Starting phenix.real_space_refine on Wed Apr 8 10:11:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nii_12360/04_2026/7nii_12360.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nii_12360/04_2026/7nii_12360.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nii_12360/04_2026/7nii_12360.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nii_12360/04_2026/7nii_12360.map" model { file = "/net/cci-nas-00/data/ceres_data/7nii_12360/04_2026/7nii_12360.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nii_12360/04_2026/7nii_12360.cif" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.006 sd= 0.079 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 P 16 5.49 5 Mg 8 5.21 5 S 113 5.16 5 C 23689 2.51 5 N 6345 2.21 5 O 7064 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37235 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "B" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "C" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Chain: "D" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "E" Number of atoms: 4050 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4050 Classifications: {'peptide': 525} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 502} Chain breaks: 3 Chain: "F" Number of atoms: 5167 Number of conformers: 1 Conformer: "" Number of residues, atoms: 663, 5167 Classifications: {'peptide': 663} Link IDs: {'PCIS': 1, 'PTRANS': 24, 'TRANS': 637} Chain breaks: 3 Chain: "G" Number of atoms: 4363 Number of conformers: 1 Conformer: "" Number of residues, atoms: 564, 4363 Classifications: {'peptide': 564} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 540} Chain breaks: 3 Chain: "H" Number of atoms: 4367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 565, 4367 Classifications: {'peptide': 565} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 541} Chain breaks: 3 Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.34, per 1000 atoms: 0.22 Number of scatterers: 37235 At special positions: 0 Unit cell: (160.826, 161.655, 172.432, 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) S 113 16.00 P 16 15.00 Mg 8 11.99 O 7064 8.00 N 6345 7.00 C 23689 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=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.53 Conformation dependent library (CDL) restraints added in 1.4 seconds 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8878 Finding SS restraints... Secondary structure from input PDB file: 176 helices and 32 sheets defined 52.3% alpha, 17.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 18 through 29 Processing helix chain 'A' and resid 29 through 51 Processing helix chain 'A' and resid 86 through 94 removed outlier: 3.762A pdb=" N ALA A 91 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 95 through 107 Processing helix chain 'A' and resid 120 through 128 Processing helix chain 'A' and resid 208 through 219 Processing helix chain 'A' and resid 240 through 266 removed outlier: 3.829A pdb=" N SER A 245 " --> pdb=" O PRO A 241 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ALA A 264 " --> pdb=" O ILE A 260 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLN A 266 " --> pdb=" O ARG A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 297 Proline residue: A 279 - end of helix Processing helix chain 'A' and resid 305 through 336 removed outlier: 3.521A pdb=" N GLN A 314 " --> pdb=" O SER A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 366 Processing helix chain 'A' and resid 368 through 404 removed outlier: 3.946A pdb=" N VAL A 374 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N SER A 403 " --> pdb=" O ASN A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 425 through 452 Processing helix chain 'A' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU A 461 " --> pdb=" O SER A 457 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 464 " --> pdb=" O GLN A 460 " (cutoff:3.500A) Processing helix chain 'A' and resid 496 through 501 Processing helix chain 'A' and resid 504 through 521 removed outlier: 3.631A pdb=" N PHE A 519 " --> pdb=" O THR A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 539 through 553 Processing helix chain 'A' and resid 569 through 575 Processing helix chain 'A' and resid 581 through 587 Processing helix chain 'A' and resid 591 through 595 removed outlier: 3.561A pdb=" N ILE A 595 " --> pdb=" O ALA A 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 591 through 595' Processing helix chain 'A' and resid 615 through 620 Processing helix chain 'A' and resid 622 through 636 removed outlier: 4.309A pdb=" N GLU A 626 " --> pdb=" O HIS A 622 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN A 634 " --> pdb=" O ASN A 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN A 635 " --> pdb=" O TRP A 631 " (cutoff:3.500A) Processing helix chain 'A' and resid 650 through 656 Processing helix chain 'A' and resid 672 through 686 removed outlier: 3.514A pdb=" N SER A 686 " --> pdb=" O ARG A 682 " (cutoff:3.500A) Processing helix chain 'A' and resid 701 through 708 removed outlier: 3.684A pdb=" N TYR A 705 " --> pdb=" O LYS A 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 18 