 720 through 745 removed outlier: 3.552A pdb=" N GLN A 724 " --> pdb=" O SER A 720 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASP A 737 " --> pdb=" O ALA A 733 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 786 Processing helix chain 'A' and resid 810 through 818 Processing helix chain 'A' and resid 828 through 847 Processing helix chain 'A' and resid 848 through 852 removed outlier: 3.687A pdb=" N GLY A 851 " --> pdb=" O TRP A 848 " (cutoff:3.500A) Processing helix chain 'A' and resid 859 through 872 Processing helix chain 'A' and resid 874 through 881 removed outlier: 4.017A pdb=" N LEU A 878 " --> pdb=" O THR A 874 " (cutoff:3.500A) Processing helix chain 'A' and resid 881 through 903 Processing helix chain 'A' and resid 907 through 927 Processing helix chain 'A' and resid 928 through 930 No H-bonds generated for 'chain 'A' and resid 928 through 930' Processing helix chain 'A' and resid 938 through 946 Processing helix chain 'A' and resid 947 through 995 removed outlier: 4.063A pdb=" N VAL A 953 " --> pdb=" O VAL A 949 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N GLN A 954 " --> pdb=" O GLU A 950 " (cutoff:3.500A) Processing helix chain 'B' and resid 268 through 277 Processing helix chain 'B' and resid 311 through 317 removed outlier: 3.508A pdb=" N VAL B 315 " --> pdb=" O PRO B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 340 through 345 removed outlier: 3.988A pdb=" N ASN B 344 " --> pdb=" O VAL B 341 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 364 removed outlier: 4.535A pdb=" N ASN B 362 " --> pdb=" O THR B 359 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N LEU B 364 " --> pdb=" O LEU B 361 " (cutoff:3.500A) Processing helix chain 'B' and resid 377 through 384 removed outlier: 3.726A pdb=" N VAL B 381 " --> pdb=" O GLY B 378 " (cutoff:3.500A) removed outlier: 4.377A pdb=" N ARG B 382 " --> pdb=" O ASP B 379 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 396 Processing helix chain 'B' and resid 581 through 583 No H-bonds generated for 'chain 'B' and resid 581 through 583' Processing helix chain 'B' and resid 584 through 590 Processing helix chain 'B' and resid 591 through 594 Processing helix chain 'B' and resid 595 through 601 removed outlier: 4.063A pdb=" N TYR B 601 " --> pdb=" O SER B 597 " (cutoff:3.500A) Processing helix chain 'B' and resid 699 through 705 Processing helix chain 'B' and resid 708 through 716 Processing helix chain 'B' and resid 717 through 719 No H-bonds generated for 'chain 'B' and resid 717 through 719' Processing helix chain 'B' and resid 720 through 745 removed outlier: 3.647A pdb=" N ASP B 737 " --> pdb=" O ALA B 733 " (cutoff:3.500A) Processing helix chain 'B' and resid 778 through 786 Processing helix chain 'B' and resid 810 through 818 Processing helix chain 'B' and resid 828 through 846 Processing helix chain 'B' and resid 848 through 852 removed outlier: 3.720A pdb=" N GLY B 851 " --> pdb=" O TRP B 848 " (cutoff:3.500A) Processing helix chain 'B' and resid 859 through 872 Processing helix chain 'B' and resid 874 through 881 removed outlier: 4.038A pdb=" N LEU B 878 " --> pdb=" O THR B 874 " (cutoff:3.500A) Processing helix chain 'B' and resid 881 through 903 Processing helix chain 'B' and resid 907 through 927 Processing helix chain 'B' and resid 928 through 930 No H-bonds generated for 'chain 'B' and resid 928 through 930' Processing helix chain 'B' and resid 938 through 946 removed outlier: 3.515A pdb=" N ILE B 942 " --> pdb=" O VAL B 938 " (cutoff:3.500A) Processing helix chain 'B' and resid 947 through 995 removed outlier: 4.061A pdb=" N VAL B 953 " --> pdb=" O VAL B 949 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N GLN B 954 " --> pdb=" O GLU B 950 " (cutoff:3.500A) Processing helix chain 'C' and resid 268 through 277 Processing helix chain 'C' and resid 311 through 317 Processing helix chain 'C' and resid 340 through 345 removed outlier: 3.981A pdb=" N ASN C 344 " --> pdb=" O VAL C 341 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 363 removed outlier: 4.527A pdb=" N ASN C 362 " --> pdb=" O THR C 359 " (cutoff:3.500A) Processing helix chain 'C' and resid 379 through 384 removed outlier: 4.380A pdb=" N ARG C 382 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing helix chain 'C' and resid 390 through 396 Processing helix chain 'C' and resid 584 through 590 Processing helix chain 'C' and resid 591 through 594 Processing helix chain 'C' and resid 595 through 601 removed outlier: 4.061A pdb=" N TYR C 601 " --> pdb=" O SER C 597 " (cutoff:3.500A) Processing helix chain 'C' and resid 699 through 705 Processing helix chain 'C' and resid 708 through 716 Processing helix chain 'C' and resid 717 through 719 No H-bonds generated for 'chain 'C' and resid 717 through 719' Processing helix chain 'C' and resid 720 through 745 removed outlier: 3.575A pdb=" N GLN C 724 " --> pdb=" O SER C 720 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LEU C 725 " --> pdb=" O PHE C 721 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP C 737 " --> pdb=" O ALA C 733 " (cutoff:3.500A) Processing helix chain 'C' and resid 778 through 786 Processing helix chain 'C' and resid 810 through 818 Processing helix chain 'C' and resid 828 through 847 Processing helix chain 'C' and resid 848 through 852 removed outlier: 3.678A pdb=" N GLY C 851 " --> pdb=" O TRP C 848 " (cutoff:3.500A) Processing helix chain 'C' and resid 859 through 872 Processing helix chain 'C' and resid 874 through 881 removed outlier: 4.029A pdb=" N LEU C 878 " --> pdb=" O THR C 874 " (cutoff:3.500A) Processing helix chain 'C' and resid 881 through 903 Processing helix chain 'C' and resid 907 through 927 Processing helix chain 'C' and resid 928 through 930 No H-bonds generated for 'chain 'C' and resid 928 through 930' Processing helix chain 'C' and resid 938 through 946 removed outlier: 3.512A pdb=" N ILE C 942 " --> pdb=" O VAL C 938 " (cutoff:3.500A) Processing helix chain 'C' and resid 947 through 995 removed outlier: 3.995A pdb=" N VAL C 953 " --> pdb=" O VAL C 949 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN C 954 " --> pdb=" O GLU C 950 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 24 through 28 removed outlier: 8.097A pdb=" N ASN A 59 " --> pdb=" O HIS A 243 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N HIS A 243 " --> pdb=" O ASN A 59 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N THR A 168 " --> pdb=" O ASP A 87 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS A 167 " --> pdb=" O TYR A 190 " (cutoff:3.500A) removed outlier: 6.094A pdb=" N LEU A 181 " --> pdb=" O LYS A 212 " (cutoff:3.500A) removed outlier: 4.352A pdb=" N LYS A 212 " --> pdb=" O LEU A 181 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N VAL A 183 " --> pdb=" O LEU A 210 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 46 through 53 removed outlier: 3.791A pdb=" N ASP A 261 " --> pdb=" O LYS A 252 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 75 through 76 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 75 through 76 current: chain 'A' and resid 107 through 112 removed outlier: 6.515A pdb=" N THR A 123 " --> pdb=" O ALA A 143 " (cutoff:3.500A) removed outlier: 4.255A pdb=" N ALA A 143 " --> pdb=" O THR A 123 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N