Starting phenix.real_space_refine on Sun Jul 5 16:11:28 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z3r_39752/07_2026/8z3r_39752.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z3r_39752/07_2026/8z3r_39752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z3r_39752/07_2026/8z3r_39752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z3r_39752/07_2026/8z3r_39752.map" model { file = "/net/cci-nas-00/data/ceres_data/8z3r_39752/07_2026/8z3r_39752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z3r_39752/07_2026/8z3r_39752.cif" } resolution = 2.28 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= 0.004 sd= 0.019 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: 6 Type Number sf(0) Gaussians Zn 6 6.06 5 P 12 5.49 5 S 132 5.16 5 C 18384 2.51 5 N 5430 2.21 5 O 5226 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 197 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 29190 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "B" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "C" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "D" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "E" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "F" Number of atoms: 4820 Number of conformers: 1 Conformer: "" Number of residues, atoms: 615, 4820 Classifications: {'peptide': 615} Link IDs: {'PTRANS': 40, 'TRANS': 574} Chain breaks: 1 Chain: "A" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' ZN': 1, 'LQJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' ZN': 1, 'LQJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' ZN': 1, 'LQJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 45 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 45 Unusual residues: {' ZN': 1, 'LQJ': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 89 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 89 Unusual residues: {' ZN': 1, 'LQJ': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 5.59, per 1000 atoms: 0.19 Number of scatterers: 29190 At special positions: 0 Unit cell: (217.92, 216, 146.88, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 6 29.99 S 132 16.00 P 12 15.00 O 5226 8.00 N 5430 7.00 C 18384 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.91 Conformation dependent library (CDL) restraints added in 1.0 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 701 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 266 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 264 " pdb="ZN ZN A 701 " - pdb=" NE2 HIS A 471 " pdb=" ZN B 701 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 264 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 266 " pdb="ZN ZN B 701 " - pdb=" NE2 HIS B 471 " pdb=" ZN C 701 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 266 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 264 " pdb="ZN ZN C 701 " - pdb=" NE2 HIS C 471 " pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 264 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 266 " pdb="ZN ZN D 701 " - pdb=" NE2 HIS D 471 " pdb=" ZN E 701 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 471 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 266 " pdb="ZN ZN E 701 " - pdb=" NE2 HIS E 264 " pdb=" ZN F 701 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 264 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 266 " pdb="ZN ZN F 701 " - pdb=" NE2 HIS F 471 " 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6816 Finding SS restraints... Secondary structure from input PDB file: 179 helices and 13 sheets defined 52.5% alpha, 10.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 17 through 23 Processing helix chain 'A' and resid 42 through 53 Processing helix chain 'A' and resid 72 through 89 removed outlier: 4.014A pdb=" N SER A 89 " --> pdb=" O TRP A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 119 Processing helix chain 'A' and resid 144 through 155 removed outlier: 3.820A pdb=" N ILE A 148 " --> pdb=" O THR A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 179 Processing helix chain 'A' and resid 198 through 217 Processing helix chain 'A' and resid 226 through 232 removed outlier: 3.571A pdb=" N LEU A 229 " --> pdb=" O PHE A 226 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 241 Processing helix chain 'A' and resid 248 through 257 Processing helix chain 'A' and resid 268 through 270 No H-bonds generated for 'chain 'A' and resid 268 through 270' Processing helix chain 'A' and resid 273 through 282 removed outlier: 3.779A pdb=" N LEU A 277 " --> pdb=" O HIS A 273 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ARG A 278 " --> pdb=" O GLY A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 310 through 317 Processing helix chain 'A' and resid 328 through 347 Processing helix chain 'A' and resid 356 through 361 removed outlier: 3.618A pdb=" N ALA A 361 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 384 Processing helix chain 'A' and resid 410 through 428 Processing helix chain 'A' and resid 446 through 453 removed outlier: 3.834A pdb=" N ARG A 450 " --> pdb=" O GLU A 447 " (cutoff:3.500A) removed outlier: 7.254A pdb=" N ALA A 451 " --> pdb=" O LYS A 448 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N HIS A 452 " --> pdb=" O THR A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 454 through 465 removed outlier: 4.541A pdb=" N ALA A 460 " --> pdb=" O GLU A 456 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N VAL A 461 " --> pdb=" O GLU A 457 " (cutoff:3.500A) Processing helix chain 'A' and resid 477 through 488 removed outlier: 4.116A pdb=" N ILE A 481 " --> pdb=" O ASP A 477 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N LEU A 488 " --> pdb=" O ALA A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 501 Processing helix chain 'A' and resid 502 through 513 Processing helix chain 'A' and resid 519 through 528 Processing helix chain 'A' and resid 553 through 561 Processing helix chain 'A' and resid 570 through 575 Processing helix chain 'A' and resid 577 through 589 Processing helix chain 'A' and resid 593 through 608 removed outlier: 3.637A pdb=" N LEU A 597 " --> pdb=" O THR A 593 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 624 Processing helix chain 'B' and resid 17 through 23 Processing helix chain 'B' and resid 42 through 52 Processing helix chain 'B' and resid 72 through 88 Processing helix chain 'B' and resid 92 through 94 No H-bonds generated for 'chain 'B' and resid 92 through 94' Processing helix chain 'B' and resid 104 through 119 removed outlier: 3.593A pdb=" N SER B 108 " --> pdb=" O PHE B 104 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N ALA B 109 " --> pdb=" O LYS B 105 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ALA B 110 " --> pdb=" O THR B 106 " (cutoff:3.500A) Processing helix chain 'B' and resid 144 through 154 removed outlier: 3.689A pdb=" N ILE B 148 " --> pdb=" O THR B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 168 through 172 removed outlier: 3.869A pdb=" N ARG B 172 " --> pdb=" O PRO B 169 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 217 Processing helix chain 'B' and resid 226 through 232 removed outlier: 3.536A pdb=" N LEU B 229 " --> pdb=" O PHE B 226 " (cutoff:3.500A) Processing helix chain 'B' and resid 233 through 241 removed outlier: 3.508A pdb=" N ARG B 241 " --> pdb=" O LEU B 237 " (cutoff:3.500A) Processing helix chain 'B' and resid 248 through 257 Processing helix chain 'B' and resid 266 through 270 removed outlier: 3.784A pdb=" N GLY B 269 " --> pdb=" O HIS B 266 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N PHE B 270 " --> pdb=" O LEU B 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 266 through 270' Processing helix chain 'B' and resid 273 through 282 removed outlier: 3.914A pdb=" N LEU B 277 " --> pdb=" O HIS B 273 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG B 278 " --> pdb=" O GLY B 274 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 290 Processing helix chain 'B' and resid 310 through 317 Processing helix chain 'B' and resid 328 through 347 Processing helix chain 'B' and resid 356 through 361 removed outlier: 3.564A pdb=" N ALA B 361 " --> pdb=" O ALA B 358 " (cutoff:3.500A) Processing helix chain 'B' and resid 365 through 384 Processing helix chain 'B' and resid 410 through 428 removed outlier: 3.592A pdb=" N ILE B 414 " --> pdb=" O TYR B 410 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N ALA B 415 " --> pdb=" O ARG B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 446 through 453 removed outlier: 3.762A pdb=" N ARG B 450 " --> pdb=" O GLU B 447 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ALA B 451 " --> pdb=" O LYS B 448 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N HIS B 452 " --> pdb=" O THR B 449 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 465 removed outlier: 4.849A pdb=" N ALA B 460 " --> pdb=" O GLU B 456 " (cutoff:3.500A) removed outlier: 4.599A pdb=" N VAL B 461 " --> pdb=" O GLU B 457 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 488 removed outlier: 4.102A pdb=" N ILE B 481 " --> pdb=" O ASP B 477 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU B 488 " --> pdb=" O ALA B 484 " (cutoff:3.500A) Processing helix chain 'B' and resid 498 through 501 Processing helix chain 'B' and resid 502 through 513 Processing helix chain 'B' and resid 519 through 527 Processing helix chain 'B' and resid 553 through 561 