through 29 Processing helix chain 'B' and resid 29 through 51 Processing helix chain 'B' and resid 87 through 94 removed outlier: 3.841A pdb=" N ALA B 91 " --> pdb=" O ALA B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 107 Processing helix chain 'B' and resid 120 through 128 Processing helix chain 'B' and resid 208 through 219 Processing helix chain 'B' and resid 240 through 278 removed outlier: 3.829A pdb=" N SER B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ASP B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 386 through 405 removed outlier: 3.525A pdb=" N ALA B 401 " --> pdb=" O GLU B 397 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 452 Processing helix chain 'B' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU B 461 " --> pdb=" O SER B 457 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE B 464 " --> pdb=" O GLN B 460 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 501 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.631A pdb=" N PHE B 519 " --> pdb=" O THR B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 539 through 553 Processing helix chain 'B' and resid 569 through 575 Processing helix chain 'B' and resid 581 through 587 Processing helix chain 'B' and resid 591 through 595 removed outlier: 3.561A pdb=" N ILE B 595 " --> pdb=" O ALA B 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 591 through 595' Processing helix chain 'B' and resid 615 through 620 Processing helix chain 'B' and resid 622 through 636 removed outlier: 4.308A pdb=" N GLU B 626 " --> pdb=" O HIS B 622 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN B 634 " --> pdb=" O ASN B 630 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN B 635 " --> pdb=" O TRP B 631 " (cutoff:3.500A) Processing helix chain 'B' and resid 650 through 656 Processing helix chain 'B' and resid 672 through 686 removed outlier: 3.513A pdb=" N SER B 686 " --> pdb=" O ARG B 682 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 708 removed outlier: 3.683A pdb=" N TYR B 705 " --> pdb=" O LYS B 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 29 Processing helix chain 'C' and resid 29 through 51 Processing helix chain 'C' and resid 86 through 94 removed outlier: 3.763A pdb=" N ALA C 91 " --> pdb=" O ALA C 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 107 Processing helix chain 'C' and resid 120 through 128 Processing helix chain 'C' and resid 208 through 219 Processing helix chain 'C' and resid 240 through 278 removed outlier: 3.829A pdb=" N SER C 245 " --> pdb=" O PRO C 241 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN C 266 " --> pdb=" O ARG C 262 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N ASP C 267 " --> pdb=" O GLN C 263 " (cutoff:3.500A) Processing helix chain 'C' and resid 385 through 405 Processing helix chain 'C' and resid 425 through 452 Processing helix chain 'C' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU C 461 " --> pdb=" O SER C 457 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE C 464 " --> pdb=" O GLN C 460 " (cutoff:3.500A) Processing helix chain 'C' and resid 496 through 501 Processing helix chain 'C' and resid 504 through 521 removed outlier: 3.632A pdb=" N PHE C 519 " --> pdb=" O THR C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 553 Processing helix chain 'C' and resid 569 through 575 Processing helix chain 'C' and resid 581 through 587 Processing helix chain 'C' and resid 591 through 595 removed outlier: 3.560A pdb=" N ILE C 595 " --> pdb=" O ALA C 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 591 through 595' Processing helix chain 'C' and resid 615 through 620 Processing helix chain 'C' and resid 622 through 636 removed outlier: 4.309A pdb=" N GLU C 626 " --> pdb=" O HIS C 622 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN C 634 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN C 635 " --> pdb=" O TRP C 631 " (cutoff:3.500A) Processing helix chain 'C' and resid 650 through 656 Processing helix chain 'C' and resid 672 through 686 removed outlier: 3.514A pdb=" N SER C 686 " --> pdb=" O ARG C 682 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 708 removed outlier: 3.683A pdb=" N TYR C 705 " --> pdb=" O LYS C 701 " (cutoff:3.500A) Processing helix chain 'D' and resid 18 through 29 Processing helix chain 'D' and resid 29 through 51 Processing helix chain 'D' and resid 86 through 94 removed outlier: 3.761A pdb=" N ALA D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 107 Processing helix chain 'D' and resid 120 through 128 Processing helix chain 'D' and resid 208 through 219 Processing helix chain 'D' and resid 240 through 267 removed outlier: 3.831A pdb=" N SER D 245 " --> pdb=" O PRO D 241 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA D 264 " --> pdb=" O ILE D 260 " (cutoff:3.500A) removed outlier: 4.166A pdb=" N ASP D 267 " --> pdb=" O GLN D 263 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 297 Proline residue: D 279 - end of helix Processing helix chain 'D' and resid 305 through 336 removed outlier: 3.521A pdb=" N GLN D 314 " --> pdb=" O SER D 310 " (cutoff:3.500A) Processing helix chain 'D' and resid 340 through 