Starting phenix.real_space_refine on Thu Oct 29 04:42:23 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.cif Found real_map, /net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.cif" model { file = "/net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7m0r_23613/10_2026/7m0r_23613.cif" } resolution = 3.7 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= 0.001 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 4 9.91 5 S 202 5.16 5 C 19538 2.51 5 N 5316 2.21 5 O 5838 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 160 residue(s): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.3rc1-6221/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 30898 Number of models: 1 Model: "" Number of chains: 5 Chain: "E" Number of atoms: 2915 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 2915 Classifications: {'peptide': 458} Incomplete info: {'truncation_to_alanine': 205} Link IDs: {'PCIS': 2, 'PTRANS': 27, 'TRANS': 428} Chain breaks: 12 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 758 Unresolved non-hydrogen angles: 973 Unresolved non-hydrogen dihedrals: 635 Unresolved non-hydrogen chiralities: 71 Planarities with less than four sites: {'GLU:plan': 18, 'ASN:plan1': 10, 'ARG:plan': 17, 'GLN:plan1': 9, 'HIS:plan': 1, 'ASP:plan': 8, 'TYR:plan': 9, 'TRP:plan': 5, 'PHE:plan': 10} Unresolved non-hydrogen planarities: 420 Chain: "C" Number of atoms: 4167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 523, 4167 Classifications: {'peptide': 523} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 31, 'TRANS': 490} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 8 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 325 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 325 Classifications: {'peptide': 65} Incomplete info: {'truncation_to_alanine': 65} Link IDs: {'TRANS': 64} Chain breaks: 5 Unresolved non-hydrogen bonds: 130 Unresolved non-hydrogen angles: 195 Unresolved non-hydrogen dihedrals: 65 Planarities with less than four sites: {'UNK:plan-1': 65} Unresolved non-hydrogen planarities: 65 Chain: "A" Number of atoms: 8040 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1133, 8040 Classifications: {'peptide': 1133} Incomplete info: {'truncation_to_alanine': 214} Link IDs: {'PCIS': 2, 'PTRANS': 61, 'TRANS': 1069} Chain breaks: 7 Unresolved non-hydrogen bonds: 858 Unresolved non-hydrogen angles: 1054 Unresolved non-hydrogen dihedrals: 693 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'ARG:plan': 29, 'GLU:plan': 45, 'HIS:plan': 5, 'TYR:plan': 2, 'ASP:plan': 14, 'ASN:plan1': 17, 'GLN:plan1': 24, 'PHE:plan': 4, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 586 Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Restraints were copied for chains: F, D, B Time building chain proxies: 13.78, per 1000 atoms: 0.45 Number of scatterers: 30898 At special positions: 0 Unit cell: (232.2, 135, 177.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 4 19.99 S 202 16.00 O 5838 8.00 N 5316 7.00 C 19538 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=70, symmetry=0 Simple disulfide: pdb=" SG CYS E 27 " - pdb=" SG CYS E 54 " distance=2.04 Simple disulfide: pdb=" SG CYS E 82 " - pdb=" SG CYS E 104 " distance=2.03 Simple disulfide: pdb=" SG CYS E 147 " - pdb=" SG CYS E 173 " distance=2.03 Simple disulfide: pdb=" SG CYS E 206 " - pdb=" SG CYS E 228 " distance=2.03 Simple disulfide: pdb=" SG CYS C 103 " - pdb=" SG CYS C 114 " distance=2.03 Simple disulfide: pdb=" SG CYS C 132 " - pdb=" SG CYS C 141 " distance=2.03 Simple disulfide: pdb=" SG CYS C 269 " - pdb=" SG CYS C 381 " distance=2.03 Simple disulfide: pdb=" SG CYS C 293 " - pdb=" SG CYS C 341 " distance=2.03 Simple disulfide: pdb=" SG CYS C 517 " - pdb=" SG CYS C 535 " distance=2.03 Simple disulfide: pdb=" SG CYS C 524 " - pdb=" SG CYS C 567 " distance=2.03 Simple disulfide: pdb=" SG CYS C 527 " - pdb=" SG CYS C 542 " distance=2.03 Simple disulfide: pdb=" SG CYS F 27 " - pdb=" SG CYS F 54 " distance=2.04 Simple disulfide: pdb=" SG CYS F 82 " - pdb=" SG CYS F 104 " distance=2.03 Simple disulfide: pdb=" SG CYS F 147 " - pdb=" SG CYS F 173 " distance=2.03 Simple disulfide: pdb=" SG CYS F 206 " - pdb=" SG CYS F 228 " distance=2.03 Simple disulfide: pdb=" SG CYS D 103 " - pdb=" SG CYS D 114 " distance=2.03 Simple disulfide: pdb=" SG CYS D 132 " - pdb=" SG CYS D 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 269 " - pdb=" SG CYS D 381 " distance=2.03 Simple disulfide: pdb=" SG CYS D 293 " - pdb=" SG CYS D 341 " distance=2.03 Simple disulfide: pdb=" SG CYS D 517 " - pdb=" SG CYS D 535 " distance=2.03 Simple disulfide: pdb=" SG CYS D 524 " - pdb=" SG CYS D 567 " distance=2.03 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 542 " distance=2.03 Simple disulfide: pdb=" SG CYS A 94 " - pdb=" SG CYS A 103 " distance=2.03 Simple disulfide: pdb=" SG CYS A 129 " - pdb=" SG CYS A 137 " distance=2.03 Simple disulfide: pdb=" SG CYS A 283 " - pdb=" SG CYS A 404 " distance=2.03 Simple disulfide: pdb=" SG CYS A 299 " - pdb=" SG CYS A 355 " distance=2.03 Simple disulfide: pdb=" SG CYS A 373 " - pdb=" SG CYS A 392 " distance=2.03 Simple disulfide: pdb=" SG CYS A 509 " - pdb=" SG CYS A 526 " distance=2.03 Simple disulfide: pdb=" SG CYS A 515 " - pdb=" SG CYS A 557 " distance=2.04 Simple disulfide: pdb=" SG CYS A 518 " - pdb=" SG CYS A 535 " distance=2.03 Simple disulfide: pdb=" SG CYS A 529 " - pdb=" SG CYS A 541 " distance=2.03 Simple disulfide: pdb=" SG CYS A 592 " - pdb=" SG CYS A 611 " distance=2.03 Simple disulfide: pdb=" SG CYS A 655 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS A 661 " - pdb=" SG CYS A 700 " distance=2.03 Simple disulfide: pdb=" SG CYS A 664 " - pdb=" SG CYS A 680 " distance=2.03 Simple disulfide: pdb=" SG CYS A 674 " - pdb=" SG CYS A 687 " distance=2.03 Simple disulfide: pdb=" SG CYS A 738 " - pdb=" SG CYS A 761 " distance=2.03 Simple disulfide: pdb=" SG CYS A 803 " - pdb=" SG CYS A 822 " distance=2.03 Simple disulfide: pdb=" SG CYS A 810 " - pdb=" SG CYS A 854 " distance=2.03 Simple disulfide: pdb=" SG CYS A 813 " - pdb=" SG CYS A 831 " distance=2.03 Simple disulfide: pdb=" SG CYS A 825 " - pdb=" SG CYS A 837 " distance=2.03 Simple disulfide: pdb=" SG CYS A 900 " - pdb=" SG CYS A 915 " distance=2.03 Simple disulfide: pdb=" SG CYS A 932 " - pdb=" SG CYS A 936 " distance=2.03 Simple disulfide: pdb=" SG CYS A 993 " - pdb=" SG CYS A1005 " distance=2.04 Simple disulfide: pdb=" SG CYS A1085 " - pdb=" SG CYS A1095 " distance=2.03 Simple disulfide: pdb=" SG CYS A1189 " - pdb=" SG CYS A1200 " distance=2.04 Simple disulfide: pdb=" SG CYS B 94 " - pdb=" SG CYS B 103 " distance=2.03 Simple disulfide: pdb=" SG CYS B 129 " - pdb=" SG CYS B 137 " distance=2.03 Simple disulfide: pdb=" SG CYS B 283 " - pdb=" SG CYS B 404 " distance=2.03 Simple disulfide: pdb=" SG CYS B 299 " - pdb=" SG CYS B 355 " distance=2.03 Simple disulfide: pdb=" SG CYS B 373 " - pdb=" SG CYS B 392 " distance=2.03 Simple disulfide: pdb=" SG CYS B 509 " - pdb=" SG CYS B 526 " distance=2.03 Simple disulfide: pdb=" SG CYS B 515 " - pdb=" SG CYS B 557 " distance=2.03 Simple disulfide: pdb=" SG CYS B 518 " - pdb=" SG CYS B 535 " distance=2.03 Simple disulfide: pdb=" SG CYS B 529 " - pdb=" SG CYS B 541 " distance=2.03 Simple disulfide: pdb=" SG CYS B 592 " - pdb=" SG CYS B 611 " distance=2.03 Simple disulfide: pdb=" SG CYS B 655 " - pdb=" SG CYS B 671 " distance=2.03 Simple disulfide: pdb=" SG CYS B 661 " - pdb=" SG CYS B 700 " distance=2.03 Simple disulfide: pdb=" SG CYS B 664 " - pdb=" SG CYS B 680 " distance=2.03 Simple disulfide: pdb=" SG CYS B 674 " - pdb=" SG CYS B 687 " distance=2.03 Simple disulfide: pdb=" SG CYS B 738 " - pdb=" SG CYS B 761 " distance=2.03 Simple disulfide: pdb=" SG CYS B 803 " - pdb=" SG CYS B 822 " distance=2.03 Simple disulfide: pdb=" SG CYS B 810 " - pdb=" SG CYS B 854 " distance=2.03 Simple disulfide: pdb=" SG CYS B 813 " - pdb=" SG CYS B 831 " distance=2.04 Simple disulfide: pdb=" SG CYS B 825 " - pdb=" SG CYS B 837 " distance=2.04 Simple disulfide: pdb=" SG CYS B 900 " - pdb=" SG CYS B 915 " distance=2.03 Simple disulfide: pdb=" SG CYS B 932 " - pdb=" SG CYS B 936 " distance=2.03 Simple disulfide: pdb=" SG CYS B 993 " - pdb=" SG CYS B1005 " distance=2.04 Simple disulfide: pdb=" SG CYS B1085 " - pdb=" SG CYS B1095 " distance=2.03 Simple disulfide: pdb=" SG CYS B1189 " - pdb=" SG CYS B1200 " distance=2.04 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 Time building additional restraints: 2.64 Conformation dependent library (CDL) restraints added in 1.5 seconds 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8092 Finding SS restraints... Secondary structure from input PDB file: 52 helices and 86 sheets defined 8.7% alpha, 36.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'E' and resid 302 through 306 Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.686A pdb=" N TYR E 429 " --> pdb=" O ILE E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 459 through 463 removed outlier: 3.590A pdb=" N ARG E 463 " --> pdb=" O GLU E 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 42 Processing helix chain 'C' and resid 96 through 107 Processing helix chain 'C' and resid 149 through 153 Processing helix chain 'C' and resid 237 through 240 Processing helix chain 'C' and resid 345 through 353 Processing helix chain 'C' and resid 391 through 395 Processing helix chain 'C' and resid 396 through 406 Processing helix chain 'C' and resid 415 through 419 removed outlier: 3.720A pdb=" N ARG C 419 " --> pdb=" O ILE C 416 " (cutoff:3.500A) Processing helix chain 'C' and resid 517 through 521 Processing helix chain 'C' and resid 523 through 530 Processing helix chain 'F' and resid 302 through 306 Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.685A pdb=" N TYR F 429 " --> pdb=" O ILE F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 459 through 463 removed outlier: 3.590A pdb=" N ARG F 463 " --> pdb=" O GLU F 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 42 Processing helix chain 'D' and resid 96 through 107 Processing helix chain 'D' and resid 149 through 153 Processing helix chain 'D' and resid 237 through 240 Processing helix chain 'D' and resid 345 through 353 Processing helix chain 'D' and resid 391 through 395 Processing helix chain 'D' and resid 396 through 406 Processing helix chain 'D' and resid 415 through 419 removed