Processing helix chain 'B' and resid 570 through 575 Processing helix chain 'B' and resid 577 through 589 Processing helix chain 'B' and resid 593 through 607 Processing helix chain 'B' and resid 611 through 624 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.643A pdb=" N LEU C 23 " --> pdb=" O PRO C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 42 through 53 removed outlier: 3.527A pdb=" N ALA C 53 " --> pdb=" O PHE C 49 " (cutoff:3.500A) Processing helix chain 'C' and resid 71 through 89 removed outlier: 4.308A pdb=" N HIS C 75 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER C 89 " --> pdb=" O TRP C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 119 Processing helix chain 'C' and resid 144 through 155 removed outlier: 3.576A pdb=" N ILE C 148 " --> pdb=" O THR C 144 " (cutoff:3.500A) Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.850A pdb=" N ARG C 172 " --> pdb=" O PRO C 169 " (cutoff:3.500A) Processing helix chain 'C' and resid 175 through 179 Processing helix chain 'C' and resid 198 through 217 Processing helix chain 'C' and resid 226 through 232 removed outlier: 3.519A pdb=" N LEU C 229 " --> pdb=" O PHE C 226 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 241 Processing helix chain 'C' and resid 248 through 257 Processing helix chain 'C' and resid 266 through 270 removed outlier: 3.659A pdb=" N GLY C 269 " --> pdb=" O HIS C 266 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N PHE C 270 " --> pdb=" O LEU C 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 266 through 270' Processing helix chain 'C' and resid 273 through 282 removed outlier: 3.806A pdb=" N LEU C 277 " --> pdb=" O HIS C 273 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N ARG C 278 " --> pdb=" O GLY C 274 " (cutoff:3.500A) Processing helix chain 'C' and resid 286 through 290 Processing helix chain 'C' and resid 310 through 317 removed outlier: 3.533A pdb=" N TYR C 314 " --> pdb=" O PRO C 310 " (cutoff:3.500A) Processing helix chain 'C' and resid 328 through 347 Processing helix chain 'C' and resid 356 through 361 removed outlier: 3.509A pdb=" N ALA C 361 " --> pdb=" O ALA C 358 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 384 Processing helix chain 'C' and resid 410 through 428 Processing helix chain 'C' and resid 446 through 453 removed outlier: 3.873A pdb=" N ARG C 450 " --> pdb=" O GLU C 447 " (cutoff:3.500A) removed outlier: 7.238A pdb=" N ALA C 451 " --> pdb=" O LYS C 448 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N HIS C 452 " --> pdb=" O THR C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 454 through 465 removed outlier: 4.864A pdb=" N ALA C 460 " --> pdb=" O GLU C 456 " (cutoff:3.500A) removed outlier: 4.586A pdb=" N VAL C 461 " --> pdb=" O GLU C 457 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 488 removed outlier: 4.104A pdb=" N ILE C 481 " --> pdb=" O ASP C 477 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU C 488 " --> pdb=" O ALA C 484 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 501 Processing helix chain 'C' and resid 502 through 513 Processing helix chain 'C' and resid 519 through 528 Processing helix chain 'C' and resid 553 through 561 Processing helix chain 'C' and resid 570 through 575 Processing helix chain 'C' and resid 577 through 589 Processing helix chain 'C' and resid 593 through 607 removed outlier: 3.551A pdb=" N LEU C 597 " --> pdb=" O THR C 593 " (cutoff:3.500A) Processing helix chain 'C' and resid 611 through 624 removed outlier: 3.518A pdb=" N SER C 624 " --> pdb=" O ARG C 620 " (cutoff:3.500A) Processing helix chain 'D' and resid 17 through 23 removed outlier: 3.706A pdb=" N LEU D 23 " --> pdb=" O PRO D 19 " (cutoff:3.500A) Processing helix chain 'D' and resid 42 through 53 Processing helix chain 'D' and resid 72 through 89 removed outlier: 3.963A pdb=" N SER D 89 " --> pdb=" O TRP D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 94 No H-bonds generated for 'chain 'D' and resid 92 through 94' Processing helix chain 'D' and resid 104 through 119 removed outlier: 3.747A pdb=" N SER D 108 " --> pdb=" O PHE D 104 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N ALA D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 155 removed outlier: 3.871A pdb=" N ILE D 148 " --> pdb=" O THR D 144 " (cutoff:3.500A) Processing helix chain 'D' and resid 198 through 217 Processing helix chain 'D' and resid 226 through 232 removed outlier: 3.551A pdb=" N LEU D 229 " --> pdb=" O PHE D 226 " (cutoff:3.500A) Processing helix chain 'D' and resid 233 through 241 removed outlier: 3.586A pdb=" N ARG D 241 " --> pdb=" O LEU D 237 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 258 Processing helix chain 'D' and resid 266 through 270 removed outlier: 3.726A pdb=" N GLY D 269 " --> pdb=" O HIS D 266 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N PHE D 270 " --> pdb=" O LEU D 267 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 266 through 270' Processing helix chain 'D' and resid 273 through 282 removed outlier: 3.798A pdb=" N LEU D 277 " --> pdb=" O HIS D 273 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ARG D 278 " --> pdb=" O GLY D 274 " (cutoff:3.500A) Processing helix chain 'D' and resid 286 through 290 Processing helix chain 'D' and resid 310 through 317 Processing helix chain 'D' and resid 328 through 346 Processing helix chain 'D' and resid 356 through 361 Processing helix chain 'D' and resid 365 through 384 Processing helix chain 'D' and resid 410 through 428 removed outlier: 3.666A pdb=" N ILE D 414 " --> pdb=" O TYR D 410 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA D 415 " --> pdb=" O ARG D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 450 through 453 Processing helix chain 'D' and resid 454 through 465 removed outlier: 4.949A pdb=" N ALA D 460 " --> pdb=" O GLU D 456 " (cutoff:3.500A) removed outlier: 4.765A pdb=" N VAL D 461 " --> pdb=" O GLU D 457 " (cutoff:3.500A) Processing helix chain 'D' and resid 477 through 488 removed outlier: 4.070A pdb=" N ILE D 481 " --> pdb=" O ASP D 477 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 488 " --> pdb=" O ALA D 484 " (cutoff:3.500A) Processing helix chain 'D' and resid 498 through 501 Processing helix chain 'D' and resid 502 through 513 Processing helix chain 'D' and resid 519 through 528 Processing helix chain 'D' and resid 553 through 561 Processing helix chain 'D' and resid 570 through 575 Processing helix chain 'D' and resid 577 through 589 Processing helix chain 'D' and resid 593 through 608 Processing helix chain 'D' and resid 611 through 624 Processing helix chain 'E' and resid 17 through 23 Processing helix chain 'E' and resid 42 through 52 Processing helix chain 'E' and resid 71 through 88 removed outlier: 4.084A pdb=" N HIS E 75 " --> pdb=" O SER E 71 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 94 No H-bonds generated for 'chain 'E' and resid 92 through 94' Processing helix chain 'E' and resid 104 through 119 Processing helix chain 'E' and resid 145 through 155 Processing helix chain 'E' and resid 168 through 172 Processing helix chain 'E' and resid 175 through 179 removed outlier: 3.523A pdb=" N PHE E 179 " --> pdb=" O PRO E 176 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 217 removed outlier: 3.506A pdb=" N THR E 202 " --> pdb=" O ARG E 198 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 232 Processing helix chain 'E' and resid 233 through 241 removed outlier: 3.536A pdb=" N ARG E 241 " --> pdb=" O LEU E 237 " (cutoff:3.500A) Processing helix chain 'E' and resid 248 through 257 Processing helix chain 'E' and resid 268 through 270 No H-bonds generated for 'chain 'E' and resid 268 through 270' Processing helix chain 'E' and resid 273 through 282 removed outlier: 3.880A pdb=" N LEU E 277 " --> pdb=" O HIS E 273 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG E 278 " --> pdb=" O GLY E 274 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 290 Processing helix chain 'E' and resid 310 through 317 Processing helix chain 'E' and resid 328 through 347 Processing helix chain 'E' and resid 356 through 361 removed outlier: 3.518A pdb=" N ALA E 361 " --> pdb=" O ALA E 358 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 384 Processing helix chain 'E' and resid 410 through 428 Processing helix chain 'E' and resid 450 through 453 Processing helix chain 'E' and resid 454 through 465 removed outlier: 4.805A pdb=" N ALA E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N VAL E 461 " --> pdb=" O GLU E 457 " (cutoff:3.500A) Processing helix chain 'E' and resid 477 through 488 removed outlier: 4.161A pdb=" N ILE E 481 " --> pdb=" O ASP E 477 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU E 488 " --> pdb=" O ALA E 484 " (cutoff:3.500A) Processing helix chain 'E' and resid 498 through 501 Processing helix chain 'E' and resid 502 through 513 Processing helix chain 'E' and resid 519 through 528 Processing helix chain 'E' and resid 553 through 561 Processing helix chain 'E' and resid 570 through 575 Processing helix chain 'E' and resid 577 through 589 Processing helix chain 'E' and resid 593 through 607 Processing helix chain 'E' and resid 611 through 624 Processing helix chain 'F' and resid 17 through 23 Processing helix chain 'F' and resid 42 through 52 Processing helix chain 'F' and resid 72 through 89 removed outlier: 3.927A pdb=" N SER F 89 " --> pdb=" O TRP F 85 