HIS A 125 " --> pdb=" O SER A 141 " (cutoff:3.500A) removed outlier: 7.237A pdb=" N LEU A 139 " --> pdb=" O CYS A 127 " (cutoff:3.500A) removed outlier: 12.683A pdb=" N THR A 129 " --> pdb=" O PRO A 137 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 285 through 288 removed outlier: 3.566A pdb=" N PHE A 608 " --> pdb=" O LEU A 615 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 302 removed outlier: 3.740A pdb=" N SER A 540 " --> pdb=" O GLY A 531 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 328 through 332 removed outlier: 3.982A pdb=" N VAL A 369 " --> pdb=" O ILE A 332 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N ASN A 368 " --> pdb=" O GLU A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 335 through 336 removed outlier: 6.673A pdb=" N CYS A 335 " --> pdb=" O CYS A 490 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 426 through 428 Processing sheet with id=AA9, first strand: chain 'A' and resid 446 through 449 Processing sheet with id=AB1, first strand: chain 'A' and resid 619 through 620 removed outlier: 6.067A pdb=" N GLU A 619 " --> pdb=" O ALA A 656 " (cutoff:3.500A) removed outlier: 8.428A pdb=" N VAL A 658 " --> pdb=" O GLU A 619 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ALA A 637 " --> pdb=" O PRO A 630 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 663 through 665 removed outlier: 6.685A pdb=" N ALA A 663 " --> pdb=" O ILE B 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'A' and resid 673 through 690 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 673 through 690 current: chain 'A' and resid 1021 through 1040 removed outlier: 3.542A pdb=" N ALA A1040 " --> pdb=" O PHE A1057 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N PHE A1057 " --> pdb=" O ALA A1040 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 695 through 698 removed outlier: 4.261A pdb=" N LYS A 695 " --> pdb=" O LEU A 823 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 749 through 751 Processing sheet with id=AB6, first strand: chain 'A' and resid 1082 through 1084 Processing sheet with id=AB7, first strand: chain 'B' and resid 24 through 28 removed outlier: 8.010A pdb=" N ASN B 59 " --> pdb=" O HIS B 243 " (cutoff:3.500A) removed outlier: 6.192A pdb=" N HIS B 243 " --> pdb=" O ASN B 59 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP B 87 " --> pdb=" O THR B 168 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N THR B 168 " --> pdb=" O ASP B 87 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N LYS B 167 " --> pdb=" O TYR B 190 " (cutoff:3.500A) removed outlier: 5.948A pdb=" N LEU B 181 " --> pdb=" O LYS B 212 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N LYS B 212 " --> pdb=" O LEU B 181 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL B 183 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 46 through 53 removed outlier: 3.761A pdb=" N ASP B 261 " --> pdb=" O LYS B 252 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 75 through 76 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 75 through 76 current: chain 'B' and resid 107 through 112 removed outlier: 6.731A pdb=" N VAL B 117 " --> pdb=" O LEU B 152 " (cutoff:3.500A) removed outlier: 7.714A pdb=" N THR B 123 " --> pdb=" O CYS B 146 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N CYS B 146 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N HIS B 125 " --> pdb=" O PHE B 144 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N PHE B 144 " --> pdb=" O HIS B 125 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N CYS B 127 " --> pdb=" O SER B 142 " (cutoff:3.500A) removed outlier: 9.710A pdb=" N SER B 142 " --> pdb=" O CYS B 127 " (cutoff:3.500A) removed outlier: 11.413A pdb=" N THR B 129 " --> pdb=" O TYR B 140 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N TYR B 140 " --> pdb=" O THR B 129 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL B 131 " --> pdb=" O HIS B 138 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 285 through 288 removed outlier: 3.578A pdb=" N PHE B 608 " --> pdb=" O LEU B 615 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 299 through 302 removed outlier: 3.676A pdb=" N SER B 540 " --> pdb=" O GLY B 531 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 328 through 332 removed outlier: 3.995A pdb=" N VAL B 369 " --> pdb=" O ILE B 332 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASN B 368 " --> pdb=" O GLU B 481 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 335 through 336 removed outlier: 6.770A pdb=" N CYS B 335 " --> pdb=" O CYS B 490 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'B' and resid 426 through 428 Processing sheet with id=AC6, first strand: chain 'B' and resid 446 through 449 Processing sheet with id=AC7, first strand: chain 'B' and resid 619 through 620 removed outlier: 6.065A pdb=" N GLU B 619 " --> pdb=" O ALA B 656 " (cutoff:3.500A) removed outlier: 8.430A pdb=" N VAL B 658 " --> pdb=" O GLU B 619 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N ILE B 635 " --> pdb=" O ILE B 631 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 663 through 665 removed outlier: 6.726A pdb=" N ALA B 663 " --> pdb=" O ILE C 750 " (cutoff:3.500A) No H-bonds generated for sheet with id=AC8 Processing sheet with id=AC9, first strand: chain 'B' and resid 673 through 690 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 673 through 690 current: chain 'B' and resid 1021 through 1040 removed outlier: 3.532A pdb=" N ALA B1040 " --> pdb=" O PHE B1057 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N PHE B1057 " --> pdb=" O ALA B1040 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 695 through 698 removed outlier: 4.211A pdb=" N LYS B 695 " --> pdb=" O LEU B 823 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 1082 through 1087 removed outlier: 6.784A pdb=" N ALA B1049 " --> pdb=" O SER B1085 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 24 through 28 removed outlier: 8.413A pdb=" N ASN C 59 " --> pdb=" O HIS C 243 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N HIS C 243 " --> pdb=" O ASN C 59 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N THR C 168 " --> pdb=" O ASP C 87 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS C 167 " --> pdb=" O TYR C 190 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N LEU C 181 " --> pdb=" O LYS C 212 " (cutoff:3.500A) removed outlier: 4.258A pdb=" N LYS C 212 " --> pdb=" O LEU C 181 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N VAL C 183 " --> pdb=" O LEU C 210 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 46 through 53 removed outlier: 3.765A pdb=" N ASP C 261 " --> pdb=" O LYS C 252 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 75 through 76 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 75 through 76 current: chain 'C' and resid 107 through 112 removed outlier: 6.774A pdb=" N VAL C 117 " --> pdb=" O LEU C 152 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N THR C 123 " --> pdb=" O CYS C 146 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N CYS C 146 " --> pdb=" O THR C 123 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N HIS C 125 " --> pdb=" O PHE C 144 " (cutoff:3.500A) removed outlier: 9.107A pdb=" N PHE C 144 " --> pdb=" O HIS C 125 