366 Processing helix chain 'D' and resid 368 through 404 removed outlier: 3.947A pdb=" N VAL D 374 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N SER D 403 " --> pdb=" O ASN D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 452 Processing helix chain 'D' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU D 461 " --> pdb=" O SER D 457 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE D 464 " --> pdb=" O GLN D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 496 through 501 Processing helix chain 'D' and resid 504 through 521 removed outlier: 3.630A pdb=" N PHE D 519 " --> pdb=" O THR D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 553 Processing helix chain 'D' and resid 569 through 575 Processing helix chain 'D' and resid 581 through 587 Processing helix chain 'D' and resid 591 through 595 removed outlier: 3.559A pdb=" N ILE D 595 " --> pdb=" O ALA D 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 591 through 595' Processing helix chain 'D' and resid 615 through 620 Processing helix chain 'D' and resid 622 through 636 removed outlier: 4.308A pdb=" N GLU D 626 " --> pdb=" O HIS D 622 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N GLN D 634 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN D 635 " --> pdb=" O TRP D 631 " (cutoff:3.500A) Processing helix chain 'D' and resid 650 through 656 Processing helix chain 'D' and resid 672 through 686 removed outlier: 3.515A pdb=" N SER D 686 " --> pdb=" O ARG D 682 " (cutoff:3.500A) Processing helix chain 'D' and resid 701 through 708 removed outlier: 3.682A pdb=" N TYR D 705 " --> pdb=" O LYS D 701 " (cutoff:3.500A) Processing helix chain 'E' and resid 18 through 29 Processing helix chain 'E' and resid 29 through 51 Processing helix chain 'E' and resid 86 through 94 removed outlier: 3.762A pdb=" N ALA E 91 " --> pdb=" O ALA E 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 95 through 107 Processing helix chain 'E' and resid 120 through 128 Processing helix chain 'E' and resid 208 through 219 Processing helix chain 'E' and resid 240 through 260 removed outlier: 3.831A pdb=" N SER E 245 " --> pdb=" O PRO E 241 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 452 Processing helix chain 'E' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU E 461 " --> pdb=" O SER E 457 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE E 464 " --> pdb=" O GLN E 460 " (cutoff:3.500A) Processing helix chain 'E' and resid 496 through 501 Processing helix chain 'E' and resid 504 through 521 removed outlier: 3.630A pdb=" N PHE E 519 " --> pdb=" O THR E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 539 through 553 Processing helix chain 'E' and resid 569 through 575 Processing helix chain 'E' and resid 581 through 587 Processing helix chain 'E' and resid 591 through 595 removed outlier: 3.561A pdb=" N ILE E 595 " --> pdb=" O ALA E 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 591 through 595' Processing helix chain 'E' and resid 615 through 620 Processing helix chain 'E' and resid 622 through 636 removed outlier: 4.308A pdb=" N GLU E 626 " --> pdb=" O HIS E 622 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N GLN E 634 " --> pdb=" O ASN E 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN E 635 " --> pdb=" O TRP E 631 " (cutoff:3.500A) Processing helix chain 'E' and resid 650 through 656 Processing helix chain 'E' and resid 672 through 686 removed outlier: 3.514A pdb=" N SER E 686 " --> pdb=" O ARG E 682 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 708 removed outlier: 3.683A pdb=" N TYR E 705 " --> pdb=" O LYS E 701 " (cutoff:3.500A) Processing helix chain 'F' and resid 18 through 29 Processing helix chain 'F' and resid 29 through 51 Processing helix chain 'F' and resid 86 through 94 removed outlier: 3.761A pdb=" N ALA F 91 " --> pdb=" O ALA F 87 " (cutoff:3.500A) Processing helix chain 'F' and resid 95 through 107 Processing helix chain 'F' and resid 120 through 128 Processing helix chain 'F' and resid 208 through 219 Processing helix chain 'F' and resid 240 through 266 removed outlier: 3.830A pdb=" N SER F 245 " --> pdb=" O PRO F 241 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N TYR F 255 " --> pdb=" O ILE F 251 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLN F 263 " --> pdb=" O ASN F 259 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA F 264 " --> pdb=" O ILE F 260 " (cutoff:3.500A) removed outlier: 4.189A pdb=" N GLN F 266 " --> pdb=" O ARG F 262 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 297 Proline residue: F 279 - end of helix Processing helix chain 'F' and resid 305 through 336 removed outlier: 3.522A pdb=" N GLN F 314 " --> pdb=" O SER F 310 " (cutoff:3.500A) Processing helix chain 'F' and resid 340 through 366 Processing helix chain 'F' and resid 368 through 404 removed outlier: 3.946A pdb=" N VAL F 374 " --> pdb=" O THR F 370 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ILE F 400 " --> pdb=" O GLN F 396 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS F 402 " --> pdb=" O LEU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 452 Processing helix chain 'F' and resid 457 