outlier: 3.721A pdb=" N ARG D 419 " --> pdb=" O ILE D 416 " (cutoff:3.500A) Processing helix chain 'D' and resid 517 through 521 Processing helix chain 'D' and resid 523 through 530 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 229 through 236 removed outlier: 3.875A pdb=" N PHE A 233 " --> pdb=" O PRO A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 326 removed outlier: 3.522A pdb=" N THR A 324 " --> pdb=" O VAL A 320 " (cutoff:3.500A) Processing helix chain 'A' and resid 359 through 375 Processing helix chain 'A' and resid 382 through 386 removed outlier: 3.559A pdb=" N LEU A 385 " --> pdb=" O LEU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 514 through 521 Processing helix chain 'A' and resid 617 through 624 removed outlier: 4.033A pdb=" N ARG A 621 " --> pdb=" O LYS A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 658 removed outlier: 3.634A pdb=" N VAL A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 661 through 667 removed outlier: 3.511A pdb=" N SER A 667 " --> pdb=" O SER A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 809 through 816 removed outlier: 3.546A pdb=" N ALA A 816 " --> pdb=" O LEU A 812 " (cutoff:3.500A) Processing helix chain 'A' and resid 817 through 821 Processing helix chain 'A' and resid 885 through 890 Processing helix chain 'A' and resid 1124 through 1129 Processing helix chain 'B' and resid 154 through 158 Processing helix chain 'B' and resid 229 through 236 removed outlier: 3.875A pdb=" N PHE B 233 " --> pdb=" O PRO B 229 " (cutoff:3.500A) Processing helix chain 'B' and resid 318 through 326 removed outlier: 3.522A pdb=" N THR B 324 " --> pdb=" O VAL B 320 " (cutoff:3.500A) Processing helix chain 'B' and resid 359 through 375 Processing helix chain 'B' and resid 382 through 386 removed outlier: 3.560A pdb=" N LEU B 385 " --> pdb=" O LEU B 382 " (cutoff:3.500A) Processing helix chain 'B' and resid 514 through 521 Processing helix chain 'B' and resid 617 through 624 removed outlier: 4.034A pdb=" N ARG B 621 " --> pdb=" O LYS B 617 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 658 removed outlier: 3.634A pdb=" N VAL B 657 " --> pdb=" O ASN B 654 " (cutoff:3.500A) Processing helix chain 'B' and resid 661 through 667 removed outlier: 3.512A pdb=" N SER B 667 " --> pdb=" O SER B 663 " (cutoff:3.500A) Processing helix chain 'B' and resid 809 through 816 removed outlier: 3.547A pdb=" N ALA B 816 " --> pdb=" O LEU B 812 " (cutoff:3.500A) Processing helix chain 'B' and resid 817 through 821 Processing helix chain 'B' and resid 885 through 890 Processing helix chain 'B' and resid 1124 through 1129 Processing sheet with id=AA1, first strand: chain 'E' and resid 29 through 32 removed outlier: 5.944A pdb=" N ASP E 91 " --> pdb=" O LEU E 99 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU E 99 " --> pdb=" O ASP E 91 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 37 through 40 Processing sheet with id=AA3, first strand: chain 'E' and resid 148 through 151 removed outlier: 6.677A pdb=" N ILE E 213 " --> pdb=" O ILE E 224 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 155 through 159 removed outlier: 6.916A pdb=" N GLY E 257 " --> pdb=" O PHE E 192 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE E 192 " --> pdb=" O GLY E 257 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER E 259 " --> pdb=" O GLU E 190 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 277 through 278 removed outlier: 7.056A pdb=" N CYS E 424 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL E 336 " --> pdb=" O CYS E 424 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG E 402 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N LEU E 332 " --> pdb=" O ILE E 400 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE E 400 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 9.512A pdb=" N ARG E 334 " --> pdb=" O PRO E 398 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL E 336 " --> pdb=" O SER E 396 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER E 396 " --> pdb=" O VAL E 336 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA E 338 " --> pdb=" O VAL E 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL E 394 " --> pdb=" O ALA E 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY E 340 " --> pdb=" O LEU E 392 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU E 392 " --> pdb=" O GLY E 340 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N THR E 357 " --> pdb=" O VAL E 409 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP E 411 " --> pdb=" O VAL E 355 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL E 355 " --> pdb=" O TRP E 411 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 433 through 434 removed outlier: 7.087A pdb=" N CYS E 583 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL E 495 " --> pdb=" O CYS E 583 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 433 through 434 removed outlier: 7.087A pdb=" N CYS E 583 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 4.970A pdb=" N VAL E 495 " --> pdb=" O CYS E 583 " (cutoff:3.500A) removed outlier: 7.681A pdb=" N ARG E 560 " --> pdb=" O LEU E 489 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASP E 491 " --> pdb=" O SER E 558 " (cutoff:3.500A) removed outlier: 9.331A pdb=" N SER E 558 " --> pdb=" O ASP E 491 " (cutoff:3.500A) removed outlier: 9.584A pdb=" N LYS E 493 " --> pdb=" O PRO E 556 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL E 495 " --> pdb=" O PHE E 554 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N PHE E 554 " --> pdb=" O VAL E 495 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N GLY E 497 " --> pdb=" O ARG E 552 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG E 552 " --> pdb=" O GLY E 497 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE E 499 " --> pdb=" O GLU E 550 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N GLU E 550 " --> pdb=" O ILE E 499 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 32 through 34 removed outlier: 6.768A pdb=" N LYS C 460 " --> pdb=" O LEU C 477 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N GLU C 479 " --> pdb=" O VAL C 458 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL C 458 " --> pdb=" O GLU C 479 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR C 457 " --> pdb=" O THR C 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN C 433 " --> pdb=" O GLY C 452 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 46 through 48 Processing sheet with id=AB1, first strand: chain 'C' and resid 60 through 63 Processing sheet with id=AB2, first strand: chain 'C' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS C 132 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 121 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR C 130 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA C 123 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS C 128 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS C 132 " --> pdb=" O LYS C 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU C 121 " --> pdb=" O TYR C 130 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR C 130 " --> pdb=" O LEU C 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA C 123 " --> pdb=" O HIS C 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS C 128 " --> pdb=" O ALA C 123 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'C' and resid 178 through 182 Processing sheet with id=AB5, first strand: chain 'C' and resid 225 through 232 removed outlier: 3.644A pdb=" N ARG C 248 " --> pdb=" O ARG C 225 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N PHE C 246 " --> pdb=" O ILE C 227 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N ALA C 229 " --> pdb=" O TYR C 244 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N TYR C 244 " --> pdb=" O ALA C 229 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N LEU C 231 " --> pdb=" O LYS C 242 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LYS C 242 " --> pdb=" O LEU C 231 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'C' and resid 294 through 296 Processing sheet with id=AB7, first strand: chain 'C' and resid 307 through 314 removed outlier: 5.808A pdb=" N LEU C 308 " --> pdb=" O THR C 329 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N THR C 329 " --> pdb=" O LEU C 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP C 310 " --> pdb=" O VAL C 327 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET C 422 " --> pdb=" O VAL C 340 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'C' and resid 535 through 537 Processing sheet with id=AB9, first strand: chain 'C' and resid 593 through 595 removed outlier: 5.258A pdb=" N UNK C 666 " --> pdb=" O UNK C 658 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N UNK C 658 " --> pdb=" O UNK C 666 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N UNK C 668 " --> pdb=" O UNK C 656 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N UNK C 656 " --> pdb=" O UNK C 668 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'C' and resid 602 through 604 Processing sheet with id=AC2, first strand: chain 'F' and resid 29 through 32 removed outlier: 5.944A pdb=" N ASP F 91 " --> pdb=" O LEU F 99 " (cutoff:3.500A) removed outlier: 5.372A pdb=" N LEU F 99 " --> pdb=" O ASP F 91 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 37 through 40 Processing sheet with id=AC4, first strand: chain 'F' and resid 148 through 151 removed outlier: 6.677A pdb=" N ILE F 213 " --> pdb=" O ILE F 224 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 155 through 159 removed outlier: 6.915A pdb=" N GLY F 257 " --> pdb=" O PHE F 192 " (cutoff:3.500A) removed outlier: 4.257A pdb=" N PHE F 192 " --> pdb=" O GLY F 257 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N SER F 259 " --> pdb=" O GLU F 190 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 277 through 278 removed outlier: 7.056A pdb=" N CYS F 424 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N VAL F 336 " --> pdb=" O CYS F 424 " (cutoff:3.500A) removed outlier: 7.114A pdb=" N ARG F 402 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 9.785A pdb=" N LEU F 332 " --> pdb=" O ILE F 400 " (cutoff:3.500A) removed outlier: 8.693A pdb=" N ILE F 400 " --> pdb=" O LEU F 332 " (cutoff:3.500A) removed outlier: 9.513A pdb=" N ARG F 334 " --> pdb=" O PRO F 398 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL F 336 " --> pdb=" O SER F 396 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N SER F 396 " --> pdb=" O VAL F 336 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ALA F 338 " --> pdb=" O VAL F 394 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N VAL F 394 " --> pdb=" O ALA F 338 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N GLY F 340 " --> pdb=" O LEU F 392 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N LEU F 392 " --> pdb=" O GLY F 340 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N THR F 357 " --> pdb=" O VAL F 409 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N TRP F 411 " --> pdb=" O VAL F 355 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N VAL F 355 " --> pdb=" O TRP F 411 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'F' and resid 433 through 434 removed outlier: 7.088A pdb=" N CYS F 583 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL F 495 " --> pdb=" O CYS F 583 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 433 through 434 removed outlier: 7.088A pdb=" N CYS F 583 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 4.969A pdb=" N VAL F 495 " --> pdb=" O CYS F 583 " (cutoff:3.500A) removed outlier: 7.680A pdb=" N ARG F 560 " --> pdb=" O LEU F 489 " (cutoff:3.500A) removed outlier: 10.392A pdb=" N ASP F 491 " --> pdb=" O SER F 558 " (cutoff:3.500A) removed outlier: 9.330A pdb=" N SER F 558 " --> pdb=" O ASP F 491 " (cutoff:3.500A) removed outlier: 9.583A pdb=" N LYS F 493 " --> pdb=" O PRO F 556 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N VAL F 495 " --> pdb=" O PHE F 554 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N PHE F 554 " --> pdb=" O VAL F 495 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N GLY F 497 " --> pdb=" O ARG F 552 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ARG F 552 " --> pdb=" O GLY F 497 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N ILE F 499 " --> pdb=" O GLU F 550 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N GLU F 550 " --> pdb=" O ILE F 499 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'D' and resid 32 through 34 removed outlier: 6.768A pdb=" N LYS D 460 " --> pdb=" O LEU D 477 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N GLU D 479 " --> pdb=" O VAL D 458 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N VAL D 458 " --> pdb=" O GLU D 479 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N THR D 457 " --> pdb=" O THR D 453 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLN D 433 " --> pdb=" O GLY D 452 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'D' and resid 46 through 48 Processing sheet with id=AD2, first strand: chain 'D' and resid 60 through 63 Processing sheet with id=AD3, first strand: chain 'D' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS D 132 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 121 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR D 130 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA D 123 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS D 128 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'D' and resid 116 through 123 removed outlier: 6.779A pdb=" N CYS D 132 " --> pdb=" O LYS D 119 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N LEU D 121 " --> pdb=" O TYR D 130 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR D 130 " --> pdb=" O LEU D 121 " (cutoff:3.500A) removed outlier: 5.436A pdb=" N ALA D 123 " --> pdb=" O HIS D 128 " (cutoff:3.500A) removed outlier: 7.684A pdb=" N HIS D 128 " --> pdb=" O ALA D 123 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'D' and resid 178 through 182 Processing sheet with id=AD6, first strand: chain 'D' and resid 225 through 232 removed outlier: 3.644A pdb=" N ARG D 248 " --> pdb=" O ARG D 225 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N PHE D 246 " --> pdb=" O ILE D 227 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N ALA D 229 " --> pdb=" O TYR D 244 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N TYR D 244 " --> pdb=" O ALA D 229 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N LEU D 231 " --> pdb=" O LYS D 242 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N LYS D 242 " --> pdb=" O LEU D 231 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'D' and resid 294 through 296 Processing sheet with id=AD8, first strand: chain 'D' and resid 307 through 314 removed outlier: 5.809A pdb=" N LEU D 308 " --> pdb=" O THR D 329 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N THR D 329 " --> pdb=" O LEU D 308 " (cutoff:3.500A) removed outlier: 4.031A pdb=" N ASP D 310 " --> pdb=" O VAL D 327 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N MET D 422 " --> pdb=" O VAL D 340 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'D' and resid 535 through 537 Processing sheet with id=AE1, first strand: chain 'D' and resid 593 through 595 removed outlier: 5.260A pdb=" N UNK D 666 " --> pdb=" O UNK D 658 " (cutoff:3.500A) removed outlier: 6.672A pdb=" N UNK D 658 " --> pdb=" O UNK D 666 " (cutoff:3.500A) removed outlier: 5.394A pdb=" N UNK D 668 " --> pdb=" O UNK D 656 " (cutoff:3.500A) removed outlier: 6.449A pdb=" N UNK D 656 " --> pdb=" O UNK D 668 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 602 through 604 Processing sheet with id=AE3, first strand: chain 'A' and resid 41 through 43 Processing sheet with id=AE4, first strand: chain 'A' and resid 50 through 55 removed outlier: 3.570A pdb=" N VAL A 81 " --> pdb=" O LYS A 72 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'A' and resid 88 through 90 Processing sheet with id=AE6, first strand: chain 'A' and resid 114 through 120 removed outlier: 3.558A pdb=" N MET A 116 " --> pdb=" O CYS A 129 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ARG A 125 " --> pdb=" O ASP A 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY A 149 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'A' and resid 168 through 173 removed outlier: 3.718A pdb=" N ILE A 198 " --> pdb=" O ILE A 226 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'A' and resid 242 through 249 removed outlier: 6.759A pdb=" N LEU A 256 " --> pdb=" O VAL A 244 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N GLY A 246 " --> pdb=" O TYR A 254 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N TYR A 254 " --> pdb=" O GLY A 246 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER A 248 " --> pdb=" O PHE A 252 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE A 252 " --> pdb=" O SER A 248 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL A 274 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 14.206A pdb=" N TYR A 275 " --> pdb=" O CYS A 299 " (cutoff:3.500A) removed outlier: 10.724A pdb=" N CYS A 299 " --> pdb=" O TYR A 275 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER A 277 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL A 418 " --> pdb=" O GLU A 294 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'A' and resid 412 through 413 removed outlier: 19.702A pdb=" N VAL A 293 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 17.152A pdb=" N ALA A 312 " --> pdb=" O VAL A 293 " (cutoff:3.500A) removed outlier: 17.418A pdb=" N VAL A 295 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 13.354A pdb=" N GLN A 310 " --> pdb=" O VAL A 295 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ILE A 297 " --> pdb=" O LEU A 308 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N LEU A 308 " --> pdb=" O ILE A 297 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL A 337 " --> pdb=" O GLN A 310 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA A 312 " --> pdb=" O PHE A 335 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE A 335 " --> pdb=" O ALA A 312 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU A 314 " --> pdb=" O LEU A 333 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N LEU A 333 " --> pdb=" O LEU A 314 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N SER A 352 " --> pdb=" O THR A 425 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR A 425 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU A 354 " --> pdb=" O VAL A 423 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'A' and resid 434 through 435 removed outlier: 6.305A pdb=" N LEU A 454 " --> pdb=" O THR A 471 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR A 471 " --> pdb=" O LEU A 454 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N LYS A 456 " --> pdb=" O TYR A 469 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'A' and resid 527 through 529 Processing sheet with id=AF3, first strand: chain 'A' and resid 559 through 562 Processing sheet with id=AF4, first strand: chain 'A' and resid 566 through 568 removed outlier: 6.329A pdb=" N THR A 644 " --> pdb=" O SER A 638 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER A 638 " --> pdb=" O THR A 644 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ALA A 646 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL A 590 " --> pdb=" O GLY A 602 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N ASP A 601 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR A 612 " --> pdb=" O ASP A 601 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'A' and resid 679 through 681 Processing sheet with id=AF6, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AF7, first strand: chain 'A' and resid 710 through 712 Processing sheet with id=AF8, first strand: chain 'A' and resid 715 through 722 removed outlier: 5.658A pdb=" N VAL A 715 " --> pdb=" O SER A 765 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER A 765 " --> pdb=" O VAL A 715 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS A 717 " --> pdb=" O ASN A 763 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN A 763 " --> pdb=" O LYS A 717 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'A' and resid 824 through 825 removed outlier: 3.779A pdb=" N GLN A 830 " --> pdb=" O CYS A 825 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'A' and resid 858 through 859 removed outlier: 5.615A pdb=" N VAL A 929 " --> pdb=" O SER A 944 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL A 893 " --> pdb=" O CYS A 900 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'A' and resid 954 through 957 removed outlier: 7.075A pdb=" N THR A 974 " --> pdb=" O ALA A 956 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N