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 94 No H-bonds generated for 'chain 'F' and resid 92 through 94' Processing helix chain 'F' and resid 104 through 119 removed outlier: 3.557A pdb=" N ALA F 109 " --> pdb=" O LYS F 105 " (cutoff:3.500A) Processing helix chain 'F' and resid 145 through 155 Processing helix chain 'F' and resid 168 through 172 removed outlier: 3.556A pdb=" N ARG F 172 " --> pdb=" O PRO F 169 " (cutoff:3.500A) Processing helix chain 'F' and resid 198 through 217 Processing helix chain 'F' and resid 226 through 232 removed outlier: 3.611A pdb=" N LEU F 229 " --> pdb=" O PHE F 226 " (cutoff:3.500A) Processing helix chain 'F' and resid 233 through 241 Processing helix chain 'F' and resid 248 through 257 Processing helix chain 'F' and resid 268 through 270 No H-bonds generated for 'chain 'F' and resid 268 through 270' Processing helix chain 'F' and resid 273 through 282 removed outlier: 3.818A pdb=" N LEU F 277 " --> pdb=" O HIS F 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 290 Processing helix chain 'F' and resid 310 through 317 removed outlier: 3.748A pdb=" N TYR F 314 " --> pdb=" O PRO F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 328 through 347 Processing helix chain 'F' and resid 356 through 361 removed outlier: 3.604A pdb=" N ALA F 361 " --> pdb=" O ALA F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 365 through 384 Processing helix chain 'F' and resid 410 through 428 removed outlier: 3.753A pdb=" N ILE F 414 " --> pdb=" O TYR F 410 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ALA F 415 " --> pdb=" O ARG F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 450 through 453 Processing helix chain 'F' and resid 454 through 465 removed outlier: 4.861A pdb=" N ALA F 460 " --> pdb=" O GLU F 456 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N VAL F 461 " --> pdb=" O GLU F 457 " (cutoff:3.500A) Processing helix chain 'F' and resid 477 through 488 removed outlier: 4.165A pdb=" N ILE F 481 " --> pdb=" O ASP F 477 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU F 488 " --> pdb=" O ALA F 484 " (cutoff:3.500A) Processing helix chain 'F' and resid 498 through 501 Processing helix chain 'F' and resid 502 through 513 Processing helix chain 'F' and resid 519 through 528 Processing helix chain 'F' and resid 553 through 561 Processing helix chain 'F' and resid 570 through 575 Processing helix chain 'F' and resid 577 through 589 Processing helix chain 'F' and resid 593 through 607 Processing helix chain 'F' and resid 611 through 624 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 161 removed outlier: 3.608A pdb=" N GLU A 122 " --> pdb=" O ARG A 96 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER A 10 " --> pdb=" O CYS A 99 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N LEU A 7 " --> pdb=" O HIS A 33 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N LEU A 35 " --> pdb=" O LEU A 7 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N VAL A 9 " --> pdb=" O LEU A 35 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL A 32 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N THR A 61 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N VAL A 34 " --> pdb=" O THR A 61 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N VAL A 63 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ILE A 60 " --> pdb=" O ARG A 191 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N VAL A 193 " --> pdb=" O ILE A 60 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ARG A 62 " --> pdb=" O VAL A 193 " (cutoff:3.500A) removed outlier: 7.353A pdb=" N GLU A 190 " --> pdb=" O GLU A 186 " (cutoff:3.500A) removed outlier: 5.058A pdb=" N GLU A 186 " --> pdb=" O GLU A 190 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ARG A 192 " --> pdb=" O VAL A 184 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N GLN A 194 " --> pdb=" O GLN A 182 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 260 through 261 removed outlier: 7.590A pdb=" N LYS A 260 " --> pdb=" O CYS A 349 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA A 351 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N CYS A 265 " --> pdb=" O ARG A 354 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 260 through 261 removed outlier: 7.590A pdb=" N LYS A 260 " --> pdb=" O CYS A 349 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N ALA A 351 " --> pdb=" O LYS A 260 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N HIS A 395 " --> pdb=" O CYS A 349 " (cutoff:3.500A) removed outlier: 8.441A pdb=" N VAL A 437 " --> pdb=" O VAL A 396 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU A 398 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL A 439 " --> pdb=" O LEU A 398 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU A 400 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 5.541A pdb=" N LEU A 441 " --> pdb=" O LEU A 400 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA A 402 " --> pdb=" O LEU A 441 " (cutoff:3.500A) removed outlier: 5.038A pdb=" N GLY A 443 " --> pdb=" O ALA A 402 " (cutoff:3.500A) removed outlier: 5.690A pdb=" N ARG A 404 " --> pdb=" O GLY A 443 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N VAL A 437 " --> pdb=" O ALA A 467 " (cutoff:3.500A) removed outlier: 8.050A pdb=" N THR A 469 " --> pdb=" O VAL A 437 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N VAL A 439 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N HIS A 471 " --> pdb=" O VAL A 439 " (cutoff:3.500A) removed outlier: 7.010A pdb=" N LEU A 441 " --> pdb=" O HIS A 471 " (cutoff:3.500A) removed outlier: 7.088A pdb=" N VAL A 468 " --> pdb=" O ARG A 492 " (cutoff:3.500A) removed outlier: 8.457A pdb=" N GLY A 494 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N VAL A 470 " --> pdb=" O GLY A 494 " (cutoff:3.500A) removed outlier: 6.928A pdb=" N LEU A 493 " --> pdb=" O GLU A 517 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 160 through 163 removed outlier: 6.457A pdb=" N VAL B 123 " --> pdb=" O LEU B 162 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER B 10 " --> pdb=" O CYS B 99 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N LEU B 7 " --> pdb=" O HIS B 33 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N LEU B 35 " --> pdb=" O LEU B 7 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N VAL B 9 " --> pdb=" O LEU B 35 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE B 60 " --> pdb=" O ARG B 191 " (cutoff:3.500A) removed outlier: 7.851A pdb=" N VAL B 193 " --> pdb=" O ILE B 60 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 62 " --> pdb=" O VAL B 193 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N GLU B 190 " --> pdb=" O GLU B 186 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N GLU B 186 " --> pdb=" O GLU B 190 " (cutoff:3.500A) removed outlier: 7.099A pdb=" N ARG B 192 " --> pdb=" O VAL B 184 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 260 through 262 removed outlier: 7.726A pdb=" N LYS B 260 " --> pdb=" O CYS B 349 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ALA B 351 " --> pdb=" O LYS B 260 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N GLU B 262 " --> pdb=" O ALA B 351 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N VAL B 353 " --> pdb=" O GLU B 262 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N VAL B 437 " --> pdb=" O VAL B 396 " (cutoff:3.500A) removed outlier: 7.652A pdb=" N LEU B 398 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N VAL B 439 " --> pdb=" O LEU B 398 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N LEU B 400 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU B 441 " --> pdb=" O LEU B 400 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ALA B 402 " --> pdb=" O LEU B 441 " (cutoff:3.500A) removed outlier: 5.092A pdb=" N GLY B 443 " --> pdb=" O ALA B 402 " (cutoff:3.500A) removed outlier: 6.041A pdb=" N ARG B 404 " --> pdb=" O GLY B 443 " (cutoff:3.500A) removed outlier: 7.351A pdb=" N VAL B 437 " --> pdb=" O ALA B 467 " (cutoff:3.500A) removed outlier: 8.030A pdb=" N THR B 469 " --> pdb=" O VAL B 437 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N VAL B 439 " --> pdb=" O THR B 469 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N HIS B 471 " --> pdb=" O VAL B 439 " (cutoff:3.500A) removed outlier: 7.039A pdb=" N LEU B 441 " --> pdb=" O HIS B 471 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL B 468 " --> pdb=" O ARG B 492 " (cutoff:3.500A) removed outlier: 8.481A pdb=" N GLY B 494 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N VAL B 470 " --> pdb=" O GLY B 494 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU B 493 " --> pdb=" O GLU B 517 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 160 through 161 removed outlier: 3.810A pdb=" N SER C 10 " --> pdb=" O CYS C 99 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N LEU C 7 " --> pdb=" O HIS C 33 " (cutoff:3.500A) removed outlier: 7.860A pdb=" N LEU C 35 " --> pdb=" O LEU C 7 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N VAL C 9 " --> pdb=" O LEU C 35 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N GLU C 190 " --> pdb=" O GLU C 186 " (cutoff:3.500A) removed outlier: 4.817A pdb=" N GLU C 186 " --> pdb=" O GLU C 190 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N ARG C 192 " --> pdb=" O VAL C 184 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN C 182 " --> pdb=" O GLN C 194 