through 464 removed outlier: 4.075A pdb=" N LEU F 461 " --> pdb=" O SER F 457 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE F 464 " --> pdb=" O GLN F 460 " (cutoff:3.500A) Processing helix chain 'F' and resid 496 through 501 Processing helix chain 'F' and resid 504 through 521 removed outlier: 3.631A pdb=" N PHE F 519 " --> pdb=" O THR F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 539 through 553 Processing helix chain 'F' and resid 569 through 575 Processing helix chain 'F' and resid 581 through 587 Processing helix chain 'F' and resid 591 through 595 removed outlier: 3.559A pdb=" N ILE F 595 " --> pdb=" O ALA F 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 591 through 595' Processing helix chain 'F' and resid 615 through 620 Processing helix chain 'F' and resid 622 through 636 removed outlier: 4.308A pdb=" N GLU F 626 " --> pdb=" O HIS F 622 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN F 634 " --> pdb=" O ASN F 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN F 635 " --> pdb=" O TRP F 631 " (cutoff:3.500A) Processing helix chain 'F' and resid 650 through 656 Processing helix chain 'F' and resid 672 through 686 removed outlier: 3.515A pdb=" N SER F 686 " --> pdb=" O ARG F 682 " (cutoff:3.500A) Processing helix chain 'F' and resid 701 through 708 removed outlier: 3.682A pdb=" N TYR F 705 " --> pdb=" O LYS F 701 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 29 Processing helix chain 'G' and resid 29 through 51 Processing helix chain 'G' and resid 86 through 94 removed outlier: 3.762A pdb=" N ALA G 91 " --> pdb=" O ALA G 87 " (cutoff:3.500A) Processing helix chain 'G' and resid 95 through 107 Processing helix chain 'G' and resid 120 through 128 Processing helix chain 'G' and resid 208 through 219 Processing helix chain 'G' and resid 240 through 278 removed outlier: 3.829A pdb=" N SER G 245 " --> pdb=" O PRO G 241 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 263 " --> pdb=" O ASN G 259 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N GLN G 266 " --> pdb=" O ARG G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 386 through 404 removed outlier: 3.928A pdb=" N SER G 403 " --> pdb=" O ASN G 399 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N SER G 404 " --> pdb=" O ILE G 400 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 452 Processing helix chain 'G' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU G 461 " --> pdb=" O SER G 457 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE G 464 " --> pdb=" O GLN G 460 " (cutoff:3.500A) Processing helix chain 'G' and resid 496 through 501 Processing helix chain 'G' and resid 504 through 521 removed outlier: 3.630A pdb=" N PHE G 519 " --> pdb=" O THR G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 539 through 553 Processing helix chain 'G' and resid 569 through 575 Processing helix chain 'G' and resid 581 through 587 Processing helix chain 'G' and resid 591 through 595 removed outlier: 3.560A pdb=" N ILE G 595 " --> pdb=" O ALA G 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 591 through 595' Processing helix chain 'G' and resid 615 through 620 Processing helix chain 'G' and resid 622 through 636 removed outlier: 4.307A pdb=" N GLU G 626 " --> pdb=" O HIS G 622 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN G 634 " --> pdb=" O ASN G 630 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ASN G 635 " --> pdb=" O TRP G 631 " (cutoff:3.500A) Processing helix chain 'G' and resid 650 through 656 Processing helix chain 'G' and resid 672 through 686 removed outlier: 3.514A pdb=" N SER G 686 " --> pdb=" O ARG G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 701 through 708 removed outlier: 3.685A pdb=" N TYR G 705 " --> pdb=" O LYS G 701 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 29 Processing helix chain 'H' and resid 29 through 51 Processing helix chain 'H' and resid 86 through 94 removed outlier: 3.762A pdb=" N ALA H 91 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 95 through 107 Processing helix chain 'H' and resid 120 through 128 Processing helix chain 'H' and resid 208 through 219 Processing helix chain 'H' and resid 240 through 278 removed outlier: 3.829A pdb=" N SER H 245 " --> pdb=" O PRO H 241 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLN H 263 " --> pdb=" O ASN H 259 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 266 " --> pdb=" O ARG H 262 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASP H 267 " --> pdb=" O GLN H 263 " (cutoff:3.500A) Processing helix chain 'H' and resid 385 through 405 removed outlier: 3.509A pdb=" N ALA H 401 " --> pdb=" O GLU H 397 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N SER H 403 " --> pdb=" O ASN H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 425 through 452 Processing helix chain 'H' and resid 457 through 464 removed outlier: 4.076A pdb=" N LEU H 461 " --> pdb=" O SER H 457 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ILE H 464 " --> pdb=" O GLN H 460 " (cutoff:3.500A) Processing helix chain 'H' and resid 496 through 501 Processing helix chain 'H' and resid 504 through 521 removed outlier: 3.632A