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N CYS C 127 " --> pdb=" O SER C 142 " (cutoff:3.500A) removed outlier: 9.765A pdb=" N SER C 142 " --> pdb=" O CYS C 127 " (cutoff:3.500A) removed outlier: 11.342A pdb=" N THR C 129 " --> pdb=" O TYR C 140 " (cutoff:3.500A) removed outlier: 8.454A pdb=" N TYR C 140 " --> pdb=" O THR C 129 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N VAL C 131 " --> pdb=" O HIS C 138 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 285 through 288 removed outlier: 3.576A pdb=" N PHE C 608 " --> pdb=" O LEU C 615 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 299 through 302 removed outlier: 3.688A pdb=" N SER C 540 " --> pdb=" O GLY C 531 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 328 through 332 removed outlier: 3.963A pdb=" N VAL C 369 " --> pdb=" O ILE C 332 " (cutoff:3.500A) removed outlier: 3.898A pdb=" N ASN C 368 " --> pdb=" O GLU C 481 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 335 through 336 removed outlier: 6.639A pdb=" N CYS C 335 " --> pdb=" O CYS C 490 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 426 through 428 Processing sheet with id=AE2, first strand: chain 'C' and resid 446 through 449 Processing sheet with id=AE3, first strand: chain 'C' and resid 619 through 620 removed outlier: 6.070A pdb=" N GLU C 619 " --> pdb=" O ALA C 656 " (cutoff:3.500A) removed outlier: 8.431A pdb=" N VAL C 658 " --> pdb=" O GLU C 619 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA C 637 " --> pdb=" O PRO C 630 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 673 through 690 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 673 through 690 current: chain 'C' and resid 1021 through 1040 removed outlier: 3.527A pdb=" N THR C1038 " --> pdb=" O SER C1059 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ALA C1040 " --> pdb=" O PHE C1057 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N PHE C1057 " --> pdb=" O ALA C1040 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 695 through 698 removed outlier: 4.282A pdb=" N LYS C 695 " --> pdb=" O LEU C 823 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 758 through 759 Processing sheet with id=AE7, first strand: chain 'C' and resid 1082 through 1084 968 hydrogen bonds defined for protein. 2637 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: 6.34 Time building geometry restraints manager: 3.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 4856 1.33 - 1.45: 7373 1.45 - 1.57: 14444 1.57 - 1.70: 0 1.70 - 1.82: 153 Bond restraints: 26826 Sorted by residual: bond pdb=" C1D BLA B1310 " pdb=" CHD BLA B1310 " ideal model delta sigma weight residual 1.440 1.363 0.077 2.00e-02 2.50e+03 1.50e+01 bond pdb=" C1D BLA A1310 " pdb=" CHD BLA A1310 " ideal model delta sigma weight residual 1.440 1.366 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C1D BLA C1310 " pdb=" CHD BLA C1310 " ideal model delta sigma weight residual 1.440 1.366 0.074 2.00e-02 2.50e+03 1.37e+01 bond pdb=" C3C BLA B1310 " pdb=" CAC BLA B1310 " ideal model delta sigma weight residual 1.458 1.394 0.064 2.00e-02 2.50e+03 1.02e+01 bond pdb=" C4A BLA B1310 " pdb=" CHB BLA B1310 " ideal model delta sigma weight residual 1.431 1.367 0.064 2.00e-02 2.50e+03 1.01e+01 ... (remaining 26821 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 35964 2.04 - 4.09: 527 4.09 - 6.13: 39 6.13 - 8.17: 21 8.17 - 10.21: 4 Bond angle restraints: 36555 Sorted by residual: angle pdb=" CA CYS C 122 " pdb=" CB CYS C 122 " pdb=" SG CYS C 122 " ideal model delta sigma weight residual 114.40 124.45 -10.05 2.30e+00 1.89e-01 1.91e+01 angle pdb=" OG1 THR A 31 " pdb=" CB THR A 31 " pdb=" CG2 THR A 31 " ideal model delta sigma weight residual 109.30 101.02 8.28 2.00e+00 2.50e-01 1.71e+01 angle pdb=" CA CYS A 122 " pdb=" CB CYS A 122 " pdb=" SG CYS A 122 " ideal model delta sigma weight residual 114.40 123.82 -9.42 2.30e+00 1.89e-01 1.68e+01 angle pdb=" CB GLU A 898 " pdb=" CG GLU A 898 " pdb=" CD GLU A 898 " ideal model delta sigma weight residual 112.60 119.14 -6.54 1.70e+00 3.46e-01 1.48e+01 angle pdb=" CB GLU C 898 " pdb=" CG GLU C 898 " pdb=" CD GLU C 898 " ideal model delta sigma weight residual 112.60 119.10 -6.50 1.70e+00 3.46e-01 1.46e+01 ... (remaining 36550 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 14863 17.92 - 35.84: 1432 35.84 - 53.76: 314 53.76 - 71.69: 90 71.69 - 89.61: 38 Dihedral angle restraints: 16737 sinusoidal: 7299 harmonic: 9438 Sorted by residual: dihedral pdb=" CB CYS C1044 " pdb=" SG CYS C1044 " pdb=" SG CYS C1088 " pdb=" CB CYS C1088 " ideal model delta sinusoidal sigma weight residual 93.00 11.85 81.15 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" CB CYS A1044 " pdb=" SG CYS A1044 " pdb=" SG CYS A1088 " pdb=" CB CYS A1088 " ideal model delta sinusoidal sigma weight residual 93.00 13.40 79.60 1 1.00e+01 1.00e-02 7.87e+01 dihedral pdb=" CB CYS B1044 " pdb=" SG CYS B1044 " pdb=" SG CYS B1088 " pdb=" CB CYS B1088 " ideal model delta sinusoidal sigma weight residual 93.00 14.75 78.25 1 1.00e+01 1.00e-02 7.64e+01 ... (remaining 16734 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 3925 0.082 - 0.164: 399 0.164 - 0.246: 8 0.246 - 0.328: 2 0.328 - 0.411: 1 Chirality restraints: 4335 Sorted by residual: chirality pdb=" C1 NAG C1314 " pdb=" ND2 ASN C 17 " pdb=" C2 NAG C1314 " pdb=" O5 NAG C1314 " both_signs ideal model delta sigma weight residual False -2.40 -1.99 -0.41 2.00e-01 2.50e+01 4.22e+00 chirality pdb=" C1 NAG C1302 " pdb=" ND2 ASN C 305 " pdb=" C2 NAG C1302 " pdb=" O5 NAG C1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.13 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" C1 NAG B1302 " pdb=" ND2 ASN B 305 " pdb=" C2 NAG B1302 " pdb=" O5 NAG B1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.14 -0.26 2.00e-01 2.50e+01 1.69e+00 ... (remaining 4332 not shown) Planarity restraints: 4668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" ND BLA B1310 " 0.469 2.00e-02 2.50e+03 2.53e-01 1.61e+03 pdb=" C1A BLA B1310 " -0.336 2.00e-02 2.50e+03 pdb=" C1D BLA B1310 " 0.019 2.00e-02 2.50e+03 pdb=" C2D BLA B1310 " 0.040 2.00e-02 2.50e+03 pdb=" C3D BLA B1310 " -0.000 2.00e-02 2.50e+03 pdb=" C4D BLA B1310 " 0.231 2.00e-02 2.50e+03 pdb=" CAD BLA B1310 " -0.252 2.00e-02 2.50e+03 pdb=" CHA BLA B1310 " 0.146 2.00e-02 2.50e+03 pdb=" CHD BLA B1310 " -0.403 2.00e-02 2.50e+03 pdb=" CMD BLA B1310 " 0.086 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA A1310 " 0.421 2.00e-02 2.50e+03 2.13e-01 1.13e+03 pdb=" C1A BLA A1310 " -0.278 2.00e-02 2.50e+03 pdb=" C1D BLA A1310 " 0.018 2.00e-02 2.50e+03 pdb=" C2D BLA A1310 " 0.026 2.00e-02 2.50e+03 pdb=" C3D BLA A1310 " 0.008 2.00e-02 2.50e+03 pdb=" C4D BLA A1310 " 0.190 2.00e-02 2.50e+03 pdb=" CAD BLA A1310 " -0.191 2.00e-02 2.50e+03 pdb=" CHA BLA A1310 " 0.088 2.00e-02 2.50e+03 pdb=" CHD BLA A1310 " -0.337 2.00e-02 2.50e+03 pdb=" CMD BLA A1310 " 0.055 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" ND BLA C1310 " 0.303 2.00e-02 2.50e+03 1.83e-01 8.38e+02 pdb=" C1A BLA C1310 " -0.165 2.00e-02 2.50e+03 pdb=" C1D BLA C1310 " -0.010 2.00e-02 2.50e+03 pdb=" C2D BLA C1310 " 0.047 2.00e-02 2.50e+03 pdb=" C3D BLA C1310 " -0.016 2.00e-02 2.50e+03 pdb=" C4D BLA C1310 " 0.143 2.00e-02 2.50e+03 pdb=" CAD BLA C1310 " -0.240 2.00e-02 2.50e+03 pdb=" CHA BLA C1310 " 