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 260 through 262 removed outlier: 7.632A pdb=" N LYS C 260 " --> pdb=" O CYS C 349 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N ALA C 351 " --> pdb=" O LYS C 260 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N GLU C 262 " --> pdb=" O ALA C 351 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N VAL C 353 " --> pdb=" O GLU C 262 " (cutoff:3.500A) removed outlier: 7.125A pdb=" N VAL C 436 " --> pdb=" O VAL C 396 " (cutoff:3.500A) removed outlier: 6.259A pdb=" N LEU C 398 " --> pdb=" O VAL C 436 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY C 438 " --> pdb=" O LEU C 398 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL C 437 " --> pdb=" O ALA C 467 " (cutoff:3.500A) removed outlier: 7.878A pdb=" N THR C 469 " --> pdb=" O VAL C 437 " (cutoff:3.500A) removed outlier: 6.332A pdb=" N VAL C 439 " --> pdb=" O THR C 469 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N HIS C 471 " --> pdb=" O VAL C 439 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N LEU C 441 " --> pdb=" O HIS C 471 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N VAL C 468 " --> pdb=" O ARG C 492 " (cutoff:3.500A) removed outlier: 8.487A pdb=" N GLY C 494 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N VAL C 470 " --> pdb=" O GLY C 494 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 160 through 163 removed outlier: 6.395A pdb=" N VAL D 123 " --> pdb=" O LEU D 162 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU D 122 " --> pdb=" O ARG D 96 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER D 10 " --> pdb=" O CYS D 99 " (cutoff:3.500A) removed outlier: 6.492A pdb=" N LEU D 7 " --> pdb=" O HIS D 33 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N LEU D 35 " --> pdb=" O LEU D 7 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL D 9 " --> pdb=" O LEU D 35 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N VAL D 34 " --> pdb=" O THR D 61 " (cutoff:3.500A) removed outlier: 8.073A pdb=" N VAL D 63 " --> pdb=" O VAL D 34 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N THR D 36 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ILE D 60 " --> pdb=" O ARG D 191 " (cutoff:3.500A) removed outlier: 7.699A pdb=" N VAL D 193 " --> pdb=" O ILE D 60 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG D 62 " --> pdb=" O VAL D 193 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N GLU D 190 " --> pdb=" O GLU D 186 " (cutoff:3.500A) removed outlier: 4.892A pdb=" N GLU D 186 " --> pdb=" O GLU D 190 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N ARG D 192 " --> pdb=" O VAL D 184 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 260 through 262 removed outlier: 7.574A pdb=" N LYS D 260 " --> pdb=" O CYS D 349 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N ALA D 351 " --> pdb=" O LYS D 260 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N GLU D 262 " --> pdb=" O ALA D 351 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N VAL D 353 " --> pdb=" O GLU D 262 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N VAL D 436 " --> pdb=" O VAL D 396 " (cutoff:3.500A) removed outlier: 6.231A pdb=" N LEU D 398 " --> pdb=" O VAL D 436 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N GLY D 438 " --> pdb=" O LEU D 398 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N VAL D 437 " --> pdb=" O ALA D 467 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N THR D 469 " --> pdb=" O VAL D 437 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N VAL D 439 " --> pdb=" O THR D 469 " (cutoff:3.500A) removed outlier: 7.955A pdb=" N HIS D 471 " --> pdb=" O VAL D 439 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU D 441 " --> pdb=" O HIS D 471 " (cutoff:3.500A) removed outlier: 7.100A pdb=" N VAL D 468 " --> pdb=" O ARG D 492 " (cutoff:3.500A) removed outlier: 8.478A pdb=" N GLY D 494 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 6.990A pdb=" N VAL D 470 " --> pdb=" O GLY D 494 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 160 through 161 removed outlier: 3.515A pdb=" N GLU E 122 " --> pdb=" O ARG E 96 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER E 10 " --> pdb=" O CYS E 99 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N LEU E 7 " --> pdb=" O HIS E 33 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N LEU E 35 " --> pdb=" O LEU E 7 " (cutoff:3.500A) removed outlier: 7.029A pdb=" N VAL E 9 " --> pdb=" O LEU E 35 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N VAL E 63 " --> pdb=" O THR E 36 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N GLU E 190 " --> pdb=" O GLU E 186 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N GLU E 186 " --> pdb=" O GLU E 190 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N ARG E 192 " --> pdb=" O VAL E 184 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 260 through 266 removed outlier: 7.616A pdb=" N LYS E 260 " --> pdb=" O CYS E 349 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ALA E 351 " --> pdb=" O LYS E 260 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N GLU E 262 " --> pdb=" O ALA E 351 " (cutoff:3.500A) removed outlier: 6.147A pdb=" N VAL E 353 " --> pdb=" O GLU E 262 " (cutoff:3.500A) removed outlier: 8.349A pdb=" N HIS E 264 " --> pdb=" O VAL E 353 " (cutoff:3.500A) removed outlier: 10.310A pdb=" N CYS E 355 " --> pdb=" O HIS E 264 " (cutoff:3.500A) removed outlier: 9.170A pdb=" N HIS E 266 " --> pdb=" O CYS E 355 " (cutoff:3.500A) removed outlier: 8.536A pdb=" N VAL E 437 " --> pdb=" O VAL E 396 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N LEU E 398 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL E 439 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N LEU E 400 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N LEU E 441 " --> pdb=" O LEU E 400 " (cutoff:3.500A) removed outlier: 6.687A pdb=" N ALA E 402 " --> pdb=" O LEU E 441 " (cutoff:3.500A) removed outlier: 5.176A pdb=" N GLY E 443 " --> pdb=" O ALA E 402 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ARG E 404 " --> pdb=" O GLY E 443 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL E 437 " --> pdb=" O ALA E 467 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N THR E 469 " --> pdb=" O VAL E 437 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL E 439 " --> pdb=" O THR E 469 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N HIS E 471 " --> pdb=" O VAL E 439 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LEU E 441 " --> pdb=" O HIS E 471 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N VAL E 468 " --> pdb=" O ARG E 492 " (cutoff:3.500A) removed outlier: 8.411A pdb=" N GLY E 494 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N VAL E 470 " --> pdb=" O GLY E 494 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'F' and resid 160 through 163 removed outlier: 5.208A pdb=" N ARG F 161 " --> pdb=" O HIS F 125 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N HIS F 125 " --> pdb=" O ARG F 161 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER F 10 " --> pdb=" O CYS F 99 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N LEU F 7 " --> pdb=" O HIS F 33 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LEU F 35 " --> pdb=" O LEU F 7 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N VAL F 9 " --> pdb=" O LEU F 35 " (cutoff:3.500A) removed outlier: 6.921A pdb=" N ILE F 60 " --> pdb=" O ARG F 191 " (cutoff:3.500A) removed outlier: 7.927A pdb=" N VAL F 193 " --> pdb=" O ILE F 60 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N ARG F 62 " --> pdb=" O VAL F 193 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLU F 190 " --> pdb=" O GLU F 186 " (cutoff:3.500A) removed outlier: 4.922A pdb=" N GLU F 186 " --> pdb=" O GLU F 190 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ARG F 192 " --> pdb=" O VAL F 184 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'F' and resid 260 through 266 removed outlier: 7.587A pdb=" N LYS F 260 " --> pdb=" O CYS F 349 " (cutoff:3.500A) removed outlier: 6.295A pdb=" N ALA F 351 " --> pdb=" O LYS F 260 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N GLU F 262 " --> pdb=" O ALA F 351 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N VAL F 353 " --> pdb=" O GLU F 262 " (cutoff:3.500A) removed outlier: 8.610A pdb=" N HIS F 264 " --> pdb=" O VAL F 353 " (cutoff:3.500A) removed outlier: 10.558A pdb=" N CYS F 355 " --> pdb=" O HIS F 264 " (cutoff:3.500A) removed outlier: 9.236A pdb=" N HIS F 266 " --> pdb=" O CYS F 355 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS F 395 " --> pdb=" O CYS F 349 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL F 436 " --> pdb=" O VAL F 396 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N LEU F 398 " --> pdb=" O VAL F 436 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N GLY F 438 " --> pdb=" O LEU F 398 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N VAL F 437 " --> pdb=" O ALA F 467 " (cutoff:3.500A) removed outlier: 7.919A pdb=" N THR F 469 " --> pdb=" O VAL F 437 " (cutoff:3.500A) removed outlier: 6.426A pdb=" N VAL F 439 " --> pdb=" O THR F 469 " (cutoff:3.500A) removed outlier: 8.097A pdb=" N HIS F 471 " --> pdb=" O VAL F 439 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU F 441 " --> pdb=" O HIS F 471 " (cutoff:3.500A) removed outlier: 6.994A pdb=" N VAL F 468 " --> pdb=" O ARG F 492 " (cutoff:3.500A) removed outlier: 8.474A pdb=" N GLY F 494 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N VAL F 470 " --> pdb=" O GLY F 494 " (cutoff:3.500A) 1333 hydrogen bonds defined for protein. 