pdb=" N PHE H 519 " --> pdb=" O THR H 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 539 through 553 Processing helix chain 'H' and resid 569 through 575 Processing helix chain 'H' and resid 581 through 587 Processing helix chain 'H' and resid 591 through 595 removed outlier: 3.561A pdb=" N ILE H 595 " --> pdb=" O ALA H 591 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 591 through 595' Processing helix chain 'H' and resid 615 through 620 Processing helix chain 'H' and resid 622 through 636 removed outlier: 4.309A pdb=" N GLU H 626 " --> pdb=" O HIS H 622 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLN H 634 " --> pdb=" O ASN H 630 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ASN H 635 " --> pdb=" O TRP H 631 " (cutoff:3.500A) Processing helix chain 'H' and resid 650 through 656 Processing helix chain 'H' and resid 672 through 686 removed outlier: 3.513A pdb=" N SER H 686 " --> pdb=" O ARG H 682 " (cutoff:3.500A) Processing helix chain 'H' and resid 701 through 708 removed outlier: 3.682A pdb=" N TYR H 705 " --> pdb=" O LYS H 701 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 220 through 223 removed outlier: 7.017A pdb=" N GLU A 56 " --> pdb=" O PRO A 421 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N ASP A 58 " --> pdb=" O PRO A 419 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N LEU A 60 " --> pdb=" O THR A 417 " (cutoff:3.500A) removed outlier: 13.148A pdb=" N THR A 417 " --> pdb=" O LEU A 60 " (cutoff:3.500A) removed outlier: 14.504A pdb=" N GLN A 62 " --> pdb=" O ALA A 415 " (cutoff:3.500A) removed outlier: 13.942A pdb=" N ALA A 415 " --> pdb=" O GLN A 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 110 through 114 Processing sheet with id=AA3, first strand: chain 'A' and resid 134 through 141 removed outlier: 7.254A pdb=" N ASN A 134 " --> pdb=" O ILE A 194 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE A 194 " --> pdb=" O ASN A 134 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N LEU A 190 " --> pdb=" O THR A 138 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU A 140 " --> pdb=" O SER A 188 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER A 188 " --> pdb=" O LEU A 140 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 468 through 473 removed outlier: 6.237A pdb=" N CYS A 693 " --> pdb=" O VAL A 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA A 470 " --> pdb=" O CYS A 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS A 662 " --> pdb=" O GLY A 692 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE A 694 " --> pdb=" O CYS A 662 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU A 664 " --> pdb=" O ILE A 694 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN A 696 " --> pdb=" O LEU A 664 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA A 666 " --> pdb=" O ASN A 696 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL A 698 " --> pdb=" O ALA A 666 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU A 559 " --> pdb=" O ILE A 640 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP A 642 " --> pdb=" O LEU A 559 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE A 561 " --> pdb=" O ASP A 642 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 220 through 223 removed outlier: 7.017A pdb=" N GLU B 56 " --> pdb=" O PRO B 421 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N ASP B 58 " --> pdb=" O PRO B 419 " (cutoff:3.500A) removed outlier: 12.839A pdb=" N LEU B 60 " --> pdb=" O THR B 417 " (cutoff:3.500A) removed outlier: 13.262A pdb=" N THR B 417 " --> pdb=" O LEU B 60 " (cutoff:3.500A) removed outlier: 14.557A pdb=" N GLN B 62 " --> pdb=" O ALA B 415 " (cutoff:3.500A) removed outlier: 14.210A pdb=" N ALA B 415 " --> pdb=" O GLN B 62 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 110 through 114 Processing sheet with id=AA7, first strand: chain 'B' and resid 134 through 141 removed outlier: 7.254A pdb=" N ASN B 134 " --> pdb=" O ILE B 194 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE B 194 " --> pdb=" O ASN B 134 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU B 190 " --> pdb=" O THR B 138 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU B 140 " --> pdb=" O SER B 188 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER B 188 " --> pdb=" O LEU B 140 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 468 through 473 removed outlier: 6.236A pdb=" N CYS B 693 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA B 470 " --> pdb=" O CYS B 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS B 662 " --> pdb=" O GLY B 692 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE B 694 " --> pdb=" O CYS B 662 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU B 664 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN B 696 " --> pdb=" O LEU B 664 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA B 666 " --> pdb=" O ASN B 696 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL B 698 " --> pdb=" O ALA B 666 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU B 559 " --> pdb=" O ILE B 640 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP B 642 " --> pdb=" O LEU B 559 