0.097 2.00e-02 2.50e+03 pdb=" CHD BLA C1310 " -0.318 2.00e-02 2.50e+03 pdb=" CMD BLA C1310 " 0.158 2.00e-02 2.50e+03 ... (remaining 4665 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.80: 7023 2.80 - 3.33: 21781 3.33 - 3.85: 44718 3.85 - 4.38: 52693 4.38 - 4.90: 90931 Nonbonded interactions: 217146 Sorted by model distance: nonbonded pdb=" O GLN A 897 " pdb=" OG1 THR A 901 " model vdw 2.280 3.040 nonbonded pdb=" O GLN C 897 " pdb=" OG1 THR C 901 " model vdw 2.288 3.040 nonbonded pdb=" OG1 THR C 874 " pdb=" OD1 ASN C 876 " model vdw 2.309 3.040 nonbonded pdb=" OG1 THR B1087 " pdb=" OD1 ASP B1089 " model vdw 2.325 3.040 nonbonded pdb=" OG SER A 765 " pdb=" OE1 GLN A 766 " model vdw 2.334 3.040 ... (remaining 217141 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' selection = chain 'B' selection = chain 'C' } ncs_group { reference = chain 'D' selection = chain 'G' selection = chain 'J' } ncs_group { reference = chain 'E' selection = chain 'F' selection = chain 'H' selection = chain 'I' selection = chain 'K' selection = chain 'L' } 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=0.00 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: 2.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 0.330 Check model and map are aligned: 0.070 Set scattering table: 0.070 Process input model: 26.870 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: 0.000 Load rotamer database and sin/cos tables:7.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.750 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 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 : 0.003 0.077 26931 Z= 0.174 Angle : 0.630 14.937 36831 Z= 0.320 Chirality : 0.045 0.411 4335 Planarity : 0.008 0.253 4617 Dihedral : 15.147 89.608 10560 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 1.25 % Allowed : 15.94 % Favored : 82.82 % 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: -0.26 (0.13), residues: 3219 helix: 0.73 (0.18), residues: 693 sheet: 0.49 (0.18), residues: 711 loop : -0.80 (0.13), residues: 1815 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 42 TYR 0.026 0.001 TYR B 227 PHE 0.037 0.001 PHE A 41 TRP 0.016 0.001 TRP B 848 HIS 0.007 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00346 (26826) covalent geometry : angle 0.58807 (36555) SS BOND : bond 0.00453 ( 39) SS BOND : angle 1.89078 ( 78) hydrogen bonds : bond 0.18980 ( 968) hydrogen bonds : angle 7.81580 ( 2637) link_ALPHA1-3 : bond 0.00923 ( 3) link_ALPHA1-3 : angle 1.07874 ( 9) link_BETA1-4 : bond 0.00453 ( 12) link_BETA1-4 : angle 1.81177 ( 36) link_NAG-ASN : bond 0.00518 ( 51) link_NAG-ASN : angle 3.18163 ( 153) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 145 time to evaluate : 1.027 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.8750 (m-80) cc_final: 0.8496 (m-80) REVERT: A 227 TYR cc_start: 0.8729 (p90) cc_final: 0.8454 (p90) REVERT: A 717 GLN cc_start: 0.8305 (mt0) cc_final: 0.7943 (mm110) REVERT: A 919 GLN cc_start: 0.8901 (tt0) cc_final: 0.8695 (tt0) REVERT: A 948 LYS cc_start: 0.8538 (OUTLIER) cc_final: 0.8304 (ttpt) REVERT: B 39 ASP cc_start: 0.8466 (t70) cc_final: 0.7880 (t0) REVERT: B 948 LYS cc_start: 0.8527 (mtpp) cc_final: 0.8322 (ttpt) REVERT: C 39 ASP cc_start: 0.8071 (OUTLIER) cc_final: 0.7667 (t0) REVERT: C 122 CYS cc_start: 0.8842 (OUTLIER) cc_final: 0.8479 (m) REVERT: C 227 TYR cc_start: 0.8687 (p90) cc_final: 0.8402 (p90) REVERT: C 795 PHE cc_start: 0.5965 (OUTLIER) cc_final: 0.5543 (m-80) REVERT: C 898 GLU cc_start: 0.8329 (mm-30) cc_final: 0.8104 (mm-30) outliers start: 35 outliers final: 27 residues processed: 176 average time/residue: 0.6296 time to fit residues: 130.7552 Evaluate side-chains 165 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 134 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 547 LEU Chi-restraints excluded: chain A residue 755 ASP Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain A residue 1068 GLN Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 122 CYS Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 641 THR Chi-restraints excluded: chain B residue 742 GLU Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 45 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 115 THR Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 315 VAL Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 755 ASP Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 796 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 197 optimal weight: 7.9990 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 0.8980 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 0.9980 chunk 207 optimal weight: 0.8980 chunk 155 optimal weight: 9.9990 chunk 244 optimal weight: 4.9990 chunk 183 optimal weight: 9.9990 chunk 298 optimal weight: 5.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 766 GLN A 897 GLN A 927 GLN A 964 GLN A1081 ASN B 863 GLN C 766 GLN C 863 GLN C 897 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.092157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.067234 restraints weight = 46982.952| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.67 r_work: 0.2835 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2722 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.0792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 26931 Z= 0.180 Angle : 0.537 8.839 36831 Z= 0.274 Chirality : 0.044 0.377 4335 Planarity : 0.004 0.043 4617 Dihedral : 6.266 59.011 4997 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.85 % Allowed : 14.87 % Favored : 83.28 % 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: 0.32 (0.14), residues: 3219 helix: 1.91 (0.20), residues: 675 sheet: 0.69 (0.19), residues: 705 loop : -0.64 (0.13), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 428 TYR 0.017 0.001 TYR C 239 PHE 0.013 0.001 PHE A 124 TRP 0.017 0.001 TRP A 848 HIS 0.005 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00411 (26826) covalent geometry : angle 0.50875 (36555) SS BOND : bond 0.00573 ( 39) SS BOND : angle 1.64134 ( 78) hydrogen bonds : bond 0.04927 ( 968) hydrogen bonds : angle 5.86678 ( 2637) link_ALPHA1-3 : bond 0.00795 ( 3) link_ALPHA1-3 : angle 1.30236 ( 9) link_BETA1-4 : bond 0.00317 ( 12) link_BETA1-4 : angle 1.83877 ( 36) link_NAG-ASN : bond 0.00355 ( 51) link_NAG-ASN : angle 2.31439 ( 153) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 145 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 314 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8249 (OUTLIER) REVERT: A 717 GLN cc_start: 0.8429 (mt0) cc_final: 0.8115 (mm110) REVERT: A 790 LEU cc_start: 0.8617 (tp) cc_final: 0.8347 (tt) REVERT: A 948 LYS cc_start: 0.8518 (mtpm) cc_final: 0.8250 (ttpt) REVERT: B 39 ASP cc_start: 0.8451 (t70) cc_final: 0.7927 (t0) REVERT: B 948 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8376 (ttpt) REVERT: C 39 ASP cc_start: 0.8070 (OUTLIER) cc_final: 0.7702 (t0) REVERT: C 314 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8350 (OUTLIER) REVERT: C 496 THR cc_start: 0.8487 (m) cc_final: 0.7993 (p) REVERT: C 795 PHE cc_start: 0.5634 (OUTLIER) cc_final: 0.5329 (m-80) outliers start: 52 outliers final: 19 residues processed: 186 average time/residue: 0.6398 time to fit residues: 140.0953 Evaluate side-chains 158 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 137 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 314 GLU Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 314 GLU Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 95 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 282 optimal weight: 3.9990 chunk 73 optimal weight: 0.5980 chunk 34 optimal weight: 4.9990 chunk 273 optimal weight: 7.9990 chunk 17 optimal weight: 9.9990 chunk 109 optimal weight: 0.7980 chunk 165 optimal weight: 5.9990 chunk 158 optimal weight: 8.9990 chunk 294 optimal weight: 0.6980 overall best weight: 2.