3732 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: 5.59 Time building geometry restraints manager: 2.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10075 1.34 - 1.46: 4339 1.46 - 1.58: 15274 1.58 - 1.70: 54 1.70 - 1.81: 174 Bond restraints: 29916 Sorted by residual: bond pdb=" C12 LQJ F 703 " pdb=" C20 LQJ F 703 " ideal model delta sigma weight residual 1.534 1.274 0.260 2.00e-02 2.50e+03 1.69e+02 bond pdb=" C12 LQJ F 702 " pdb=" C20 LQJ F 702 " ideal model delta sigma weight residual 1.534 1.276 0.258 2.00e-02 2.50e+03 1.67e+02 bond pdb=" C12 LQJ A 702 " pdb=" C20 LQJ A 702 " ideal model delta sigma weight residual 1.534 1.277 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C12 LQJ C 702 " pdb=" C20 LQJ C 702 " ideal model delta sigma weight residual 1.534 1.277 0.257 2.00e-02 2.50e+03 1.65e+02 bond pdb=" C12 LQJ D 702 " pdb=" C20 LQJ D 702 " ideal model delta sigma weight residual 1.534 1.278 0.256 2.00e-02 2.50e+03 1.64e+02 ... (remaining 29911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.45: 40312 3.45 - 6.91: 341 6.91 - 10.36: 67 10.36 - 13.82: 13 13.82 - 17.27: 7 Bond angle restraints: 40740 Sorted by residual: angle pdb=" CA PRO C 135 " pdb=" N PRO C 135 " pdb=" CD PRO C 135 " ideal model delta sigma weight residual 112.00 97.09 14.91 1.40e+00 5.10e-01 1.13e+02 angle pdb=" CA PRO B 142 " pdb=" N PRO B 142 " pdb=" CD PRO B 142 " ideal model delta sigma weight residual 112.00 98.91 13.09 1.40e+00 5.10e-01 8.74e+01 angle pdb=" CA PRO E 135 " pdb=" N PRO E 135 " pdb=" CD PRO E 135 " ideal model delta sigma weight residual 112.00 100.34 11.66 1.40e+00 5.10e-01 6.94e+01 angle pdb=" CA PRO D 142 " pdb=" N PRO D 142 " pdb=" CD PRO D 142 " ideal model delta sigma weight residual 112.00 100.52 11.48 1.40e+00 5.10e-01 6.73e+01 angle pdb=" N VAL D 363 " pdb=" CA VAL D 363 " pdb=" C VAL D 363 " ideal model delta sigma weight residual 113.53 107.64 5.89 9.80e-01 1.04e+00 3.62e+01 ... (remaining 40735 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 15910 17.99 - 35.99: 1603 35.99 - 53.98: 216 53.98 - 71.97: 40 71.97 - 89.96: 21 Dihedral angle restraints: 17790 sinusoidal: 7236 harmonic: 10554 Sorted by residual: dihedral pdb=" CA VAL E 63 " pdb=" C VAL E 63 " pdb=" N ALA E 64 " pdb=" CA ALA E 64 " ideal model delta harmonic sigma weight residual 180.00 146.61 33.39 0 5.00e+00 4.00e-02 4.46e+01 dihedral pdb=" CA VAL A 63 " pdb=" C VAL A 63 " pdb=" N ALA A 64 " pdb=" CA ALA A 64 " ideal model delta harmonic sigma weight residual 180.00 152.53 27.47 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA GLN F 154 " pdb=" C GLN F 154 " pdb=" N GLY F 155 " pdb=" CA GLY F 155 " ideal model delta harmonic sigma weight residual 180.00 154.21 25.79 0 5.00e+00 4.00e-02 2.66e+01 ... (remaining 17787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.076: 4026 0.076 - 0.152: 390 0.152 - 0.228: 29 0.228 - 0.305: 6 0.305 - 0.381: 13 Chirality restraints: 4464 Sorted by residual: chirality pdb=" C20 LQJ F 702 " pdb=" C12 LQJ F 702 " pdb=" C19 LQJ F 702 " pdb=" O9 LQJ F 702 " both_signs ideal model delta sigma weight residual False -2.67 -2.29 -0.38 2.00e-01 2.50e+01 3.62e+00 chirality pdb=" C20 LQJ A 702 " pdb=" C12 LQJ A 702 " pdb=" C19 LQJ A 702 " pdb=" O9 LQJ A 702 " both_signs ideal model delta sigma weight residual False -2.67 -2.30 -0.37 2.00e-01 2.50e+01 3.48e+00 chirality pdb=" C20 LQJ F 703 " pdb=" C12 LQJ F 703 " pdb=" C19 LQJ F 703 " pdb=" O9 LQJ F 703 " both_signs ideal model delta sigma weight residual False -2.67 -2.30 -0.37 2.00e-01 2.50e+01 3.45e+00 ... (remaining 4461 not shown) Planarity restraints: 5358 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO B 141 " 0.097 5.00e-02 4.00e+02 1.36e-01 2.96e+01 pdb=" N PRO B 142 " -0.235 5.00e-02 4.00e+02 pdb=" CA PRO B 142 " 0.067 5.00e-02 4.00e+02 pdb=" CD PRO B 142 " 0.070 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 92 " 0.075 5.00e-02 4.00e+02 1.12e-01 1.99e+01 pdb=" N PRO A 93 " -0.193 5.00e-02 4.00e+02 pdb=" CA PRO A 93 " 0.058 5.00e-02 4.00e+02 pdb=" CD PRO A 93 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 134 " -0.077 5.00e-02 4.00e+02 1.05e-01 1.78e+01 pdb=" N PRO C 135 " 0.182 5.00e-02 4.00e+02 pdb=" CA PRO C 135 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO C 135 " -0.058 5.00e-02 4.00e+02 ... (remaining 5355 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 379 2.68 - 3.24: 26842 3.24 - 3.79: 43252 3.79 - 4.35: 58921 4.35 - 4.90: 99246 Nonbonded interactions: 228640 Sorted by model distance: nonbonded pdb=" NE2 GLN A 182 " pdb=" OE2 GLU A 196 " model vdw 2.127 3.120 nonbonded pdb=" NH1 ARG F 278 " pdb=" OE2 GLU F 295 " model vdw 2.177 3.120 nonbonded pdb=" NH1 ARG B 278 " pdb=" OE2 GLU B 295 " model vdw 2.180 3.120 nonbonded pdb=" NH1 ARG A 278 " pdb=" OE2 GLU A 295 " model vdw 2.194 3.120 nonbonded pdb=" OG1 THR D 101 " pdb=" ND1 HIS D 125 " model vdw 2.242 3.120 ... (remaining 228635 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: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 2 through 701) selection = (chain 'B' and resid 2 through 701) selection = (chain 'C' and resid 2 through 701) selection = (chain 'D' and resid 2 through 701) selection = chain 'E' selection = (chain 'F' and resid 2 through 701) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 10.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 26.700 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.050 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:7.350 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9055 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 : 0.010 0.260 29935 Z= 0.481 Angle : 0.853 17.274 40740 Z= 0.406 Chirality : 0.049 0.381 4464 Planarity : 0.009 0.136 5358 Dihedral : 13.962 89.964 10974 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.32 % Favored : 94.52 % Rotamer: Outliers : 0.07 % Allowed : 0.44 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3666 helix: 1.85 (0.13), residues: 1632 sheet: -0.56 (0.23), residues: 564 loop : -1.36 (0.15), residues: 1470 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.026 0.000 ARG A 463 TYR 0.013 0.001 TYR A 521 PHE 0.022 0.001 PHE F 203 TRP 0.021 0.002 TRP F 302 HIS 0.010 0.001 HIS D 417 Details of bonding type rmsd/Z covalent geometry : bond 0.00991 / 0.48 (29916) covalent geometry : angle 0.85305 / 0.41 (40740) hydrogen bonds : bond 0.17807 / 12.31 ( 1333) hydrogen bonds : angle 5.95898 / 4.16 ( 3732) metal coordination : bond 0.00164 / 0.11 ( 18) Misc. bond : bond 0.00074 / 0.04 ( 1) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 306 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 304 time to evaluate : 1.104 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 275 GLU cc_start: 0.7867 (tp30) cc_final: 0.7609 (tp30) REVERT: E 275 GLU cc_start: 0.7938 (tp30) cc_final: 0.7485 (tp30) outliers start: 2 outliers final: 0 residues processed: 306 average time/residue: 1.2022 time to fit residues: 400.6294 Evaluate side-chains 201 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 201 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 197 optimal weight: 0.3980 chunk 215 optimal weight: 0.3980 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.7980 chunk 261 optimal weight: 0.0670 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 1.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 3.9990 chunk 183 optimal weight: 3.9990 chunk 298 optimal weight: 1.9990 overall best weight: 0.5118 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 52 HIS B 33 HIS ** B 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 335 GLN C 601 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 417 HIS D 452 HIS E 2 ASN E 475 ASN ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 205 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.057179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.049358 restraints weight = 79634.744| |-----------------------------------------------------------------------------| r_work (start): 0.3121 rms_B_bonded: 1.88 r_work: 0.3017 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.2899 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2899 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9091 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 29935 Z= 0.135 Angle : 0.644 7.946 40740 Z= 0.325 Chirality : 0.043 0.207 4464 Planarity : 0.007 0.080 5358 Dihedral : 5.051 46.117 4122 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 4.01 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 0.98 % Allowed : 7.27 % Favored : 91.