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE B 561 " --> pdb=" O ASP B 642 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 220 through 223 removed outlier: 7.018A pdb=" N GLU C 56 " --> pdb=" O PRO C 421 " (cutoff:3.500A) removed outlier: 12.073A pdb=" N ASP C 58 " --> pdb=" O PRO C 419 " (cutoff:3.500A) removed outlier: 12.865A pdb=" N LEU C 60 " --> pdb=" O THR C 417 " (cutoff:3.500A) removed outlier: 13.424A pdb=" N THR C 417 " --> pdb=" O LEU C 60 " (cutoff:3.500A) removed outlier: 14.687A pdb=" N GLN C 62 " --> pdb=" O ALA C 415 " (cutoff:3.500A) removed outlier: 14.100A pdb=" N ALA C 415 " --> pdb=" O GLN C 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 110 through 114 Processing sheet with id=AB2, first strand: chain 'C' and resid 134 through 141 removed outlier: 7.254A pdb=" N ASN C 134 " --> pdb=" O ILE C 194 " (cutoff:3.500A) removed outlier: 5.349A pdb=" N ILE C 194 " --> pdb=" O ASN C 134 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU C 190 " --> pdb=" O THR C 138 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU C 140 " --> pdb=" O SER C 188 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER C 188 " --> pdb=" O LEU C 140 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'C' and resid 468 through 473 removed outlier: 6.236A pdb=" N CYS C 693 " --> pdb=" O VAL C 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA C 470 " --> pdb=" O CYS C 693 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N CYS C 662 " --> pdb=" O GLY C 692 " (cutoff:3.500A) removed outlier: 8.116A pdb=" N ILE C 694 " --> pdb=" O CYS C 662 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N LEU C 664 " --> pdb=" O ILE C 694 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN C 696 " --> pdb=" O LEU C 664 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA C 666 " --> pdb=" O ASN C 696 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL C 698 " --> pdb=" O ALA C 666 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU C 559 " --> pdb=" O ILE C 640 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N ASP C 642 " --> pdb=" O LEU C 559 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE C 561 " --> pdb=" O ASP C 642 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 220 through 223 removed outlier: 7.016A pdb=" N GLU D 56 " --> pdb=" O PRO D 421 " (cutoff:3.500A) removed outlier: 12.072A pdb=" N ASP D 58 " --> pdb=" O PRO D 419 " (cutoff:3.500A) removed outlier: 12.844A pdb=" N LEU D 60 " --> pdb=" O THR D 417 " (cutoff:3.500A) removed outlier: 13.147A pdb=" N THR D 417 " --> pdb=" O LEU D 60 " (cutoff:3.500A) removed outlier: 14.382A pdb=" N GLN D 62 " --> pdb=" O ALA D 415 " (cutoff:3.500A) removed outlier: 13.806A pdb=" N ALA D 415 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 110 through 114 Processing sheet with id=AB6, first strand: chain 'D' and resid 134 through 141 removed outlier: 7.254A pdb=" N ASN D 134 " --> pdb=" O ILE D 194 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE D 194 " --> pdb=" O ASN D 134 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU D 190 " --> pdb=" O THR D 138 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N LEU D 140 " --> pdb=" O SER D 188 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N SER D 188 " --> pdb=" O LEU D 140 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 468 through 473 removed outlier: 6.236A pdb=" N CYS D 693 " --> pdb=" O VAL D 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA D 470 " --> pdb=" O CYS D 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS D 662 " --> pdb=" O GLY D 692 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N ILE D 694 " --> pdb=" O CYS D 662 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU D 664 " --> pdb=" O ILE D 694 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN D 696 " --> pdb=" O LEU D 664 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA D 666 " --> pdb=" O ASN D 696 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL D 698 " --> pdb=" O ALA D 666 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU D 559 " --> pdb=" O ILE D 640 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP D 642 " --> pdb=" O LEU D 559 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE D 561 " --> pdb=" O ASP D 642 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 220 through 223 removed outlier: 7.018A pdb=" N GLU E 56 " --> pdb=" O PRO E 421 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N ASP E 58 " --> pdb=" O PRO E 419 " (cutoff:3.500A) removed outlier: 12.846A pdb=" N LEU E 60 " --> pdb=" O THR E 417 " (cutoff:3.500A) removed outlier: 13.147A pdb=" N THR E 417 " --> pdb=" O LEU E 60 " (cutoff:3.500A) removed outlier: 14.383A pdb=" N GLN E 62 " --> pdb=" O ALA E 415 " (cutoff:3.500A) removed outlier: 13.807A pdb=" N ALA E 415 " --> pdb=" O GLN E 62 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 110 through 114 Processing sheet with id=AC1, first strand: chain 'E' and resid 134 through 141 removed outlier: 7.254A pdb=" N ASN E 134 " --> pdb=" O ILE E 194 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ILE E 194 " --> pdb=" O ASN E 134 