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 232 ASN A 798 GLN A 964 GLN B 798 GLN B1081 ASN C 927 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3380 r_free = 0.3380 target = 0.091281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2992 r_free = 0.2992 target = 0.066235 restraints weight = 46981.503| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.68 r_work: 0.2813 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2700 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8716 moved from start: 0.1043 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 26931 Z= 0.195 Angle : 0.538 8.814 36831 Z= 0.275 Chirality : 0.045 0.359 4335 Planarity : 0.003 0.042 4617 Dihedral : 6.068 59.853 4965 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 2.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 1.93 % Allowed : 15.01 % Favored : 83.07 % 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: 0.47 (0.14), residues: 3219 helix: 2.04 (0.20), residues: 675 sheet: 0.73 (0.19), residues: 699 loop : -0.51 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 962 TYR 0.017 0.001 TYR A 239 PHE 0.013 0.001 PHE B 124 TRP 0.015 0.001 TRP A 848 HIS 0.004 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00451 (26826) covalent geometry : angle 0.51000 (36555) SS BOND : bond 0.00615 ( 39) SS BOND : angle 1.88737 ( 78) hydrogen bonds : bond 0.04936 ( 968) hydrogen bonds : angle 5.63179 ( 2637) link_ALPHA1-3 : bond 0.00854 ( 3) link_ALPHA1-3 : angle 1.29216 ( 9) link_BETA1-4 : bond 0.00273 ( 12) link_BETA1-4 : angle 1.74982 ( 36) link_NAG-ASN : bond 0.00369 ( 51) link_NAG-ASN : angle 2.19653 ( 153) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 143 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8081 (t0) cc_final: 0.7576 (t0) REVERT: A 302 ARG cc_start: 0.8917 (OUTLIER) cc_final: 0.8546 (mmp-170) REVERT: A 496 THR cc_start: 0.8719 (m) cc_final: 0.8139 (p) REVERT: A 717 GLN cc_start: 0.8460 (mt0) cc_final: 0.8168 (mm110) REVERT: A 790 LEU cc_start: 0.8633 (tp) cc_final: 0.8363 (tt) REVERT: A 948 LYS cc_start: 0.8558 (mtpm) cc_final: 0.8295 (ttpt) REVERT: B 39 ASP cc_start: 0.8534 (OUTLIER) cc_final: 0.8075 (t0) REVERT: B 681 THR cc_start: 0.9253 (OUTLIER) cc_final: 0.8902 (p) REVERT: B 948 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8370 (ttpt) REVERT: C 39 ASP cc_start: 0.8087 (OUTLIER) cc_final: 0.7726 (t0) REVERT: C 254 ASP cc_start: 0.8677 (t0) cc_final: 0.8320 (t0) REVERT: C 496 THR cc_start: 0.8505 (m) cc_final: 0.8080 (p) REVERT: C 795 PHE cc_start: 0.5649 (OUTLIER) cc_final: 0.5343 (m-80) outliers start: 54 outliers final: 28 residues processed: 186 average time/residue: 0.5470 time to fit residues: 121.2589 Evaluate side-chains 169 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 136 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 249 MET Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 39 ASP Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 5 optimal weight: 8.9990 chunk 161 optimal weight: 0.8980 chunk 236 optimal weight: 3.9990 chunk 257 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 223 optimal weight: 0.4980 chunk 26 optimal weight: 5.9990 chunk 195 optimal weight: 6.9990 chunk 303 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 143 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN A1081 ASN C 927 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3011 r_free = 0.3011 target = 0.067214 restraints weight = 46821.315| |-----------------------------------------------------------------------------| r_work (start): 0.2949 rms_B_bonded: 2.66 r_work: 0.2826 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2714 rms_B_bonded: 4.53 restraints_weight: 0.2500 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 26931 Z= 0.144 Angle : 0.505 9.293 36831 Z= 0.258 Chirality : 0.044 0.348 4335 Planarity : 0.003 0.041 4617 Dihedral : 6.014 89.380 4965 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 2.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.28 % Allowed : 15.72 % Favored : 82.99 % 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: 0.55 (0.14), residues: 3219 helix: 2.14 (0.20), residues: 681 sheet: 0.71 (0.19), residues: 705 loop : -0.45 (0.14), residues: 1833 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 962 TYR 0.015 0.001 TYR C 239 PHE 0.014 0.001 PHE C 124 TRP 0.012 0.001 TRP A 848 HIS 0.003 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00327 (26826) covalent geometry : angle 0.47785 (36555) SS BOND : bond 0.00536 ( 39) SS BOND : angle 1.98379 ( 78) hydrogen bonds : bond 0.04375 ( 968) hydrogen bonds : angle 5.46611 ( 2637) link_ALPHA1-3 : bond 0.00733 ( 3) link_ALPHA1-3 : angle 1.19659 ( 9) link_BETA1-4 : bond 0.00311 ( 12) link_BETA1-4 : angle 1.63750 ( 36) link_NAG-ASN : bond 0.00335 ( 51) link_NAG-ASN : angle 2.05441 ( 153) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 144 time to evaluate : 0.886 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 59 ASN cc_start: 0.8160 (t0) cc_final: 0.7745 (t0) REVERT: A 496 THR cc_start: 0.8635 (m) cc_final: 0.8090 (p) REVERT: A 717 GLN cc_start: 0.8431 (mt0) cc_final: 0.8134 (mm110) REVERT: A 790 LEU cc_start: 0.8629 (tp) cc_final: 0.8351 (tt) REVERT: A 948 LYS cc_start: 0.8524 (mtpm) cc_final: 0.8208 (ttpt) REVERT: B 39 ASP cc_start: 0.8500 (t70) cc_final: 0.8065 (t0) REVERT: C 39 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7743 (t0) REVERT: C 254 ASP cc_start: 0.8662 (t0) cc_final: 0.8320 (t0) REVERT: C 496 THR cc_start: 0.8482 (m) cc_final: 0.8110 (p) REVERT: C 795 PHE cc_start: 0.5552 (OUTLIER) cc_final: 0.5252 (m-80) outliers start: 36 outliers final: 24 residues processed: 176 average time/residue: 0.5668 time to fit residues: 118.9960 Evaluate side-chains 161 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 135 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 783 LEU Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 209 optimal weight: 0.0870 chunk 34 optimal weight: 5.9990 chunk 240 optimal weight: 4.9990 chunk 106 optimal weight: 8.9990 chunk 287 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 199 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 140 optimal weight: 2.9990 chunk 262 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.8166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN B1081 ASN C 927 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.091604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2995 r_free = 0.2995 target = 0.066554 restraints weight = 46158.260| |-----------------------------------------------------------------------------| r_work (start): 0.2937 rms_B_bonded: 2.66 r_work: 0.2814 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 26931 Z= 0.168 Angle : 0.521 11.610 36831 Z= 0.266 Chirality : 0.044 0.350 4335 Planarity : 0.003 0.041 4617 Dihedral : 5.972 75.552 4964 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 1.89 % Allowed : 15.19 % Favored : 82.92 % 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: 0.59 (0.14), residues: 3219 helix: 2.18 (0.20), residues: 675 sheet: 0.72 (0.19), residues: 699 loop : -0.41 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C1001 TYR 0.017 0.001 TYR A 239 PHE 0.019 0.001 PHE A 124 TRP 0.011 0.001 TRP A 848 HIS 0.003 0.001 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00387 (26826) covalent geometry : angle 0.49278 (36555) SS BOND : bond 0.00568 ( 39) SS BOND : angle 2.17199 ( 78) hydrogen bonds : bond 0.04476 ( 968) hydrogen bonds : angle 5.39995 ( 2637) link_ALPHA1-3 : bond 0.00749 ( 3) link_ALPHA1-3 : angle 1.24201 ( 9) link_BETA1-4 : bond 0.00263 ( 12) link_BETA1-4 : angle 1.66166 ( 36) link_NAG-ASN : bond 0.00340 ( 51) link_NAG-ASN : angle 2.06660 ( 153) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 137 time to evaluate : 0.879 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 302 ARG cc_start: 0.8926 (OUTLIER) cc_final: 0.8580 (mmp-170) REVERT: A 496 THR cc_start: 0.8635 (m) cc_final: 0.8178 (p) REVERT: A 681 THR cc_start: 0.9279 (OUTLIER) cc_final: 0.8996 (p) REVERT: A 717 GLN cc_start: 0.8458 (mt0) cc_final: 0.8161 (mm110) REVERT: A 790 LEU cc_start: 0.8631 (tp) cc_final: 0.8367 (tt) REVERT: A 948 LYS cc_start: 0.8540 (OUTLIER) cc_final: 0.8291 (ttpt) REVERT: B 39 ASP cc_start: 0.8441 (t70) cc_final: 0.8031 (t0) REVERT: B 496 THR cc_start: 0.8638 (m) cc_final: 0.8044 (p) REVERT: B 681 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.8946 (p) REVERT: C 39 ASP cc_start: 0.8064 (OUTLIER) cc_final: 0.7719 (t0) REVERT: C 254 ASP cc_start: 0.8658 (t0) cc_final: 0.8323 (t0) REVERT: C 496 THR cc_start: 0.8534 (m) cc_final: 0.8186 (p) REVERT: C 795 PHE cc_start: 0.5628 (OUTLIER) cc_final: 0.5365 (m-80) outliers start: 53 outliers final: 31 residues processed: 180 average time/residue: 0.5479 time to fit residues: 118.0763 Evaluate side-chains 169 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 132 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 302 ARG Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 681 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 122 optimal weight: 2.9990 chunk 251 optimal weight: 0.7980 chunk 310 optimal weight: 0.7980 chunk 308 optimal weight: 0.9980 chunk 106 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 227 optimal weight: 0.4980 chunk 206 optimal weight: 2.9990 chunk 170 optimal weight: 6.9990 chunk 183 optimal weight: 10.0000 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN A1081 ASN C 927 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.092412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.067573 restraints weight = 46886.981| |-----------------------------------------------------------------------------| r_work (start): 0.2959 rms_B_bonded: 2.67 r_work: 0.2836 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2724 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2724 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8698 moved from start: 0.1188 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 26931 Z= 0.126 Angle : 0.490 9.584 36831 Z= 0.250 Chirality : 0.043 0.342 4335 Planarity : 0.003 0.040 4617 Dihedral : 5.786 69.615 4964 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 3.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.39 % Allowed : 15.76 % Favored : 82.85 % 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: 0.63 (0.14), residues: 3219 helix: 2.25 (0.20), residues: 681 sheet: 0.65 (0.19), residues: 690 loop : -0.36 (0.14), residues: 1848 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 382 TYR 0.020 0.001 TYR B 557 PHE 0.014 0.001 PHE A 41 TRP 0.011 0.001 TRP A 848 HIS 0.003 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00286 (26826) covalent geometry : angle 0.46485 (36555) SS BOND : bond 0.00474 ( 39) SS BOND : angle 1.82087 ( 78) hydrogen bonds : bond 0.04113 ( 968) hydrogen bonds : angle 5.29772 ( 2637) link_ALPHA1-3 : bond 0.00697 ( 3) link_ALPHA1-3 : angle 1.20576 ( 9) link_BETA1-4 : bond 0.00315 ( 12) link_BETA1-4 : angle 1.57147 ( 36) link_NAG-ASN : bond 0.00317 ( 51) link_NAG-ASN : angle 1.96944 ( 153) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 143 time to evaluate : 0.962 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 THR cc_start: 0.8644 (m) cc_final: 0.8168 (p) REVERT: A 717 GLN cc_start: 0.8413 (mt0) cc_final: 0.8106 (mm110) REVERT: A 790 LEU cc_start: 0.8592 (tp) cc_final: 0.8316 (tt) REVERT: A 948 LYS cc_start: 0.8521 (OUTLIER) cc_final: 0.8276 (ttpt) REVERT: B 39 ASP cc_start: 0.8446 (t70) cc_final: 0.8036 (t0) REVERT: B 496 THR cc_start: 0.8588 (m) cc_final: 0.8016 (p) REVERT: B 681 THR cc_start: 0.9255 (OUTLIER) cc_final: 0.8974 (p) REVERT: C 39 ASP cc_start: 0.8029 (OUTLIER) cc_final: 0.7705 (t0) REVERT: C 254 ASP cc_start: 0.8644 (t0) cc_final: 0.8340 (t0) REVERT: C 496 THR cc_start: 0.8543 (m) cc_final: 0.8218 (p) REVERT: C 795 PHE cc_start: 0.5492 (OUTLIER) cc_final: 0.5264 (m-80) outliers start: 39 outliers final: 28 residues processed: 178 average time/residue: 0.5060 time to fit residues: 107.6934 Evaluate side-chains 168 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 136 time to evaluate : 0.695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 CYS Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain B residue 48 LEU Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 185 optimal weight: 0.0370 chunk 14 optimal weight: 8.9990 chunk 258 optimal weight: 9.9990 chunk 312 optimal weight: 0.9980 chunk 240 optimal weight: 5.9990 chunk 191 optimal weight: 5.9990 chunk 319 optimal weight: 0.9990 chunk 219 optimal weight: 6.9990 chunk 104 optimal weight: 4.9990 chunk 114 optimal weight: 8.9990 chunk 127 optimal weight: 1.9990 overall best weight: 1.8064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN B1081 ASN C 611 GLN C 927 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.091634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.066712 restraints weight = 46719.506| |-----------------------------------------------------------------------------| r_work (start): 0.2938 rms_B_bonded: 2.67 r_work: 0.2815 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2702 rms_B_bonded: 4.52 restraints_weight: 0.2500 r_work (final): 0.2702 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 26931 Z= 0.165 Angle : 0.515 9.886 36831 Z= 0.263 Chirality : 0.044 0.348 4335 Planarity : 0.003 0.041 4617 Dihedral : 5.785 65.617 4963 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 3.