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3666 helix: 2.13 (0.13), residues: 1638 sheet: -0.57 (0.22), residues: 564 loop : -1.19 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG E 51 TYR 0.014 0.001 TYR E 552 PHE 0.016 0.001 PHE A 86 TRP 0.014 0.001 TRP A 85 HIS 0.008 0.001 HIS F 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.13 (29916) covalent geometry : angle 0.64443 / 0.32 (40740) hydrogen bonds : bond 0.04979 / 3.40 ( 1333) hydrogen bonds : angle 4.60487 / 3.21 ( 3732) metal coordination : bond 0.00174 / 0.10 ( 18) Misc. bond : bond 0.00152 / 0.08 ( 1) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 199 time to evaluate : 1.201 Fit side-chains revert: symmetry clash REVERT: B 220 MET cc_start: 0.8392 (OUTLIER) cc_final: 0.7606 (ptp) REVERT: B 275 GLU cc_start: 0.8249 (tp30) cc_final: 0.7930 (tp30) REVERT: B 448 LYS cc_start: 0.9201 (OUTLIER) cc_final: 0.8931 (ptmm) REVERT: C 112 GLN cc_start: 0.8986 (OUTLIER) cc_final: 0.8142 (tt0) REVERT: E 275 GLU cc_start: 0.8370 (tp30) cc_final: 0.7881 (tp30) REVERT: F 447 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7895 (tp30) outliers start: 29 outliers final: 9 residues processed: 210 average time/residue: 1.1008 time to fit residues: 254.7397 Evaluate side-chains 204 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 192 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain B residue 145 LEU Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain B residue 448 LYS Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 207 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 88 optimal weight: 3.9990 chunk 249 optimal weight: 1.9990 chunk 321 optimal weight: 0.9980 chunk 53 optimal weight: 0.0000 chunk 51 optimal weight: 0.8980 chunk 269 optimal weight: 0.4980 chunk 153 optimal weight: 0.9980 chunk 298 optimal weight: 0.7980 chunk 218 optimal weight: 1.9990 chunk 213 optimal weight: 2.9990 chunk 157 optimal weight: 1.9990 overall best weight: 0.6384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 136 GLN B 205 GLN B 570 ASN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 342 HIS E 475 ASN E 601 GLN F 95 GLN F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.056513 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.048658 restraints weight = 79532.115| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 1.88 r_work: 0.2996 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2877 rms_B_bonded: 3.75 restraints_weight: 0.2500 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9109 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 29935 Z= 0.136 Angle : 0.618 7.303 40740 Z= 0.312 Chirality : 0.043 0.219 4464 Planarity : 0.006 0.066 5358 Dihedral : 5.060 48.646 4122 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 1.18 % Allowed : 8.42 % Favored : 90.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3666 helix: 2.25 (0.13), residues: 1638 sheet: -0.60 (0.22), residues: 564 loop : -1.15 (0.15), residues: 1464 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 297 TYR 0.015 0.001 TYR A 444 PHE 0.014 0.001 PHE B 66 TRP 0.016 0.001 TRP A 85 HIS 0.007 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00333 / 0.14 (29916) covalent geometry : angle 0.61758 / 0.31 (40740) hydrogen bonds : bond 0.04859 / 3.32 ( 1333) hydrogen bonds : angle 4.34592 / 3.03 ( 3732) metal coordination : bond 0.00203 / 0.12 ( 18) Misc. bond : bond 0.00242 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 200 time to evaluate : 1.112 Fit side-chains revert: symmetry clash REVERT: A 530 ARG cc_start: 0.8782 (OUTLIER) cc_final: 0.8557 (mpp-170) REVERT: B 275 GLU cc_start: 0.8246 (tp30) cc_final: 0.7973 (tp30) REVERT: C 112 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8129 (tt0) REVERT: C 161 ARG cc_start: 0.8938 (OUTLIER) cc_final: 0.8394 (mtp85) REVERT: C 220 MET cc_start: 0.8445 (OUTLIER) cc_final: 0.7335 (ppp) REVERT: D 327 ARG cc_start: 0.8585 (OUTLIER) cc_final: 0.7715 (mpt-90) REVERT: E 275 GLU cc_start: 0.8354 (tp30) cc_final: 0.7868 (tp30) REVERT: F 220 MET cc_start: 0.8513 (OUTLIER) cc_final: 0.7607 (ppp) REVERT: F 223 GLU cc_start: 0.8224 (OUTLIER) cc_final: 0.8022 (mp0) REVERT: F 447 GLU cc_start: 0.8150 (tm-30) cc_final: 0.7909 (tp30) outliers start: 35 outliers final: 9 residues processed: 222 average time/residue: 1.1324 time to fit residues: 277.7127 Evaluate side-chains 210 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 194 time to evaluate : 1.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 MET Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 161 ARG Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 220 MET Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 304 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 133 optimal weight: 0.9980 chunk 333 optimal weight: 3.9990 chunk 338 optimal weight: 2.9990 chunk 149 optimal weight: 3.9990 chunk 96 optimal weight: 0.7980 chunk 129 optimal weight: 2.9990 chunk 293 optimal weight: 3.9990 chunk 192 optimal weight: 2.9990 chunk 265 optimal weight: 2.9990 chunk 334 optimal weight: 3.9990 chunk 346 optimal weight: 3.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 570 ASN A 581 ASN B 95 GLN C 501 GLN C 581 ASN D 95 GLN ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 417 HIS F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 286 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.052475 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.044520 restraints weight = 79536.635| |-----------------------------------------------------------------------------| r_work (start): 0.2978 rms_B_bonded: 1.92 r_work: 0.2867 rms_B_bonded: 2.20 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9207 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.069 29935 Z= 0.320 Angle : 0.775 7.709 40740 Z= 0.396 Chirality : 0.052 0.279 4464 Planarity : 0.007 0.066 5358 Dihedral : 5.668 52.591 4122 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.14 % Favored : 93.70 % Rotamer: Outliers : 1.18 % Allowed : 9.33 % Favored : 89.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.33 (0.14), residues: 3666 helix: 1.90 (0.13), residues: 1644 sheet: -0.56 (0.22), residues: 540 loop : -1.45 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG E 492 TYR 0.023 0.002 TYR E 552 PHE 0.031 0.003 PHE D 66 TRP 0.023 0.002 TRP C 85 HIS 0.015 0.002 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00811 / 0.32 (29916) covalent geometry : angle 0.77484 / 0.40 (40740) hydrogen bonds : bond 0.08146 / 5.56 ( 1333) hydrogen bonds : angle 4.82974 / 3.39 ( 3732) metal coordination : bond 0.00519 / 0.29 ( 18) Misc. bond : bond 0.00644 / 0.34 ( 1) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 0.945 Fit side-chains revert: symmetry clash REVERT: A 530 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8447 (mpp-170) REVERT: B 220 MET cc_start: 0.8628 (OUTLIER) cc_final: 0.8000 (ptp) REVERT: B 275 GLU cc_start: 0.8354 (tp30) cc_final: 0.8030 (tp30) REVERT: B 447 GLU cc_start: 0.8683 (tt0) cc_final: 0.8413 (tm-30) REVERT: C 112 GLN cc_start: 0.9104 (OUTLIER) cc_final: 0.8319 (tt0) REVERT: C 316 LYS cc_start: 0.9316 (OUTLIER) cc_final: 0.9101 (ptpp) REVERT: D 140 MET cc_start: 0.7586 (ppp) cc_final: 0.7364 (ppp) REVERT: D 327 ARG cc_start: 0.8785 (OUTLIER) cc_final: 0.7945 (mpt-90) REVERT: E 275 GLU cc_start: 0.8377 (tp30) cc_final: 0.7878 (tp30) REVERT: F 125 HIS cc_start: 0.7332 (OUTLIER) cc_final: 0.7000 (p90) REVERT: F 223 GLU cc_start: 0.8457 (OUTLIER) cc_final: 0.8146 (mp0) REVERT: F 327 ARG cc_start: 0.8738 (OUTLIER) cc_final: 0.8155 (ttp80) REVERT: F 447 GLU cc_start: 0.8265 (tm-30) cc_final: 0.7980 (tp30) outliers start: 35 outliers final: 12 residues processed: 227 average time/residue: 1.1187 time to fit residues: 279.5396 Evaluate side-chains 214 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 194 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LEU Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 316 LYS Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 290 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 223 GLU Chi-restraints excluded: chain F residue 327 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 28 optimal weight: 0.9980 chunk 262 optimal weight: 0.6980 chunk 92 optimal weight: 0.6980 chunk 58 optimal weight: 0.5980 chunk 122 optimal weight: 1.9990 chunk 318 optimal weight: 7.9990 chunk 163 optimal weight: 1.9990 chunk 300 optimal weight: 0.7980 chunk 230 optimal weight: 1.9990 chunk 289 optimal weight: 0.7980 chunk 147 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 95 GLN B 452 HIS C 286 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN E 378 GLN ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 209 GLN F 567 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.054663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.046835 restraints weight = 79099.723| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.87 r_work: 0.2942 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2821 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9155 moved from start: 0.1771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 29935 Z= 0.147 Angle : 0.640 7.216 40740 Z= 0.328 Chirality : 0.044 0.240 4464 Planarity : 0.006 0.060 5358 Dihedral : 5.338 48.735 4122 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.65 % Favored : 94.19 % Rotamer: Outliers : 1.28 % Allowed : 10.67 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3666 helix: 2.09 (0.13), residues: 1644 sheet: -0.50 (0.22), residues: 540 loop : -1.40 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 297 TYR 0.015 0.001 TYR A 444 PHE 0.015 0.001 PHE B 66 TRP 0.017 0.001 TRP A 85 HIS 0.011 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00356 / 0.15 (29916) covalent geometry : angle 0.64042 / 0.33 (40740) hydrogen bonds : bond 0.05310 / 3.62 ( 1333) hydrogen bonds : angle 4.42350 / 3.09 ( 3732) metal coordination : bond 0.00157 / 0.08 ( 18) Misc. bond : bond 0.00250 / 0.13 ( 1) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 198 time to evaluate : 1.059 Fit side-chains revert: symmetry clash REVERT: A 