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU E 190 " --> pdb=" O THR E 138 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU E 140 " --> pdb=" O SER E 188 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER E 188 " --> pdb=" O LEU E 140 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 468 through 473 removed outlier: 6.234A pdb=" N CYS E 693 " --> pdb=" O VAL E 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA E 470 " --> pdb=" O CYS E 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS E 662 " --> pdb=" O GLY E 692 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE E 694 " --> pdb=" O CYS E 662 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU E 664 " --> pdb=" O ILE E 694 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN E 696 " --> pdb=" O LEU E 664 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA E 666 " --> pdb=" O ASN E 696 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL E 698 " --> pdb=" O ALA E 666 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU E 559 " --> pdb=" O ILE E 640 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP E 642 " --> pdb=" O LEU E 559 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N ILE E 561 " --> pdb=" O ASP E 642 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 220 through 223 removed outlier: 7.016A pdb=" N GLU F 56 " --> pdb=" O PRO F 421 " (cutoff:3.500A) removed outlier: 12.074A pdb=" N ASP F 58 " --> pdb=" O PRO F 419 " (cutoff:3.500A) removed outlier: 12.845A pdb=" N LEU F 60 " --> pdb=" O THR F 417 " (cutoff:3.500A) removed outlier: 13.148A pdb=" N THR F 417 " --> pdb=" O LEU F 60 " (cutoff:3.500A) removed outlier: 14.383A pdb=" N GLN F 62 " --> pdb=" O ALA F 415 " (cutoff:3.500A) removed outlier: 13.805A pdb=" N ALA F 415 " --> pdb=" O GLN F 62 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'F' and resid 110 through 114 Processing sheet with id=AC5, first strand: chain 'F' and resid 134 through 141 removed outlier: 7.252A pdb=" N ASN F 134 " --> pdb=" O ILE F 194 " (cutoff:3.500A) removed outlier: 5.346A pdb=" N ILE F 194 " --> pdb=" O ASN F 134 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N LEU F 190 " --> pdb=" O THR F 138 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU F 140 " --> pdb=" O SER F 188 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER F 188 " --> pdb=" O LEU F 140 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'F' and resid 468 through 473 removed outlier: 6.234A pdb=" N CYS F 693 " --> pdb=" O VAL F 468 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA F 470 " --> pdb=" O CYS F 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS F 662 " --> pdb=" O GLY F 692 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE F 694 " --> pdb=" O CYS F 662 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU F 664 " --> pdb=" O ILE F 694 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N ASN F 696 " --> pdb=" O LEU F 664 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N ALA F 666 " --> pdb=" O ASN F 696 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N VAL F 698 " --> pdb=" O ALA F 666 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N LEU F 559 " --> pdb=" O ILE F 640 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP F 642 " --> pdb=" O LEU F 559 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE F 561 " --> pdb=" O ASP F 642 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 220 through 223 removed outlier: 8.448A pdb=" N ILE G 54 " --> pdb=" O ASP G 418 " (cutoff:3.500A) removed outlier: 8.483A pdb=" N ASP G 418 " --> pdb=" O ILE G 54 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N GLU G 56 " --> pdb=" O VAL G 416 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL G 416 " --> pdb=" O GLU G 56 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ASP G 58 " --> pdb=" O ASN G 414 " (cutoff:3.500A) removed outlier: 5.857A pdb=" N ASN G 414 " --> pdb=" O ASP G 58 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N LEU G 60 " --> pdb=" O ILE G 412 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 110 through 114 Processing sheet with id=AC9, first strand: chain 'G' and resid 134 through 141 removed outlier: 7.253A pdb=" N ASN G 134 " --> pdb=" O ILE G 194 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE G 194 " --> pdb=" O ASN G 134 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU G 190 " --> pdb=" O THR G 138 " (cutoff:3.500A) removed outlier: 4.144A pdb=" N LEU G 140 " --> pdb=" O SER G 188 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER G 188 " --> pdb=" O LEU G 140 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 468 through 473 removed outlier: 6.235A pdb=" N CYS G 693 " --> pdb=" O VAL G 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA G 470 " --> pdb=" O CYS G 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS G 662 " --> pdb=" O GLY G 692 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE G 694 " --> pdb=" O CYS G 662 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N LEU G 664 " --> pdb=" O ILE G 694 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N ASN G 696 " --> pdb=" O LEU G 664 