ASN A1006 " --> pdb=" O PHE A 995 " (cutoff:3.500A) removed outlier: 5.167A pdb=" N PHE A 995 " --> pdb=" O ASN A1006 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'A' and resid 962 through 963 Processing sheet with id=AG4, first strand: chain 'A' and resid 987 through 988 Processing sheet with id=AG5, first strand: chain 'A' and resid 1040 through 1044 removed outlier: 5.282A pdb=" N ILE A1041 " --> pdb=" O THR A1062 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR A1062 " --> pdb=" O ILE A1041 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE A1084 " --> pdb=" O GLN A1096 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N GLU A1116 " --> pdb=" O LYS A1075 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'A' and resid 1048 through 1050 removed outlier: 6.020A pdb=" N SER A1049 " --> pdb=" O TYR A1138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AG6 Processing sheet with id=AG7, first strand: chain 'A' and resid 1142 through 1143 Processing sheet with id=AG8, first strand: chain 'A' and resid 1180 through 1183 Processing sheet with id=AG9, first strand: chain 'B' and resid 41 through 43 Processing sheet with id=AH1, first strand: chain 'B' and resid 50 through 55 removed outlier: 3.571A pdb=" N VAL B 81 " --> pdb=" O LYS B 72 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'B' and resid 88 through 90 Processing sheet with id=AH3, first strand: chain 'B' and resid 114 through 120 removed outlier: 3.557A pdb=" N MET B 116 " --> pdb=" O CYS B 129 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG B 125 " --> pdb=" O ASP B 120 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N GLY B 149 " --> pdb=" O LEU B 139 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'B' and resid 168 through 173 removed outlier: 3.718A pdb=" N ILE B 198 " --> pdb=" O ILE B 226 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'B' and resid 242 through 249 removed outlier: 6.759A pdb=" N LEU B 256 " --> pdb=" O VAL B 244 " (cutoff:3.500A) removed outlier: 4.511A pdb=" N GLY B 246 " --> pdb=" O TYR B 254 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N TYR B 254 " --> pdb=" O GLY B 246 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N SER B 248 " --> pdb=" O PHE B 252 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N PHE B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N VAL B 274 " --> pdb=" O GLU B 261 " (cutoff:3.500A) removed outlier: 14.206A pdb=" N TYR B 275 " --> pdb=" O CYS B 299 " (cutoff:3.500A) removed outlier: 10.723A pdb=" N CYS B 299 " --> pdb=" O TYR B 275 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N SER B 277 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 8.853A pdb=" N VAL B 418 " --> pdb=" O GLU B 294 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'B' and resid 412 through 413 removed outlier: 19.702A pdb=" N VAL B 293 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 17.152A pdb=" N ALA B 312 " --> pdb=" O VAL B 293 " (cutoff:3.500A) removed outlier: 17.418A pdb=" N VAL B 295 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 13.354A pdb=" N GLN B 310 " --> pdb=" O VAL B 295 " (cutoff:3.500A) removed outlier: 10.069A pdb=" N ILE B 297 " --> pdb=" O LEU B 308 " (cutoff:3.500A) removed outlier: 6.109A pdb=" N LEU B 308 " --> pdb=" O ILE B 297 " (cutoff:3.500A) removed outlier: 6.508A pdb=" N VAL B 337 " --> pdb=" O GLN B 310 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA B 312 " --> pdb=" O PHE B 335 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N PHE B 335 " --> pdb=" O ALA B 312 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N LEU B 314 " --> pdb=" O LEU B 333 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N LEU B 333 " --> pdb=" O LEU B 314 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N SER B 352 " --> pdb=" O THR B 425 " (cutoff:3.500A) removed outlier: 4.763A pdb=" N THR B 425 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.795A pdb=" N LEU B 354 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'B' and resid 434 through 435 removed outlier: 6.305A pdb=" N LEU B 454 " --> pdb=" O THR B 471 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N THR B 471 " --> pdb=" O LEU B 454 " (cutoff:3.500A) removed outlier: 7.116A pdb=" N LYS B 456 " --> pdb=" O TYR B 469 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'B' and resid 527 through 529 Processing sheet with id=AH9, first strand: chain 'B' and resid 559 through 562 Processing sheet with id=AI1, first strand: chain 'B' and resid 566 through 568 removed outlier: 6.329A pdb=" N THR B 644 " --> pdb=" O SER B 638 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N SER B 638 " --> pdb=" O THR B 644 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N ALA B 646 " --> pdb=" O LEU B 636 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL B 590 " --> pdb=" O GLY B 602 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ASP B 601 " --> pdb=" O TYR B 612 " (cutoff:3.500A) removed outlier: 5.673A pdb=" N TYR B 612 " --> pdb=" O ASP B 601 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'B' and resid 679 through 681 Processing sheet with id=AI3, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AI4, first strand: chain 'B' and resid 710 through 712 Processing sheet with id=AI5, first strand: chain 'B' and resid 715 through 722 removed outlier: 5.657A pdb=" N VAL B 715 " --> pdb=" O SER B 765 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N SER B 765 " --> pdb=" O VAL B 715 " (cutoff:3.500A) removed outlier: 5.772A pdb=" N LYS B 717 " --> pdb=" O ASN B 763 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASN B 763 " --> pdb=" O LYS B 717 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'B' and resid 824 through 825 removed outlier: 3.779A pdb=" N GLN B 830 " --> pdb=" O CYS B 825 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'B' and resid 858 through 859 removed outlier: 5.615A pdb=" N VAL B 929 " --> pdb=" O SER B 944 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL B 893 " --> pdb=" O CYS B 900 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'B' and resid 954 through 957 removed outlier: 7.075A pdb=" N THR B 974 " --> pdb=" O ALA B 956 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ASN B1006 " --> pdb=" O PHE B 995 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N PHE B 995 " --> pdb=" O ASN B1006 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'B' and resid 962 through 963 Processing sheet with id=AJ1, first strand: chain 'B' and resid 987 through 988 Processing sheet with id=AJ2, first strand: chain 'B' and resid 1040 through 1044 removed outlier: 5.282A pdb=" N ILE B1041 " --> pdb=" O THR B1062 " (cutoff:3.500A) removed outlier: 6.068A pdb=" N THR B1062 " --> pdb=" O ILE B1041 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE B1084 " --> pdb=" O GLN B1096 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N GLU B1116 " --> pdb=" O LYS B1075 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'B' and resid 1048 through 1050 removed outlier: 6.020A pdb=" N SER B1049 " --> pdb=" O TYR B1138 " (cutoff:3.500A) No H-bonds generated for sheet with id=AJ3 Processing sheet with id=AJ4, first strand: chain 'B' and resid 1142 through 1143 Processing sheet with id=AJ5, first strand: chain 'B' and resid 1180 through 1183 1088 hydrogen bonds defined for protein. 2760 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: 8.12 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 10292 1.35 - 1.47: 7588 1.47 - 1.59: 13410 1.59 - 1.71: 0 1.71 - 1.83: 262 Bond restraints: 31552 Sorted by residual: bond pdb=" N ALA A 896 " pdb=" CA ALA A 896 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" N ALA B 896 " pdb=" CA ALA B 896 " ideal model delta sigma weight residual 1.458 1.483 -0.025 1.23e-02 6.61e+03 4.06e+00 bond pdb=" C HIS D 406 " pdb=" N PRO D 407 " ideal model delta sigma weight residual 1.331 1.316 0.015 7.90e-03 1.60e+04 3.75e+00 bond pdb=" N ALA A1025 " pdb=" CA ALA A1025 " ideal model delta sigma weight residual 1.457 1.479 -0.022 1.17e-02 7.31e+03 3.53e+00 bond pdb=" C SER D 188 " pdb=" N GLY D 189 " ideal model delta sigma weight residual 1.332 1.323 0.009 5.00e-03 4.00e+04 3.50e+00 ... (remaining 31547 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.78: 41766 1.78 - 3.57: 1151 3.57 - 5.35: 108 5.35 - 7.13: 23 7.13 - 8.91: 6 Bond angle restraints: 43054 Sorted by residual: angle pdb=" N PRO C 465 " pdb=" CA PRO C 465 " pdb=" CB PRO C 465 " ideal model delta sigma weight residual 103.00 110.41 -7.41 1.10e+00 8.26e-01 4.54e+01 angle pdb=" N PRO D 465 " pdb=" CA PRO D 465 " pdb=" CB PRO D 465 " ideal model delta sigma weight residual 103.00 110.40 -7.40 1.10e+00 8.26e-01 4.53e+01 angle pdb=" N GLY E 101 " pdb=" CA GLY E 101 " pdb=" C GLY E 101 " ideal model delta sigma weight residual 111.37 116.93 -5.56 1.29e+00 6.01e-01 1.86e+01 angle pdb=" N GLY F 101 " pdb=" CA GLY F 101 " pdb=" C GLY F 101 " ideal model delta sigma weight residual 111.37 116.91 -5.54 1.29e+00 6.01e-01 1.84e+01 angle pdb=" N VAL A 895 " pdb=" CA VAL A 895 " pdb=" C VAL A 895 " ideal model delta sigma weight residual 109.58 104.98 4.60 1.29e+00 6.01e-01 1.27e+01 ... (remaining 43049 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.00: 17354 18.00 - 36.00: 1172 36.00 - 54.01: 216 54.01 - 72.01: 54 72.01 - 90.01: 28 Dihedral angle restraints: 18824 sinusoidal: 6276 harmonic: 12548 Sorted by residual: dihedral pdb=" CB CYS A 825 " pdb=" SG CYS A 825 " pdb=" SG CYS A 837 " pdb=" CB CYS A 837 " ideal model delta sinusoidal sigma weight residual -86.00 -176.01 90.01 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B 825 " pdb=" SG CYS B 825 " pdb=" SG CYS B 837 " pdb=" CB CYS B 837 " ideal model delta sinusoidal sigma weight residual -86.00 -176.00 90.00 1 1.00e+01 1.00e-02 9.60e+01 dihedral pdb=" CB CYS B 993 " pdb=" SG CYS B 993 " pdb=" SG CYS B1005 " pdb=" CB CYS B1005 " ideal model delta sinusoidal sigma weight residual 93.00 177.80 -84.80 1 1.00e+01 1.00e-02 8.73e+01 ... (remaining 18821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 3806 0.047 - 0.095: 809 0.095 - 0.142: 332 0.142 - 0.189: 19 0.189 - 0.237: 4 Chirality restraints: 4970 Sorted by residual: chirality pdb=" CA PRO C 465 " pdb=" N PRO C 465 " pdb=" C PRO C 465 " pdb=" CB PRO C 465 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CA PRO