381 MET cc_start: 0.9204 (mtp) cc_final: 0.8956 (mtp) REVERT: A 530 ARG cc_start: 0.8792 (OUTLIER) cc_final: 0.8515 (mpp-170) REVERT: B 220 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.7741 (ppp) REVERT: B 275 GLU cc_start: 0.8328 (tp30) cc_final: 0.8026 (tp30) REVERT: C 112 GLN cc_start: 0.8997 (OUTLIER) cc_final: 0.8138 (tt0) REVERT: D 140 MET cc_start: 0.7464 (ppp) cc_final: 0.7254 (ppp) REVERT: D 327 ARG cc_start: 0.8660 (OUTLIER) cc_final: 0.7808 (mpt-90) REVERT: E 275 GLU cc_start: 0.8325 (tp30) cc_final: 0.7846 (tp30) REVERT: F 289 LYS cc_start: 0.9023 (mttm) cc_final: 0.8792 (mptt) REVERT: F 327 ARG cc_start: 0.8627 (OUTLIER) cc_final: 0.7966 (ttp80) REVERT: F 447 GLU cc_start: 0.8227 (tm-30) cc_final: 0.7962 (tp30) outliers start: 38 outliers final: 18 residues processed: 220 average time/residue: 1.0525 time to fit residues: 255.7552 Evaluate side-chains 214 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 191 time to evaluate : 1.148 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain D residue 432 ASN Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 327 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 204 optimal weight: 1.9990 chunk 320 optimal weight: 3.9990 chunk 220 optimal weight: 0.5980 chunk 316 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 309 optimal weight: 0.0870 chunk 339 optimal weight: 2.9990 chunk 225 optimal weight: 3.9990 chunk 242 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 29 optimal weight: 0.0370 overall best weight: 1.1440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 95 GLN B 495 HIS ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3253 r_free = 0.3253 target = 0.053983 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.046089 restraints weight = 79570.273| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 1.89 r_work: 0.2919 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.2797 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9172 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 29935 Z= 0.190 Angle : 0.671 7.895 40740 Z= 0.341 Chirality : 0.045 0.254 4464 Planarity : 0.006 0.060 5358 Dihedral : 5.354 49.676 4122 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.84 % Rotamer: Outliers : 1.21 % Allowed : 10.98 % Favored : 87.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.14), residues: 3666 helix: 2.11 (0.13), residues: 1644 sheet: -0.52 (0.22), residues: 540 loop : -1.42 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 297 TYR 0.016 0.001 TYR A 444 PHE 0.018 0.002 PHE D 66 TRP 0.018 0.002 TRP A 85 HIS 0.008 0.001 HIS A 452 Details of bonding type rmsd/Z covalent geometry : bond 0.00479 / 0.19 (29916) covalent geometry : angle 0.67105 / 0.34 (40740) hydrogen bonds : bond 0.05911 / 4.03 ( 1333) hydrogen bonds : angle 4.44514 / 3.10 ( 3732) metal coordination : bond 0.00273 / 0.15 ( 18) Misc. bond : bond 0.00386 / 0.20 ( 1) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 198 time to evaluate : 1.118 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 530 ARG cc_start: 0.8787 (OUTLIER) cc_final: 0.8485 (mpp-170) REVERT: B 144 THR cc_start: 0.8439 (p) cc_final: 0.8209 (p) REVERT: B 220 MET cc_start: 0.8503 (OUTLIER) cc_final: 0.7736 (ppp) REVERT: B 275 GLU cc_start: 0.8321 (tp30) cc_final: 0.8040 (tp30) REVERT: C 112 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8171 (tt0) REVERT: C 429 ARG cc_start: 0.8883 (OUTLIER) cc_final: 0.8545 (mtm180) REVERT: D 140 MET cc_start: 0.7607 (ppp) cc_final: 0.7392 (ppp) REVERT: D 327 ARG cc_start: 0.8680 (OUTLIER) cc_final: 0.7818 (mpt-90) REVERT: E 275 GLU cc_start: 0.8350 (tp30) cc_final: 0.7878 (tp30) REVERT: F 125 HIS cc_start: 0.7078 (OUTLIER) cc_final: 0.6846 (p90) REVERT: F 327 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.8000 (ttp80) REVERT: F 447 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7986 (tp30) outliers start: 36 outliers final: 14 residues processed: 218 average time/residue: 1.0389 time to fit residues: 250.3161 Evaluate side-chains 212 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 191 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain B residue 220 MET Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 311 LEU Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Chi-restraints excluded: chain F residue 327 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 173 optimal weight: 1.9990 chunk 65 optimal weight: 0.3980 chunk 148 optimal weight: 0.9980 chunk 318 optimal weight: 6.9990 chunk 214 optimal weight: 0.9980 chunk 359 optimal weight: 0.9980 chunk 292 optimal weight: 0.6980 chunk 139 optimal weight: 0.5980 chunk 321 optimal weight: 0.6980 chunk 174 optimal weight: 0.9980 chunk 176 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 95 GLN C 286 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 209 GLN E 2 ASN ** F 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.055077 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.047224 restraints weight = 79138.899| |-----------------------------------------------------------------------------| r_work (start): 0.3055 rms_B_bonded: 1.88 r_work: 0.2949 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.70 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29935 Z= 0.141 Angle : 0.637 10.971 40740 Z= 0.323 Chirality : 0.043 0.244 4464 Planarity : 0.005 0.059 5358 Dihedral : 5.215 48.348 4122 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.81 % Favored : 94.03 % Rotamer: Outliers : 0.98 % Allowed : 11.55 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3666 helix: 2.19 (0.13), residues: 1644 sheet: -0.51 (0.22), residues: 540 loop : -1.38 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG F 297 TYR 0.016 0.001 TYR A 444 PHE 0.013 0.001 PHE D 66 TRP 0.016 0.001 TRP A 85 HIS 0.007 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00344 / 0.14 (29916) covalent geometry : angle 0.63669 / 0.32 (40740) hydrogen bonds : bond 0.04973 / 3.39 ( 1333) hydrogen bonds : angle 4.29332 / 2.99 ( 3732) metal coordination : bond 0.00165 / 0.09 ( 18) Misc. bond : bond 0.00217 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.074 Fit side-chains REVERT: A 530 ARG cc_start: 0.8768 (OUTLIER) cc_final: 0.8469 (mpp-170) REVERT: B 145 LEU cc_start: 0.8363 (mt) cc_final: 0.8147 (mt) REVERT: B 275 GLU cc_start: 0.8306 (tp30) cc_final: 0.8013 (tp30) REVERT: C 112 GLN cc_start: 0.8991 (OUTLIER) cc_final: 0.8106 (tt0) REVERT: C 530 ARG cc_start: 0.8644 (mmt180) cc_final: 0.8398 (mpt180) REVERT: D 140 MET cc_start: 0.7592 (ppp) cc_final: 0.7373 (ppp) REVERT: D 327 ARG cc_start: 0.8671 (OUTLIER) cc_final: 0.7796 (mpt-90) REVERT: E 275 GLU cc_start: 0.8324 (tp30) cc_final: 0.7845 (tp30) REVERT: F 220 MET cc_start: 0.8619 (OUTLIER) cc_final: 0.8228 (ppp) REVERT: F 447 GLU cc_start: 0.8224 (tm-30) cc_final: 0.7967 (tp30) outliers start: 29 outliers final: 15 residues processed: 209 average time/residue: 1.0519 time to fit residues: 243.2653 Evaluate side-chains 212 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 193 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain F residue 3 VAL Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 125 HIS Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 357 optimal weight: 3.9990 chunk 288 optimal weight: 4.9990 chunk 161 optimal weight: 3.9990 chunk 137 optimal weight: 2.9990 chunk 46 optimal weight: 0.0870 chunk 247 optimal weight: 0.8980 chunk 330 optimal weight: 0.8980 chunk 305 optimal weight: 3.9990 chunk 99 optimal weight: 3.9990 chunk 126 optimal weight: 0.6980 chunk 139 optimal weight: 0.6980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055304 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.047470 restraints weight = 79466.022| |-----------------------------------------------------------------------------| r_work (start): 0.3063 rms_B_bonded: 1.89 r_work: 0.2956 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2836 rms_B_bonded: 3.72 restraints_weight: 0.2500 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.1884 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 29935 Z= 0.139 Angle : 0.634 8.361 40740 Z= 0.322 Chirality : 0.043 0.243 4464 Planarity : 0.006 0.069 5358 Dihedral : 5.133 47.792 4122 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 0.91 % Allowed : 12.22 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.67 (0.14), residues: 3666 helix: 2.23 (0.13), residues: 1650 sheet: -0.48 (0.22), residues: 540 loop : -1.33 (0.15), residues: 1476 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG F 297 TYR 0.016 0.001 TYR A 444 PHE 0.014 0.001 PHE A 49 TRP 0.015 0.001 TRP A 85 HIS 0.006 0.001 HIS F 125 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.14 (29916) covalent geometry : angle 0.63429 / 0.32 (40740) hydrogen bonds : bond 0.04747 / 3.24 ( 1333) hydrogen bonds : angle 4.21169 / 2.93 ( 3732) metal coordination : bond 0.00167 / 0.09 ( 18) Misc. bond : bond 0.00212 / 0.11 ( 1) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 1.157 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 530 ARG cc_start: 0.8776 (OUTLIER) cc_final: 0.8481 (mpp-170) REVERT: B 275 GLU cc_start: 0.8291 (tp30) cc_final: 0.7988 (tp30) REVERT: C 112 GLN cc_start: 0.8984 (OUTLIER) cc_final: 0.8087 (tt0) REVERT: C 530 ARG cc_start: 0.8660 (mmt180) cc_final: 0.8413 (mpt180) REVERT: D 140 MET cc_start: 0.7638 (ppp) cc_final: 0.7420 (ppp) REVERT: D 327 ARG cc_start: 0.8659 (OUTLIER) cc_final: 0.7779 (mpt-90) REVERT: E 275 GLU cc_start: 0.8334 (tp30) cc_final: 0.7844 (tp30) REVERT: F 220 MET cc_start: 0.8631 (OUTLIER) cc_final: 0.8171 (ppp) REVERT: F 447 GLU cc_start: 0.8232 (tm-30) cc_final: 0.7963 (tp30) outliers start: 27 outliers final: 15 residues processed: 210 average time/residue: 1.0658 time to fit residues: 247.6948 Evaluate side-chains 207 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 188 time to evaluate : 1.