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.57 % Allowed : 15.69 % Favored : 82.75 % 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: 0.61 (0.14), residues: 3219 helix: 2.23 (0.20), residues: 675 sheet: 0.72 (0.19), residues: 699 loop : -0.40 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 382 TYR 0.023 0.001 TYR B 557 PHE 0.013 0.001 PHE A 41 TRP 0.013 0.001 TRP C 848 HIS 0.003 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00383 (26826) covalent geometry : angle 0.48828 (36555) SS BOND : bond 0.00570 ( 39) SS BOND : angle 2.08667 ( 78) hydrogen bonds : bond 0.04425 ( 968) hydrogen bonds : angle 5.34506 ( 2637) link_ALPHA1-3 : bond 0.00646 ( 3) link_ALPHA1-3 : angle 1.20019 ( 9) link_BETA1-4 : bond 0.00278 ( 12) link_BETA1-4 : angle 1.64437 ( 36) link_NAG-ASN : bond 0.00326 ( 51) link_NAG-ASN : angle 2.00313 ( 153) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 THR cc_start: 0.8678 (m) cc_final: 0.8201 (p) REVERT: A 717 GLN cc_start: 0.8450 (mt0) cc_final: 0.8133 (mm110) REVERT: A 790 LEU cc_start: 0.8591 (tp) cc_final: 0.8369 (tp) REVERT: A 948 LYS cc_start: 0.8531 (OUTLIER) cc_final: 0.8301 (ttpt) REVERT: B 39 ASP cc_start: 0.8452 (t70) cc_final: 0.8048 (t0) REVERT: B 496 THR cc_start: 0.8669 (m) cc_final: 0.8104 (p) REVERT: B 681 THR cc_start: 0.9283 (OUTLIER) cc_final: 0.9007 (p) REVERT: C 39 ASP cc_start: 0.8106 (OUTLIER) cc_final: 0.7757 (t0) REVERT: C 246 ARG cc_start: 0.8843 (tpt90) cc_final: 0.8580 (mmt-90) REVERT: C 254 ASP cc_start: 0.8645 (t0) cc_final: 0.8337 (t0) REVERT: C 496 THR cc_start: 0.8597 (m) cc_final: 0.8285 (p) outliers start: 44 outliers final: 33 residues processed: 177 average time/residue: 0.5977 time to fit residues: 126.2121 Evaluate side-chains 168 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 132 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 71 SER Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 317 ASN Chi-restraints excluded: chain A residue 333 SER Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 115 THR Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 518 THR Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 681 THR Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 39 ASP Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 122 CYS Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 333 SER Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain C residue 902 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 301 optimal weight: 0.8980 chunk 272 optimal weight: 5.9990 chunk 35 optimal weight: 0.7980 chunk 78 optimal weight: 5.9990 chunk 38 optimal weight: 0.0770 chunk 155 optimal weight: 4.9990 chunk 203 optimal weight: 0.8980 chunk 102 optimal weight: 0.6980 chunk 99 optimal weight: 0.9990 chunk 10 optimal weight: 8.9990 chunk 2 optimal weight: 0.2980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN A1081 ASN C 927 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.093893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.069245 restraints weight = 46821.362| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 2.67 r_work: 0.2869 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8672 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 26931 Z= 0.091 Angle : 0.466 8.828 36831 Z= 0.236 Chirality : 0.042 0.328 4335 Planarity : 0.003 0.040 4617 Dihedral : 5.423 59.053 4960 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.07 % Allowed : 16.26 % Favored : 82.67 % 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: 0.63 (0.14), residues: 3219 helix: 2.34 (0.20), residues: 684 sheet: 0.59 (0.19), residues: 681 loop : -0.37 (0.14), residues: 1854 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 962 TYR 0.023 0.001 TYR B 557 PHE 0.022 0.001 PHE B 41 TRP 0.018 0.001 TRP A 848 HIS 0.002 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00195 (26826) covalent geometry : angle 0.44407 (36555) SS BOND : bond 0.00349 ( 39) SS BOND : angle 1.49748 ( 78) hydrogen bonds : bond 0.03638 ( 968) hydrogen bonds : angle 5.14735 ( 2637) link_ALPHA1-3 : bond 0.00701 ( 3) link_ALPHA1-3 : angle 1.22840 ( 9) link_BETA1-4 : bond 0.00382 ( 12) link_BETA1-4 : angle 1.44346 ( 36) link_NAG-ASN : bond 0.00333 ( 51) link_NAG-ASN : angle 1.85736 ( 153) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 151 time to evaluate : 0.997 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 THR cc_start: 0.8653 (m) cc_final: 0.8198 (p) REVERT: A 717 GLN cc_start: 0.8352 (mt0) cc_final: 0.8005 (mm110) REVERT: A 790 LEU cc_start: 0.8576 (tp) cc_final: 0.8364 (tp) REVERT: A 948 LYS cc_start: 0.8470 (mtpm) cc_final: 0.8240 (ttpt) REVERT: B 39 ASP cc_start: 0.8445 (t70) cc_final: 0.7989 (t0) REVERT: B 496 THR cc_start: 0.8545 (m) cc_final: 0.8006 (p) REVERT: C 39 ASP cc_start: 0.7989 (m-30) cc_final: 0.7743 (t0) REVERT: C 246 ARG cc_start: 0.8865 (tpt90) cc_final: 0.8589 (mmt-90) REVERT: C 254 ASP cc_start: 0.8616 (t0) cc_final: 0.8354 (t0) REVERT: C 496 THR cc_start: 0.8587 (m) cc_final: 0.8272 (p) REVERT: C 795 PHE cc_start: 0.5501 (OUTLIER) cc_final: 0.5298 (m-80) REVERT: C 1081 ASN cc_start: 0.8918 (m-40) cc_final: 0.8652 (m110) outliers start: 30 outliers final: 23 residues processed: 179 average time/residue: 0.5913 time to fit residues: 126.3514 Evaluate side-chains 165 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 141 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Chi-restraints excluded: chain C residue 902 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 42 optimal weight: 2.9990 chunk 197 optimal weight: 4.9990 chunk 219 optimal weight: 4.9990 chunk 269 optimal weight: 4.9990 chunk 210 optimal weight: 6.9990 chunk 161 optimal weight: 0.7980 chunk 94 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 116 optimal weight: 0.0670 chunk 133 optimal weight: 0.8980 chunk 313 optimal weight: 8.9990 overall best weight: 1.7522 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN B 927 GLN C 578 GLN C 927 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3392 r_free = 0.3392 target = 0.092000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3006 r_free = 0.3006 target = 0.067020 restraints weight = 46766.441| |-----------------------------------------------------------------------------| r_work (start): 0.2948 rms_B_bonded: 2.68 r_work: 0.2823 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2710 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 26931 Z= 0.164 Angle : 0.547 26.412 36831 Z= 0.270 Chirality : 0.047 1.084 4335 Planarity : 0.003 0.040 4617 Dihedral : 5.581 59.788 4954 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.28 % Allowed : 16.08 % Favored : 82.64 % 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: 0.72 (0.14), residues: 3219 helix: 2.34 (0.20), residues: 681 sheet: 0.75 (0.19), residues: 699 loop : -0.34 (0.14), residues: 1839 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 440 TYR 0.024 0.001 TYR B 557 PHE 0.023 0.001 PHE B 41 TRP 0.024 0.001 TRP B 848 HIS 0.002 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00381 (26826) covalent geometry : angle 0.49645 (36555) SS BOND : bond 0.00540 ( 39) SS BOND : angle 2.24141 ( 78) hydrogen bonds : bond 0.04253 ( 968) hydrogen bonds : angle 5.24228 ( 2637) link_ALPHA1-3 : bond 0.00636 ( 3) link_ALPHA1-3 : angle 1.23859 ( 9) link_BETA1-4 : bond 0.00260 ( 12) link_BETA1-4 : angle 1.62720 ( 36) link_NAG-ASN : bond 0.00433 ( 51) link_NAG-ASN : angle 3.12594 ( 153) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 143 time to evaluate : 0.