D 465 " pdb=" N PRO D 465 " pdb=" C PRO D 465 " pdb=" CB PRO D 465 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CA VAL A 783 " pdb=" N VAL A 783 " pdb=" C VAL A 783 " pdb=" CB VAL A 783 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.21e-01 ... (remaining 4967 not shown) Planarity restraints: 5652 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASP C 318 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.84e+00 pdb=" N PRO C 319 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO C 319 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO C 319 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP D 318 " 0.028 5.00e-02 4.00e+02 4.21e-02 2.83e+00 pdb=" N PRO D 319 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO D 319 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO D 319 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 295 " 0.027 5.00e-02 4.00e+02 4.01e-02 2.58e+00 pdb=" N PRO B 296 " -0.069 5.00e-02 4.00e+02 pdb=" CA PRO B 296 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 296 " 0.022 5.00e-02 4.00e+02 ... (remaining 5649 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.62: 495 2.62 - 3.19: 28224 3.19 - 3.76: 48924 3.76 - 4.33: 66806 4.33 - 4.90: 108093 Nonbonded interactions: 252542 Sorted by model distance: nonbonded pdb=" O ILE F 253 " pdb="CA CA F 602 " model vdw 2.056 2.510 nonbonded pdb=" O ILE E 253 " pdb="CA CA E 602 " model vdw 2.056 2.510 nonbonded pdb=" OG1 THR B 41 " pdb=" OE1 GLN B 500 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" OE1 GLN A 500 " model vdw 2.160 3.040 nonbonded pdb=" OH TYR A 768 " pdb=" O ILE A 773 " model vdw 2.173 3.040 ... (remaining 252537 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: 0.09 Found NCS groups: ncs_group { reference = chain 'E' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.580 Check model and map are aligned: 0.100 Set scattering table: 0.080 Process input model: 37.760 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8206 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 : 0.004 0.043 31622 Z= 0.213 Angle : 0.715 8.913 43194 Z= 0.422 Chirality : 0.046 0.237 4970 Planarity : 0.004 0.042 5652 Dihedral : 12.838 89.852 10522 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 16.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.04 % Allowed : 6.44 % Favored : 92.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -2.49 (0.12), residues: 4132 helix: -2.20 (0.25), residues: 292 sheet: -1.13 (0.13), residues: 1368 loop : -1.94 (0.11), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 301 TYR 0.020 0.001 TYR B 653 PHE 0.023 0.002 PHE E 189 TRP 0.015 0.002 TRP C 537 HIS 0.008 0.001 HIS E 130 Details of bonding type rmsd/Z covalent geometry : bond 0.00423 / 0.21 (31552) covalent geometry : angle 0.71054 / 0.42 (43054) SS BOND : bond 0.00358 / 0.26 ( 70) SS BOND : angle 1.60141 / 1.16 ( 140) hydrogen bonds : bond 0.16660 / 11.03 ( 1038) hydrogen bonds : angle 8.51835 / 5.90 ( 2760) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 237 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 207 time to evaluate : 1.049 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 262 MET cc_start: 0.7152 (ttp) cc_final: 0.6799 (ptm) REVERT: A 346 MET cc_start: 0.8376 (tpt) cc_final: 0.7576 (pmm) REVERT: A 554 MET cc_start: 0.8305 (mmm) cc_final: 0.8016 (tpp) REVERT: B 262 MET cc_start: 0.7309 (ttp) cc_final: 0.6769 (ptm) REVERT: B 346 MET cc_start: 0.8467 (tpt) cc_final: 0.7607 (pmm) REVERT: B 554 MET cc_start: 0.8221 (mmm) cc_final: 0.7900 (tpp) outliers start: 30 outliers final: 8 residues processed: 237 average time/residue: 0.2143 time to fit residues: 79.2608 Evaluate side-chains 124 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 116 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain D residue 543 SER Chi-restraints excluded: chain A residue 891 SER Chi-restraints excluded: chain B residue 891 SER Chi-restraints excluded: chain B residue 1124 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [197, 388, 215, 20, 132, 261, 248, 207, 401, 424, 155] chunk 197 optimal weight: 5.9990 chunk 388 optimal weight: 6.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 0.0170 chunk 132 optimal weight: 20.0000 chunk 261 optimal weight: 20.0000 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 40.0000 chunk 424 optimal weight: 3.9990 chunk 155 optimal weight: 0.7980 overall best weight: 3.3624 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 59 GLN E 130 HIS E 149 GLN E 150 ASN E 223 HIS C 44 ASN C 76 HIS C 209 HIS ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 358 HIS C 411 ASN C 433 GLN C 445 GLN C 566 HIS F 59 GLN F 130 HIS F 149 GLN F 150 ASN F 223 HIS D 44 ASN D 76 HIS D 209 HIS ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 358 HIS D 411 ASN D 445 GLN D 566 HIS A 51 ASN A 114 ASN A 218 HIS A 273 GLN A 371 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 977 ASN A 979 ASN B 51 ASN B 114 ASN B 218 HIS B 273 GLN B 371 GLN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 977 ASN B 979 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.076512 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 81)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.049979 restraints weight = 187200.931| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.051065 restraints weight = 88728.390| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.051703 restraints weight = 55691.622| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.052102 restraints weight = 41888.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.052302 restraints weight = 35801.262| |-----------------------------------------------------------------------------| r_work (final): 0.3271 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 31622 Z= 0.170 Angle : 0.609 7.969 43194 Z= 0.318 Chirality : 0.046 0.217 4970 Planarity : 0.004 0.044 5652 Dihedral : 5.366 58.331 4592 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % Rotamer: Outliers : 1.87 % Allowed : 11.50 % Favored : 86.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.91 (0.12), residues: 4132 helix: -1.56 (0.28), residues: 306 sheet: -0.73 (0.14), residues: 1354 loop : -1.57 (0.12), residues: 2472 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 484 TYR 0.020 0.001 TYR A 653 PHE 0.017 0.001 PHE B 652 TRP 0.017 0.002 TRP C 537 HIS 0.007 0.001 HIS D 216 Details of bonding type rmsd/Z covalent geometry : bond 0.00382 / 0.17 (31552) covalent geometry : angle 0.60468 / 0.32 (43054) SS BOND : bond 0.00327 / 0.23 ( 70) SS BOND : angle 1.45170 / 1.10 ( 140) hydrogen bonds : bond 0.03741 / 2.52 ( 1038) hydrogen bonds : angle 6.78581 / 4.68 ( 2760) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 125 time to evaluate : 1.272 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 346 MET cc_start: 0.8448 (tpt) cc_final: 0.7596 (pmm) REVERT: A 489 ASP cc_start: 0.7703 (p0) cc_final: 0.7499 (p0) REVERT: B 346 MET cc_start: 0.8513 (tpt) cc_final: 0.7610 (pmm) REVERT: B 417 MET cc_start: 0.8591 (tmm) cc_final: 0.7752 (tmm) outliers start: 54 outliers final: 24 residues processed: 173 average time/residue: 0.1737 time to fit residues: 51.4160 Evaluate side-chains 141 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 117 time to evaluate : 0.986 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 488 THR Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 488 THR Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [14, 318, 109, 131, 430, 321, 218, 298, 178, 17, 47] chunk 14 optimal weight: 20.0000 chunk 318 optimal weight: 9.9990 chunk 109 optimal weight: 8.9990 chunk 131 optimal weight: 40.0000 chunk 430 optimal weight: 50.0000 chunk 321 optimal weight: 8.9990 chunk 218 optimal weight: 0.8980 chunk 298 optimal weight: 7.9990 chunk 178 optimal weight: 6.9990 chunk 17 optimal weight: 8.9990 chunk 47 optimal weight: 9.9990 overall best weight: 6.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 256 HIS C 281 ASN C 406 HIS ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 433 GLN A 124 ASN A 206 ASN ** A 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 725 ASN A 733 GLN ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN B 124 ASN ** B 630 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.075304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3241 r_free = 0.3241 target = 0.050437 restraints weight = 189079.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3322 r_free = 0.3322 target = 0.051807 restraints weight = 102392.159| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3300 r_free = 0.3300 target = 0.051625 restraints weight = 59222.230| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.051686 restraints weight = 45133.075| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.051744 restraints weight = 44651.781| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.092 31622 Z= 0.290 Angle : 0.668 7.770 43194 Z= 0.348 Chirality : 0.047 0.193 4970 Planarity : 0.005 0.049 5652 Dihedral : 5.422 57.435 4588 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 14.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 3.32 % Allowed : 14.37 % Favored : 82.