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 327 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 234 optimal weight: 1.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 345 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 221 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 191 optimal weight: 1.9990 chunk 307 optimal weight: 0.0670 overall best weight: 1.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 95 GLN C 286 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN E 2 ASN F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.053180 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.045270 restraints weight = 79407.561| |-----------------------------------------------------------------------------| r_work (start): 0.3008 rms_B_bonded: 1.92 r_work: 0.2893 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9196 moved from start: 0.2010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 29935 Z= 0.247 Angle : 0.719 9.963 40740 Z= 0.366 Chirality : 0.048 0.278 4464 Planarity : 0.006 0.066 5358 Dihedral : 5.432 51.117 4122 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.22 % Favored : 93.62 % Rotamer: Outliers : 0.98 % Allowed : 12.19 % Favored : 86.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.47 (0.14), residues: 3666 helix: 2.08 (0.13), residues: 1644 sheet: -0.55 (0.22), residues: 540 loop : -1.45 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG F 297 TYR 0.018 0.002 TYR A 444 PHE 0.021 0.002 PHE D 66 TRP 0.018 0.002 TRP C 85 HIS 0.008 0.002 HIS C 471 Details of bonding type rmsd/Z covalent geometry : bond 0.00629 / 0.25 (29916) covalent geometry : angle 0.71925 / 0.37 (40740) hydrogen bonds : bond 0.06753 / 4.61 ( 1333) hydrogen bonds : angle 4.52466 / 3.17 ( 3732) metal coordination : bond 0.00372 / 0.21 ( 18) Misc. bond : bond 0.00342 / 0.18 ( 1) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 192 time to evaluate : 1.191 Fit side-chains revert: symmetry clash REVERT: A 530 ARG cc_start: 0.8828 (OUTLIER) cc_final: 0.8486 (mpp-170) REVERT: B 275 GLU cc_start: 0.8331 (tp30) cc_final: 0.7996 (tp30) REVERT: C 112 GLN cc_start: 0.9086 (OUTLIER) cc_final: 0.8256 (tt0) REVERT: C 429 ARG cc_start: 0.8931 (OUTLIER) cc_final: 0.8601 (mtm180) REVERT: C 530 ARG cc_start: 0.8724 (mmt180) cc_final: 0.8455 (mpt180) REVERT: D 140 MET cc_start: 0.7757 (ppp) cc_final: 0.7518 (ppp) REVERT: D 327 ARG cc_start: 0.8735 (OUTLIER) cc_final: 0.7861 (mpt-90) REVERT: E 275 GLU cc_start: 0.8358 (tp30) cc_final: 0.7855 (tp30) REVERT: F 220 MET cc_start: 0.8730 (OUTLIER) cc_final: 0.8306 (ppp) REVERT: F 447 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7965 (tp30) outliers start: 29 outliers final: 15 residues processed: 208 average time/residue: 1.1163 time to fit residues: 257.2439 Evaluate side-chains 206 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 186 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain A residue 564 VAL Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 112 GLN Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain C residue 429 ARG Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 145 LEU Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 129 optimal weight: 0.9990 chunk 269 optimal weight: 0.5980 chunk 157 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 320 optimal weight: 0.5980 chunk 195 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 228 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 211 optimal weight: 0.2980 chunk 244 optimal weight: 2.9990 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 95 GLN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 2 ASN F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.055299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.047492 restraints weight = 78734.545| |-----------------------------------------------------------------------------| r_work (start): 0.3064 rms_B_bonded: 1.87 r_work: 0.2958 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9143 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 29935 Z= 0.136 Angle : 0.645 8.701 40740 Z= 0.328 Chirality : 0.043 0.237 4464 Planarity : 0.005 0.063 5358 Dihedral : 5.181 47.629 4122 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.56 % Favored : 94.27 % Rotamer: Outliers : 0.77 % Allowed : 12.56 % Favored : 86.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.61 (0.14), residues: 3666 helix: 2.21 (0.13), residues: 1644 sheet: -0.48 (0.22), residues: 540 loop : -1.39 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 297 TYR 0.017 0.001 TYR A 444 PHE 0.012 0.001 PHE A 49 TRP 0.015 0.001 TRP A 85 HIS 0.006 0.001 HIS D 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.14 (29916) covalent geometry : angle 0.64463 / 0.33 (40740) hydrogen bonds : bond 0.04661 / 3.19 ( 1333) hydrogen bonds : angle 4.22718 / 2.95 ( 3732) metal coordination : bond 0.00138 / 0.08 ( 18) Misc. bond : bond 0.00150 / 0.08 ( 1) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7332 Ramachandran restraints generated. 3666 Oldfield, 0 Emsley, 3666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 194 time to evaluate : 1.182 Fit side-chains revert: symmetry clash REVERT: A 530 ARG cc_start: 0.8759 (OUTLIER) cc_final: 0.8435 (mpp-170) REVERT: B 275 GLU cc_start: 0.8290 (tp30) cc_final: 0.8001 (tp30) REVERT: C 530 ARG cc_start: 0.8643 (mmt180) cc_final: 0.8407 (mpt180) REVERT: D 140 MET cc_start: 0.7753 (ppp) cc_final: 0.7534 (ppp) REVERT: D 327 ARG cc_start: 0.8664 (OUTLIER) cc_final: 0.7797 (mpt-90) REVERT: E 275 GLU cc_start: 0.8334 (tp30) cc_final: 0.7846 (tp30) REVERT: F 220 MET cc_start: 0.8618 (OUTLIER) cc_final: 0.8099 (ppp) REVERT: F 447 GLU cc_start: 0.8238 (tm-30) cc_final: 0.7916 (tp30) outliers start: 23 outliers final: 14 residues processed: 206 average time/residue: 1.1144 time to fit residues: 253.7327 Evaluate side-chains 201 residues out of total 2970 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 162 LEU Chi-restraints excluded: chain A residue 530 ARG Chi-restraints excluded: chain B residue 125 HIS Chi-restraints excluded: chain C residue 32 VAL Chi-restraints excluded: chain C residue 162 LEU Chi-restraints excluded: chain C residue 289 LYS Chi-restraints excluded: chain D residue 58 LEU Chi-restraints excluded: chain D residue 74 ASP Chi-restraints excluded: chain D residue 327 ARG Chi-restraints excluded: chain E residue 82 MET Chi-restraints excluded: chain E residue 206 ASP Chi-restraints excluded: chain E residue 286 ASN Chi-restraints excluded: chain E residue 316 LYS Chi-restraints excluded: chain F residue 58 LEU Chi-restraints excluded: chain F residue 140 MET Chi-restraints excluded: chain F residue 207 LEU Chi-restraints excluded: chain F residue 220 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 366 random chunks: chunk 205 optimal weight: 0.4980 chunk 355 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 103 optimal weight: 1.9990 chunk 13 optimal weight: 0.1980 chunk 221 optimal weight: 2.9990 chunk 258 optimal weight: 0.5980 chunk 270 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.4980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 205 GLN B 95 GLN C 286 ASN ** D 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 475 ASN E 2 ASN F 125 HIS ** F 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.055072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3058 r_free = 0.3058 target = 0.047232 restraints weight = 79341.860| |-----------------------------------------------------------------------------| r_work (start): 0.3056 rms_B_bonded: 1.88 r_work: 0.2949 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2829 rms_B_bonded: 3.71 restraints_weight: 0.2500 r_work (final): 0.2829 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9149 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 29935 Z= 0.149 Angle : 0.652 8.886 40740 Z= 0.330 Chirality : 0.043 0.250 4464 Planarity : 0.006 0.068 5358 Dihedral : 5.159 47.970 4122 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 3.33 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.95 % Favored : 93.89 % Rotamer: Outliers : 0.74 % Allowed : 12.66 % Favored : 86.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.14), residues: 3666 helix: 2.22 (0.13), residues: 1644 sheet: -0.47 (0.22), residues: 540 loop : -1.37 (0.15), residues: 1482 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG F 297 TYR 0.018 0.001 TYR A 444 PHE 0.013 0.001 PHE A 49 TRP 0.016 0.001 TRP A 85 HIS 0.009 0.001 HIS F 156 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (29916) covalent geometry : angle 0.65204 / 0.33 (40740) hydrogen bonds : bond 0.04939 / 3.37 ( 1333) hydrogen bonds : angle 4.22579 / 2.94 ( 3732) metal coordination : bond 0.00186 / 0.11 ( 18) Misc. bond : bond 0.00223 / 0.12 ( 1) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 13988.37 seconds wall clock time: 237 minutes 23.86 seconds (14243.86 seconds total)