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 THR cc_start: 0.8690 (m) cc_final: 0.8223 (p) REVERT: A 717 GLN cc_start: 0.8425 (mt0) cc_final: 0.8084 (mm110) REVERT: A 790 LEU cc_start: 0.8552 (tp) cc_final: 0.8344 (tp) REVERT: A 948 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8280 (ttpt) REVERT: B 39 ASP cc_start: 0.8469 (t70) cc_final: 0.8037 (t0) REVERT: B 496 THR cc_start: 0.8635 (m) cc_final: 0.8091 (p) REVERT: C 39 ASP cc_start: 0.8134 (m-30) cc_final: 0.7806 (t0) REVERT: C 246 ARG cc_start: 0.8840 (tpt90) cc_final: 0.8569 (mmt-90) REVERT: C 254 ASP cc_start: 0.8624 (t0) cc_final: 0.8337 (t0) REVERT: C 402 ASP cc_start: 0.9058 (p0) cc_final: 0.8764 (p0) REVERT: C 496 THR cc_start: 0.8607 (m) cc_final: 0.8300 (p) REVERT: C 795 PHE cc_start: 0.5611 (OUTLIER) cc_final: 0.5384 (m-80) outliers start: 36 outliers final: 26 residues processed: 177 average time/residue: 0.6110 time to fit residues: 128.5489 Evaluate side-chains 167 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 139 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 795 PHE Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 14 optimal weight: 20.0000 chunk 35 optimal weight: 0.7980 chunk 162 optimal weight: 4.9990 chunk 202 optimal weight: 1.9990 chunk 289 optimal weight: 2.9990 chunk 296 optimal weight: 5.9990 chunk 47 optimal weight: 2.9990 chunk 293 optimal weight: 0.0870 chunk 153 optimal weight: 0.9990 chunk 249 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 overall best weight: 1.1764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 964 GLN B1081 ASN C 927 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3406 r_free = 0.3406 target = 0.092818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.068053 restraints weight = 46648.389| |-----------------------------------------------------------------------------| r_work (start): 0.2967 rms_B_bonded: 2.66 r_work: 0.2845 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2732 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.062 26931 Z= 0.126 Angle : 0.515 16.280 36831 Z= 0.259 Chirality : 0.045 0.674 4335 Planarity : 0.003 0.041 4617 Dihedral : 5.511 59.064 4954 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 3.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 1.07 % Allowed : 16.43 % Favored : 82.50 % 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: 0.68 (0.14), residues: 3219 helix: 2.35 (0.20), residues: 681 sheet: 0.60 (0.19), residues: 675 loop : -0.31 (0.14), residues: 1863 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 962 TYR 0.025 0.001 TYR B 557 PHE 0.022 0.001 PHE B 41 TRP 0.021 0.001 TRP B 848 HIS 0.003 0.000 HIS A 24 Details of bonding type rmsd covalent geometry : bond 0.00288 (26826) covalent geometry : angle 0.47864 (36555) SS BOND : bond 0.00478 ( 39) SS BOND : angle 2.25704 ( 78) hydrogen bonds : bond 0.03971 ( 968) hydrogen bonds : angle 5.20241 ( 2637) link_ALPHA1-3 : bond 0.00666 ( 3) link_ALPHA1-3 : angle 1.22085 ( 9) link_BETA1-4 : bond 0.00286 ( 12) link_BETA1-4 : angle 1.52292 ( 36) link_NAG-ASN : bond 0.00354 ( 51) link_NAG-ASN : angle 2.44601 ( 153) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 6438 Ramachandran restraints generated. 3219 Oldfield, 0 Emsley, 3219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 143 time to evaluate : 0.770 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 496 THR cc_start: 0.8674 (m) cc_final: 0.8219 (p) REVERT: A 717 GLN cc_start: 0.8391 (mt0) cc_final: 0.8059 (mm110) REVERT: A 948 LYS cc_start: 0.8502 (OUTLIER) cc_final: 0.8284 (ttpt) REVERT: B 496 THR cc_start: 0.8601 (m) cc_final: 0.8060 (p) REVERT: C 39 ASP cc_start: 0.8121 (m-30) cc_final: 0.7780 (t0) REVERT: C 246 ARG cc_start: 0.8865 (tpt90) cc_final: 0.8594 (mmt-90) REVERT: C 254 ASP cc_start: 0.8605 (t0) cc_final: 0.8342 (t0) REVERT: C 402 ASP cc_start: 0.9051 (p0) cc_final: 0.8747 (p0) REVERT: C 496 THR cc_start: 0.8589 (m) cc_final: 0.8294 (p) REVERT: C 1081 ASN cc_start: 0.8906 (m-40) cc_final: 0.8647 (m110) outliers start: 30 outliers final: 26 residues processed: 170 average time/residue: 0.5550 time to fit residues: 112.1063 Evaluate side-chains 165 residues out of total 2805 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 138 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 156 ARG Chi-restraints excluded: chain A residue 177 GLN Chi-restraints excluded: chain A residue 231 ASP Chi-restraints excluded: chain A residue 518 THR Chi-restraints excluded: chain A residue 580 VAL Chi-restraints excluded: chain A residue 597 SER Chi-restraints excluded: chain A residue 641 THR Chi-restraints excluded: chain A residue 836 THR Chi-restraints excluded: chain A residue 948 LYS Chi-restraints excluded: chain B residue 45 THR Chi-restraints excluded: chain B residue 72 VAL Chi-restraints excluded: chain B residue 75 SER Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 131 VAL Chi-restraints excluded: chain B residue 231 ASP Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 375 VAL Chi-restraints excluded: chain B residue 580 VAL Chi-restraints excluded: chain B residue 597 SER Chi-restraints excluded: chain B residue 836 THR Chi-restraints excluded: chain C residue 75 SER Chi-restraints excluded: chain C residue 156 ARG Chi-restraints excluded: chain C residue 231 ASP Chi-restraints excluded: chain C residue 518 THR Chi-restraints excluded: chain C residue 580 VAL Chi-restraints excluded: chain C residue 641 THR Chi-restraints excluded: chain C residue 836 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 321 random chunks: chunk 62 optimal weight: 5.9990 chunk 278 optimal weight: 8.9990 chunk 85 optimal weight: 2.9990 chunk 149 optimal weight: 6.9990 chunk 49 optimal weight: 7.9990 chunk 236 optimal weight: 3.9990 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 89 optimal weight: 6.9990 chunk 266 optimal weight: 1.9990 chunk 264 optimal weight: 5.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 590 HIS A1081 ASN B 590 HIS B1081 ASN C 927 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3368 r_free = 0.3368 target = 0.090527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2979 r_free = 0.2979 target = 0.065598 restraints weight = 46707.281| |-----------------------------------------------------------------------------| r_work (start): 0.2918 rms_B_bonded: 2.66 r_work: 0.2793 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2678 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 26931 Z= 0.242 Angle : 0.590 12.736 36831 Z= 0.299 Chirality : 0.047 0.554 4335 Planarity : 0.003 0.040 4617 Dihedral : 5.855 59.504 4954 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.32 % Allowed : 16.01 % Favored : 82.67 % 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: 0.57 (0.14), residues: 3219 helix: 2.15 (0.20), residues: 675 sheet: 0.68 (0.19), residues: 699 loop : -0.40 (0.14), residues: 1845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 382 TYR 0.025 0.001 TYR B 557 PHE 0.022 0.001 PHE B 41 TRP 0.023 0.002 TRP B 848 HIS 0.003 0.001 HIS C 243 Details of bonding type rmsd covalent geometry : bond 0.00566 (26826) covalent geometry : angle 0.55151 (36555) SS BOND : bond 0.00694 ( 39) SS BOND : angle 2.97414 ( 78) hydrogen bonds : bond 0.04934 ( 968) hydrogen bonds : angle 5.43074 ( 2637) link_ALPHA1-3 : bond 0.00649 ( 3) link_ALPHA1-3 : angle 1.19674 ( 9) link_BETA1-4 : bond 0.00241 ( 12) link_BETA1-4 : angle 1.74569 ( 36) link_NAG-ASN : bond 0.00386 ( 51) link_NAG-ASN : angle 2.42182 ( 153) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10286.45 seconds wall clock time: 175 minutes 46.76 seconds (10546.76 seconds total)