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.77 (0.13), residues: 4132 helix: -1.29 (0.30), residues: 294 sheet: -0.74 (0.14), residues: 1340 loop : -1.42 (0.12), residues: 2498 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG B 548 TYR 0.016 0.002 TYR A 653 PHE 0.021 0.002 PHE A1033 TRP 0.015 0.002 TRP B 824 HIS 0.007 0.002 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00652 / 0.29 (31552) covalent geometry : angle 0.66425 / 0.35 (43054) SS BOND : bond 0.00398 / 0.29 ( 70) SS BOND : angle 1.39702 / 1.06 ( 140) hydrogen bonds : bond 0.03859 / 2.60 ( 1038) hydrogen bonds : angle 6.72796 / 4.64 ( 2760) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 96 poor density : 117 time to evaluate : 1.160 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.8904 (mmm) cc_final: 0.8624 (mmp) REVERT: C 267 GLN cc_start: 0.9210 (OUTLIER) cc_final: 0.8261 (pp30) REVERT: F 182 MET cc_start: 0.5092 (mmt) cc_final: 0.4830 (mmt) REVERT: F 245 MET cc_start: 0.8895 (mmm) cc_final: 0.8627 (mmp) REVERT: D 409 MET cc_start: 0.9044 (OUTLIER) cc_final: 0.8721 (mmm) REVERT: A 212 MET cc_start: 0.8443 (mmm) cc_final: 0.8226 (mmm) REVERT: A 489 ASP cc_start: 0.7874 (p0) cc_final: 0.7563 (p0) REVERT: A 833 LEU cc_start: 0.2411 (OUTLIER) cc_final: 0.2185 (pp) REVERT: B 212 MET cc_start: 0.8451 (mmm) cc_final: 0.8238 (mmm) REVERT: B 496 MET cc_start: 0.8227 (ttp) cc_final: 0.7915 (ppp) REVERT: B 833 LEU cc_start: 0.2900 (OUTLIER) cc_final: 0.2694 (pp) outliers start: 96 outliers final: 47 residues processed: 204 average time/residue: 0.1591 time to fit residues: 57.1844 Evaluate side-chains 163 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 112 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 267 GLN Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain C residue 541 SER Chi-restraints excluded: chain D residue 47 THR Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 256 HIS Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 409 MET Chi-restraints excluded: chain D residue 436 VAL Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain D residue 541 SER Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 624 THR Chi-restraints excluded: chain A residue 833 LEU Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 198 ILE Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 833 LEU Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 984 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [183, 202, 330, 92, 203, 43, 104, 5, 421, 39, 231] chunk 183 optimal weight: 0.0870 chunk 202 optimal weight: 50.0000 chunk 330 optimal weight: 9.9990 chunk 92 optimal weight: 2.9990 chunk 203 optimal weight: 40.0000 chunk 43 optimal weight: 0.0970 chunk 104 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 421 optimal weight: 40.0000 chunk 39 optimal weight: 20.0000 chunk 231 optimal weight: 2.9990 overall best weight: 1.8362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 215 GLN C 256 HIS ** D 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 630 HIS ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN B 630 HIS B 733 GLN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 792 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.076354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.049722 restraints weight = 187047.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.050707 restraints weight = 88911.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.051340 restraints weight = 56229.051| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.051684 restraints weight = 42949.089| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.051903 restraints weight = 36800.843| |-----------------------------------------------------------------------------| r_work (final): 0.3260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2153 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.082 31622 Z= 0.121 Angle : 0.566 7.537 43194 Z= 0.295 Chirality : 0.045 0.180 4970 Planarity : 0.004 0.046 5652 Dihedral : 5.041 56.074 4587 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 3.19 % Allowed : 15.58 % Favored : 81.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.52 (0.13), residues: 4132 helix: -1.20 (0.29), residues: 304 sheet: -0.54 (0.14), residues: 1334 loop : -1.26 (0.12), residues: 2494 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 210 TYR 0.015 0.001 TYR A 653 PHE 0.030 0.001 PHE A 652 TRP 0.016 0.001 TRP B 824 HIS 0.015 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (31552) covalent geometry : angle 0.56294 / 0.29 (43054) SS BOND : bond 0.00392 / 0.27 ( 70) SS BOND : angle 1.15614 / 0.82 ( 140) hydrogen bonds : bond 0.03021 / 2.04 ( 1038) hydrogen bonds : angle 6.21105 / 4.30 ( 2760) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 121 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: F 182 MET cc_start: 0.5417 (mmt) cc_final: 0.5098 (mmt) REVERT: A 417 MET cc_start: 0.8979 (tmm) cc_final: 0.8676 (tmm) REVERT: A 489 ASP cc_start: 0.7854 (p0) cc_final: 0.7567 (p0) REVERT: A 496 MET cc_start: 0.8245 (ttp) cc_final: 0.7936 (ppp) REVERT: A 895 VAL cc_start: 0.1843 (OUTLIER) cc_final: 0.1622 (t) REVERT: B 496 MET cc_start: 0.8153 (ttp) cc_final: 0.7801 (ppp) outliers start: 92 outliers final: 38 residues processed: 204 average time/residue: 0.1547 time to fit residues: 55.4990 Evaluate side-chains 156 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 117 time to evaluate : 1.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 480 MET Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 984 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [15, 361, 109, 243, 74, 21, 363, 398, 258, 354, 224] chunk 15 optimal weight: 1.9990 chunk 361 optimal weight: 7.9990 chunk 109 optimal weight: 7.9990 chunk 243 optimal weight: 8.9990 chunk 74 optimal weight: 6.9990 chunk 21 optimal weight: 5.9990 chunk 363 optimal weight: 10.0000 chunk 398 optimal weight: 50.0000 chunk 258 optimal weight: 4.9990 chunk 354 optimal weight: 9.9990 chunk 224 optimal weight: 10.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 216 HIS C 256 HIS D 215 GLN D 216 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN B 725 ASN ** B 775 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 979 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.075243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3226 r_free = 0.3226 target = 0.048433 restraints weight = 187961.771| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.049341 restraints weight = 91874.726| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 66)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.050016 restraints weight = 58531.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3302 r_free = 0.3302 target = 0.050372 restraints weight = 44374.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.050537 restraints weight = 37895.048| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 31622 Z= 0.241 Angle : 0.625 10.153 43194 Z= 0.322 Chirality : 0.046 0.180 4970 Planarity : 0.005 0.048 5652 Dihedral : 5.121 58.525 4585 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.22 % Allowed : 17.11 % Favored : 79.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.51 (0.13), residues: 4132 helix: -1.13 (0.29), residues: 306 sheet: -0.54 (0.14), residues: 1340 loop : -1.25 (0.12), residues: 2486 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG E 210 TYR 0.013 0.002 TYR A 653 PHE 0.024 0.002 PHE A 652 TRP 0.013 0.001 TRP A 673 HIS 0.007 0.001 HIS A 836 Details of bonding type rmsd/Z covalent geometry : bond 0.00549 / 0.24 (31552) covalent geometry : angle 0.62066 / 0.32 (43054) SS BOND : bond 0.00438 / 0.31 ( 70) SS BOND : angle 1.42251 / 1.10 ( 140) hydrogen bonds : bond 0.03377 / 2.28 ( 1038) hydrogen bonds : angle 6.26382 / 4.33 ( 2760) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 205 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 112 time to evaluate : 1.186 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.8867 (mmm) cc_final: 0.8283 (mmm) REVERT: F 212 GLU cc_start: 0.7842 (OUTLIER) cc_final: 0.7518 (mm-30) REVERT: F 245 MET cc_start: 0.8911 (mmm) cc_final: 0.8502 (mmm) REVERT: A 212 MET cc_start: 0.8477 (mmm) cc_final: 0.8243 (mmm) REVERT: A 489 ASP cc_start: 0.7893 (p0) cc_final: 0.7589 (p0) REVERT: A 496 MET cc_start: 0.8334 (ttp) cc_final: 0.7901 (ppp) REVERT: B 212 MET cc_start: 0.8474 (mmm) cc_final: 0.8233 (mmm) REVERT: B 489 ASP cc_start: 0.8592 (p0) cc_final: 0.8383 (p0) REVERT: B 496 MET cc_start: 0.8286 (ttp) cc_final: 0.7915 (ppp) outliers start: 93 outliers final: 64 residues processed: 194 average time/residue: 0.1521 time to fit residues: 52.6429 Evaluate side-chains 177 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 112 time to evaluate : 1.197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 129 THR Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 47 THR Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 401 THR Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 401 THR Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 917 MET Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 917 MET Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [87, 423, 105, 61, 156, 295, 188, 14, 403, 315, 8] chunk 87 optimal weight: 5.9990 chunk 423 optimal weight: 9.9990 chunk 105 optimal weight: 9.9990 chunk 61 optimal weight: 0.9980 chunk 156 optimal weight: 3.9990 chunk 295 optimal weight: 40.0000 chunk 188 optimal weight: 3.9990 chunk 14 optimal weight: 20.0000 chunk 403 optimal weight: 50.0000 chunk 315 optimal weight: 0.0980 chunk 8 optimal weight: 20.0000 overall best weight: 3.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 775 ASN A 979 ASN B 775 ASN B 979 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.075833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 67)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.049202 restraints weight = 187316.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.050134 restraints weight = 88603.161| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.050756 restraints weight = 56104.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.051000 restraints weight = 42682.173| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.051269 restraints weight = 37725.782| |-----------------------------------------------------------------------------| r_work (final): 0.3236 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 31622 Z= 0.145 Angle : 0.563 7.279 43194 Z= 0.291 Chirality : 0.045 0.153 4970 Planarity : 0.004 0.049 5652 Dihedral : 4.911 52.707 4585 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 11.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.94 % Allowed : 18.35 % Favored : 78.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.35 (0.13), residues: 4132 helix: -0.58 (0.31), residues: 280 sheet: -0.47 (0.14), residues: 1344 loop : -1.19 (0.12), residues: 2508 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 753 TYR 0.016 0.001 TYR A 653 PHE 0.022 0.001 PHE A 652 TRP 0.025 0.001 TRP A 824 HIS 0.022 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.14 (31552) covalent geometry : angle 0.55983 / 0.29 (43054) SS BOND : bond 0.00425 / 0.26 ( 70) SS BOND : angle 1.14383 / 0.85 ( 140) hydrogen bonds : bond 0.02951 / 2.00 ( 1038) hydrogen bonds : angle 5.97707 / 4.13 ( 2760) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 118 time to evaluate : 1.171 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.8772 (mmm) cc_final: 0.8324 (mmm) REVERT: F 245 MET cc_start: 0.8878 (mmm) cc_final: 0.8528 (mmm) REVERT: A 417 MET cc_start: 0.9101 (tmm) cc_final: 0.8768 (tmm) REVERT: A 489 ASP cc_start: 0.7971 (p0) cc_final: 0.7664 (p0) REVERT: A 496 MET cc_start: 0.8242 (ttp) cc_final: 0.7857 (ppp) REVERT: A 936 CYS cc_start: 0.1512 (OUTLIER) cc_final: 0.0913 (t) REVERT: B 212 MET cc_start: 0.8479 (mmm) cc_final: 0.8276 (mmm) REVERT: B 489 ASP cc_start: 0.8526 (p0) cc_final: 0.8230 (p0) REVERT: B 496 MET cc_start: 0.8213 (ttp) cc_final: 0.7905 (ppp) REVERT: B 936 CYS cc_start: 0.1534 (OUTLIER) cc_final: 0.0912 (t) outliers start: 85 outliers final: 60 residues processed: 194 average time/residue: 0.1564 time to fit residues: 54.4514 Evaluate side-chains 172 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 110 time to evaluate : 0.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 265 ILE Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 567 ILE Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 936 CYS Chi-restraints excluded: chain A residue 979 ASN Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 936 CYS Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [5, 123, 24, 382, 300, 270, 306, 53, 315, 128, 305] chunk 5 optimal weight: 1.9990 chunk 123 optimal weight: 0.0050 chunk 24 optimal weight: 50.0000 chunk 382 optimal weight: 6.9990 chunk 300 optimal weight: 0.3980 chunk 270 optimal weight: 20.0000 chunk 306 optimal weight: 9.9990 chunk 53 optimal weight: 6.9990 chunk 315 optimal weight: 1.9990 chunk 128 optimal weight: 7.9990 chunk 305 optimal weight: 9.9990 overall best weight: 2.2800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS ** A 733 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 465 ASN ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3990 r_free = 0.3990 target = 0.075966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.049527 restraints weight = 185486.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.050579 restraints weight = 87119.424| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 68)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.051217 restraints weight = 55004.382| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 47)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.051586 restraints weight = 41606.189| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.051714 restraints weight = 35417.758| |-----------------------------------------------------------------------------| r_work (final): 0.3251 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 31622 Z= 0.130 Angle : 0.560 9.451 43194 Z= 0.288 Chirality : 0.045 0.146 4970 Planarity : 0.004 0.046 5652 Dihedral : 4.792 42.469 4585 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.14 % Favored : 95.86 % Rotamer: Outliers : 3.19 % Allowed : 18.01 % Favored : 78.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.25 (0.13), residues: 4132 helix: -0.45 (0.31), residues: 280 sheet: -0.39 (0.14), residues: 1356 loop : -1.13 (0.12), residues: 2496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 516 TYR 0.016 0.001 TYR A 653 PHE 0.020 0.001 PHE A 652 TRP 0.015 0.001 TRP A 824 HIS 0.004 0.001 HIS B 629 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.13 (31552) covalent geometry : angle 0.55460 / 0.29 (43054) SS BOND : bond 0.00460 / 0.33 ( 70) SS BOND : angle 1.43155 / 1.07 ( 140) hydrogen bonds : bond 0.02934 / 1.99 ( 1038) hydrogen bonds : angle 5.79228 / 4.00 ( 2760) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 92 poor density : 115 time to evaluate : 1.267 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.9024 (mmm) cc_final: 0.8699 (mmm) REVERT: C 409 MET cc_start: 0.9059 (mmp) cc_final: 0.8768 (mmt) REVERT: F 212 GLU cc_start: 0.7577 (OUTLIER) cc_final: 0.7364 (mm-30) REVERT: F 245 MET cc_start: 0.8988 (mmm) cc_final: 0.8651 (mmm) REVERT: A 417 MET cc_start: 0.9124 (tmm) cc_final: 0.8871 (tmm) REVERT: A 489 ASP cc_start: 0.7990 (p0) cc_final: 0.7664 (p0) REVERT: A 496 MET cc_start: 0.8152 (ttp) cc_final: 0.7808 (ppp) REVERT: B 212 MET cc_start: 0.8467 (mmm) cc_final: 0.8241 (mmm) REVERT: B 489 ASP cc_start: 0.8427 (p0) cc_final: 0.8042 (p0) REVERT: B 496 MET cc_start: 0.8186 (ttp) cc_final: 0.7867 (ppp) outliers start: 92 outliers final: 62 residues processed: 201 average time/residue: 0.1623 time to fit residues: 57.9685 Evaluate side-chains 174 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 111 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 204 MET Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 141 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 256 HIS Chi-restraints excluded: chain C residue 391 SER Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 204 MET Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [232, 52, 147, 15, 53, 6, 287, 133, 167, 37, 95] chunk 232 optimal weight: 10.0000 chunk 52 optimal weight: 2.9990 chunk 147 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 53 optimal weight: 5.9990 chunk 6 optimal weight: 8.9990 chunk 287 optimal weight: 40.0000 chunk 133 optimal weight: 50.0000 chunk 167 optimal weight: 0.0000 chunk 37 optimal weight: 20.0000 chunk 95 optimal weight: 9.9990 overall best weight: 5.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 206 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.075111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.048578 restraints weight = 188383.323| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.049503 restraints weight = 90926.403| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 54)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.050140 restraints weight = 58198.370| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.050459 restraints weight = 44494.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.050680 restraints weight = 38269.933| |-----------------------------------------------------------------------------| r_work (final): 0.3216 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 31622 Z= 0.231 Angle : 0.620 7.869 43194 Z= 0.319 Chirality : 0.046 0.212 4970 Planarity : 0.004 0.048 5652 Dihedral : 5.040 35.161 4585 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 12.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 3.57 % Allowed : 17.69 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.35 (0.13), residues: 4132 helix: -0.57 (0.31), residues: 282 sheet: -0.51 (0.14), residues: 1384 loop : -1.16 (0.12), residues: 2466 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 548 TYR 0.014 0.001 TYR A 653 PHE 0.019 0.002 PHE A 652 TRP 0.027 0.001 TRP B 824 HIS 0.040 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 (31552) covalent geometry : angle 0.61443 / 0.32 (43054) SS BOND : bond 0.00411 / 0.29 ( 70) SS BOND : angle 1.60826 / 1.23 ( 140) hydrogen bonds : bond 0.03277 / 2.21 ( 1038) hydrogen bonds : angle 5.99833 / 4.13 ( 2760) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 110 time to evaluate : 1.251 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.8935 (mmm) cc_final: 0.8568 (mmm) REVERT: E 256 GLU cc_start: 0.5943 (OUTLIER) cc_final: 0.5087 (pp20) REVERT: F 212 GLU cc_start: 0.7676 (OUTLIER) cc_final: 0.7372 (mm-30) REVERT: F 245 MET cc_start: 0.9008 (mmm) cc_final: 0.8623 (mmm) REVERT: D 267 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.8522 (pp30) REVERT: A 212 MET cc_start: 0.8400 (mmm) cc_final: 0.8144 (mmm) REVERT: A 489 ASP cc_start: 0.7973 (p0) cc_final: 0.7660 (p0) REVERT: A 496 MET cc_start: 0.8175 (ttp) cc_final: 0.7888 (ppp) REVERT: B 212 MET cc_start: 0.8556 (mmm) cc_final: 0.8294 (mmm) REVERT: B 489 ASP cc_start: 0.8420 (p0) cc_final: 0.8055 (p0) REVERT: B 496 MET cc_start: 0.8150 (ttp) cc_final: 0.7876 (ppp) outliers start: 103 outliers final: 74 residues processed: 205 average time/residue: 0.1535 time to fit residues: 55.8930 Evaluate side-chains 187 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 110 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 187 LEU Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain C residue 45 VAL Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 132 CYS Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 434 ILE Chi-restraints excluded: chain F residue 129 THR Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 267 GLN Chi-restraints excluded: chain D residue 268 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 484 MET Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 893 VAL Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 567 ILE Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [6, 103, 259, 92, 282, 185, 230, 153, 154, 289, 143] chunk 6 optimal weight: 8.9990 chunk 103 optimal weight: 30.0000 chunk 259 optimal weight: 30.0000 chunk 92 optimal weight: 7.9990 chunk 282 optimal weight: 50.0000 chunk 185 optimal weight: 0.8980 chunk 230 optimal weight: 0.9990 chunk 153 optimal weight: 0.6980 chunk 154 optimal weight: 2.9990 chunk 289 optimal weight: 30.0000 chunk 143 optimal weight: 20.0000 overall best weight: 2.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.075660 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.049091 restraints weight = 187897.002| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 54)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.050121 restraints weight = 88788.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.050744 restraints weight = 56104.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.050962 restraints weight = 42409.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 51)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.051281 restraints weight = 37924.627| |-----------------------------------------------------------------------------| r_work (final): 0.3235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3103 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 31622 Z= 0.138 Angle : 0.573 11.165 43194 Z= 0.294 Chirality : 0.045 0.168 4970 Planarity : 0.004 0.049 5652 Dihedral : 4.835 28.771 4584 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 11.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Rotamer: Outliers : 2.67 % Allowed : 18.28 % Favored : 79.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.26 (0.13), residues: 4132 helix: -0.45 (0.31), residues: 280 sheet: -0.42 (0.14), residues: 1352 loop : -1.11 (0.12), residues: 2500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 210 TYR 0.016 0.001 TYR A 653 PHE 0.018 0.001 PHE A 652 TRP 0.020 0.001 TRP B 824 HIS 0.019 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00321 / 0.14 (31552) covalent geometry : angle 0.56397 / 0.29 (43054) SS BOND : bond 0.00382 / 0.26 ( 70) SS BOND : angle 1.86376 / 1.28 ( 140) hydrogen bonds : bond 0.02911 / 1.98 ( 1038) hydrogen bonds : angle 5.77698 / 3.99 ( 2760) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 114 time to evaluate : 1.366 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.8983 (mmm) cc_final: 0.8573 (mmm) REVERT: E 256 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5259 (pp20) REVERT: F 212 GLU cc_start: 0.7607 (OUTLIER) cc_final: 0.7333 (mm-30) REVERT: F 245 MET cc_start: 0.9057 (mmm) cc_final: 0.8612 (mmm) REVERT: A 417 MET cc_start: 0.9120 (tmm) cc_final: 0.8866 (tmm) REVERT: A 489 ASP cc_start: 0.7915 (p0) cc_final: 0.7588 (p0) REVERT: A 496 MET cc_start: 0.8099 (ttp) cc_final: 0.7786 (ppp) REVERT: B 212 MET cc_start: 0.8531 (mmm) cc_final: 0.8268 (mmm) REVERT: B 417 MET cc_start: 0.9130 (tmm) cc_final: 0.8875 (tmm) REVERT: B 489 ASP cc_start: 0.8390 (p0) cc_final: 0.8030 (p0) REVERT: B 496 MET cc_start: 0.8084 (ttp) cc_final: 0.7795 (ppp) outliers start: 77 outliers final: 64 residues processed: 184 average time/residue: 0.1568 time to fit residues: 51.3783 Evaluate side-chains 177 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 111 time to evaluate : 0.999 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 68 MET Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 268 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain C residue 492 MET Chi-restraints excluded: chain F residue 68 MET Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [305, 326, 385, 87, 337, 277, 144, 398, 134, 421, 303] chunk 305 optimal weight: 40.0000 chunk 326 optimal weight: 0.8980 chunk 385 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 337 optimal weight: 10.0000 chunk 277 optimal weight: 20.0000 chunk 144 optimal weight: 50.0000 chunk 398 optimal weight: 8.9990 chunk 134 optimal weight: 10.0000 chunk 421 optimal weight: 20.0000 chunk 303 optimal weight: 40.0000 overall best weight: 7.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 979 ASN ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.074511 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.047874 restraints weight = 187053.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.048774 restraints weight = 91301.560| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.049391 restraints weight = 59145.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 50)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.049705 restraints weight = 45547.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.049913 restraints weight = 39343.711| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.3331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.099 31622 Z= 0.302 Angle : 0.681 9.309 43194 Z= 0.351 Chirality : 0.048 0.247 4970 Planarity : 0.005 0.053 5652 Dihedral : 5.257 28.760 4584 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 14.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Rotamer: Outliers : 2.80 % Allowed : 18.28 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.49 (0.13), residues: 4132 helix: -0.50 (0.32), residues: 270 sheet: -0.69 (0.14), residues: 1400 loop : -1.22 (0.12), residues: 2462 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG B 548 TYR 0.017 0.002 TYR F 262 PHE 0.022 0.002 PHE A1033 TRP 0.023 0.002 TRP D 105 HIS 0.008 0.002 HIS D 515 Details of bonding type rmsd/Z covalent geometry : bond 0.00681 / 0.30 (31552) covalent geometry : angle 0.67455 / 0.35 (43054) SS BOND : bond 0.00437 / 0.31 ( 70) SS BOND : angle 1.74425 / 1.27 ( 140) hydrogen bonds : bond 0.03567 / 2.40 ( 1038) hydrogen bonds : angle 6.25730 / 4.31 ( 2760) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8264 Ramachandran restraints generated. 4132 Oldfield, 0 Emsley, 4132 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 113 time to evaluate : 0.911 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 245 MET cc_start: 0.8930 (mmm) cc_final: 0.8530 (mmm) REVERT: E 256 GLU cc_start: 0.6140 (OUTLIER) cc_final: 0.5292 (pp20) REVERT: F 212 GLU cc_start: 0.7751 (OUTLIER) cc_final: 0.7313 (mm-30) REVERT: F 245 MET cc_start: 0.8978 (mmm) cc_final: 0.8536 (mmm) REVERT: A 489 ASP cc_start: 0.7953 (p0) cc_final: 0.7637 (p0) REVERT: A 496 MET cc_start: 0.8192 (ttp) cc_final: 0.7821 (ppp) REVERT: B 417 MET cc_start: 0.9187 (tmm) cc_final: 0.8944 (tmm) REVERT: B 496 MET cc_start: 0.8099 (ttp) cc_final: 0.7848 (ppp) outliers start: 81 outliers final: 68 residues processed: 186 average time/residue: 0.1483 time to fit residues: 49.2077 Evaluate side-chains 180 residues out of total 3732 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 110 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 130 HIS Chi-restraints excluded: chain E residue 137 ARG Chi-restraints excluded: chain E residue 158 ILE Chi-restraints excluded: chain E residue 256 GLU Chi-restraints excluded: chain C residue 98 THR Chi-restraints excluded: chain C residue 195 MET Chi-restraints excluded: chain C residue 252 ILE Chi-restraints excluded: chain C residue 432 THR Chi-restraints excluded: chain F residue 130 HIS Chi-restraints excluded: chain F residue 158 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain F residue 253 ILE Chi-restraints excluded: chain D residue 98 THR Chi-restraints excluded: chain D residue 110 ILE Chi-restraints excluded: chain D residue 132 CYS Chi-restraints excluded: chain D residue 141 CYS Chi-restraints excluded: chain D residue 161 HIS Chi-restraints excluded: chain D residue 195 MET Chi-restraints excluded: chain D residue 252 ILE Chi-restraints excluded: chain D residue 391 SER Chi-restraints excluded: chain D residue 432 THR Chi-restraints excluded: chain D residue 434 ILE Chi-restraints excluded: chain D residue 455 VAL Chi-restraints excluded: chain A residue 40 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 54 VAL Chi-restraints excluded: chain A residue 82 THR Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 173 VAL Chi-restraints excluded: chain A residue 236 ILE Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 441 ASN Chi-restraints excluded: chain A residue 486 PHE Chi-restraints excluded: chain A residue 495 ILE Chi-restraints excluded: chain A residue 530 VAL Chi-restraints excluded: chain A residue 558 VAL Chi-restraints excluded: chain A residue 854 CYS Chi-restraints excluded: chain A residue 892 HIS Chi-restraints excluded: chain A residue 895 VAL Chi-restraints excluded: chain A residue 986 VAL Chi-restraints excluded: chain A residue 1072 ILE Chi-restraints excluded: chain A residue 1136 THR Chi-restraints excluded: chain A residue 1182 VAL Chi-restraints excluded: chain A residue 1215 VAL Chi-restraints excluded: chain B residue 40 VAL Chi-restraints excluded: chain B residue 53 LEU Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 119 ILE Chi-restraints excluded: chain B residue 173 VAL Chi-restraints excluded: chain B residue 236 ILE Chi-restraints excluded: chain B residue 256 LEU Chi-restraints excluded: chain B residue 362 ILE Chi-restraints excluded: chain B residue 441 ASN Chi-restraints excluded: chain B residue 486 PHE Chi-restraints excluded: chain B residue 495 ILE Chi-restraints excluded: chain B residue 530 VAL Chi-restraints excluded: chain B residue 558 VAL Chi-restraints excluded: chain B residue 854 CYS Chi-restraints excluded: chain B residue 892 HIS Chi-restraints excluded: chain B residue 893 VAL Chi-restraints excluded: chain B residue 895 VAL Chi-restraints excluded: chain B residue 986 VAL Chi-restraints excluded: chain B residue 1022 VAL Chi-restraints excluded: chain B residue 1072 ILE Chi-restraints excluded: chain B residue 1136 THR Chi-restraints excluded: chain B residue 1182 VAL Chi-restraints excluded: chain B residue 1200 CYS Chi-restraints excluded: chain B residue 1215 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: [115, 225, 42, 78, 192, 348, 21, 67, 5, 199, 428] chunk 115 optimal weight: 8.9990 chunk 225 optimal weight: 0.9990 chunk 42 optimal weight: 40.0000 chunk 78 optimal weight: 2.9990 chunk 192 optimal weight: 6.9990 chunk 348 optimal weight: 10.0000 chunk 21 optimal weight: 40.0000 chunk 67 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 199 optimal weight: 7.9990 chunk 428 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 256 HIS ** A 465 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 785 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 892 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3972 r_free = 0.3972 target = 0.075292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.048859 restraints weight = 187127.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.049857 restraints weight = 89638.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.050537 restraints weight = 56988.044| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.050851 restraints weight = 42723.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.051061 restraints weight = 36998.993| |-----------------------------------------------------------------------------| r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8267 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 31622 Z= 0.161 Angle : 0.588 8.970 43194 Z= 0.303 Chirality : 0.046 0.187 4970 Planarity : 0.004 0.052 5652 Dihedral : 5.004 28.398 4584 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 2.77 % Allowed : 18.56 % Favored : 78.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.07 % 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: -1.40 (0.13), residues: 4132 helix: -0.51 (0.31), residues: 282 sheet: -0.58 (0.14), residues: 1362 loop : -1.18 (0.12), residues: 2488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 428 TYR 0.017 0.001 TYR A 653 PHE 0.018 0.001 PHE A 652 TRP 0.018 0.001 TRP B 824 HIS 0.005 0.001 HIS C 256 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.16 (31552) covalent geometry : angle 0.58338 / 0.30 (43054) SS BOND : bond 0.00359 / 0.24 ( 70) SS BOND : angle 1.39232 / 1.02 ( 140) hydrogen bonds : bond 0.02988 / 2.02 ( 1038) hydrogen bonds : angle 5.92285 / 4.09 ( 2760) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6880.08 seconds wall clock time: 118 minutes 34.38 seconds (7114.38 seconds total)