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA G 666 " --> pdb=" O ASN G 696 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N VAL G 698 " --> pdb=" O ALA G 666 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU G 559 " --> pdb=" O ILE G 640 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N ASP G 642 " --> pdb=" O LEU G 559 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N ILE G 561 " --> pdb=" O ASP G 642 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 220 through 223 removed outlier: 8.449A pdb=" N ILE H 54 " --> pdb=" O ASP H 418 " (cutoff:3.500A) removed outlier: 8.484A pdb=" N ASP H 418 " --> pdb=" O ILE H 54 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU H 56 " --> pdb=" O VAL H 416 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL H 416 " --> pdb=" O GLU H 56 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ASP H 58 " --> pdb=" O ASN H 414 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N ASN H 414 " --> pdb=" O ASP H 58 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N LEU H 60 " --> pdb=" O ILE H 412 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'H' and resid 110 through 114 Processing sheet with id=AD4, first strand: chain 'H' and resid 134 through 141 removed outlier: 7.255A pdb=" N ASN H 134 " --> pdb=" O ILE H 194 " (cutoff:3.500A) removed outlier: 5.347A pdb=" N ILE H 194 " --> pdb=" O ASN H 134 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LEU H 190 " --> pdb=" O THR H 138 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LEU H 140 " --> pdb=" O SER H 188 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N SER H 188 " --> pdb=" O LEU H 140 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 468 through 473 removed outlier: 6.235A pdb=" N CYS H 693 " --> pdb=" O VAL H 468 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N ALA H 470 " --> pdb=" O CYS H 693 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N CYS H 662 " --> pdb=" O GLY H 692 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N ILE H 694 " --> pdb=" O CYS H 662 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N LEU H 664 " --> pdb=" O ILE H 694 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N ASN H 696 " --> pdb=" O LEU H 664 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA H 666 " --> pdb=" O ASN H 696 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N VAL H 698 " --> pdb=" O ALA H 666 " (cutoff:3.500A) removed outlier: 6.256A pdb=" N LEU H 559 " --> pdb=" O ILE H 640 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ASP H 642 " --> pdb=" O LEU H 559 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ILE H 561 " --> pdb=" O ASP H 642 " (cutoff:3.500A) 2100 hydrogen bonds defined for protein. 6183 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 8.44 Time building geometry restraints manager: 3.48 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: 12263 1.34 - 1.46: 4449 1.46 - 1.57: 20851 1.57 - 1.69: 24 1.69 - 1.81: 210 Bond restraints: 37797 Sorted by residual: bond pdb=" C ASP B 58 " pdb=" N ALA B 59 " ideal model delta sigma weight residual 1.330 1.523 -0.194 1.41e-02 5.03e+03 1.88e+02 bond pdb=" C6 ADP C1000 " pdb=" N6 ADP C1000 " ideal model delta sigma weight residual 1.355 1.463 -0.108 2.00e-02 2.50e+03 2.91e+01 bond pdb=" C6 ADP H1000 " pdb=" N6 ADP H1000 " ideal model delta sigma weight residual 1.355 1.463 -0.108 2.00e-02 2.50e+03 2.90e+01 bond pdb=" C6 ADP B1000 " pdb=" N6 ADP B1000 " ideal model delta sigma weight residual 1.355 1.462 -0.107 2.00e-02 2.50e+03 2.89e+01 bond pdb=" C6 ADP G1000 " pdb=" N6 ADP G1000 " ideal model delta sigma weight residual 1.355 1.462 -0.107 2.00e-02 2.50e+03 2.87e+01 ... (remaining 37792 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.24: 50462 2.24 - 4.48: 588 4.48 - 6.72: 89 6.72 - 8.96: 36 8.96 - 11.19: 33 Bond angle restraints: 51208 Sorted by residual: angle pdb=" N SER G 403 " pdb=" CA SER G 403 " pdb=" C SER G 403 " ideal model delta sigma weight residual 111.36 118.58 -7.22 1.09e+00 8.42e-01 4.38e+01 angle pdb=" C ASP B 58 " pdb=" N ALA B 59 " pdb=" CA ALA B 59 " ideal model delta sigma weight residual 122.81 112.65 10.16 1.68e+00 3.54e-01 3.66e+01 angle pdb=" N ASN B 408 " pdb=" CA ASN B 408 " pdb=" C ASN B 408 " ideal model delta sigma weight residual 111.28 104.73 6.55 1.09e+00 8.42e-01 3.61e+01 angle pdb=" N ALA D 265 " pdb=" CA ALA D 265 " pdb=" C ALA D 265 " ideal model delta sigma weight residual 111.28 117.09 -5.81 1.09e+00 8.42e-01 2.85e+01 angle pdb=" N GLY C 407 " pdb=" CA GLY C 407 " pdb=" C GLY C 407 " ideal model delta sigma weight residual 110.56 118.93 -8.37 1.66e+00 3.63e-01 2.54e+01 ... (remaining 51203 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 23.28: 22424 23.28 - 46.55: 566 46.55 - 69.83: 56 69.83 - 93.11: 32 93.11 - 116.39: 8 Dihedral angle restraints: 23086 sinusoidal: 9308 harmonic: 13778 Sorted by residual: dihedral pdb=" C5' ADP H1000 " pdb=" O5' ADP H1000 " pdb=" PA ADP H1000 " pdb=" O2A ADP H1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.39 -116.39 1 2.00e+01 2.50e-03 3.47e+01 dihedral pdb=" C5' ADP G1000 " pdb=" O5' ADP G1000 " pdb=" PA ADP G1000 " pdb=" O2A ADP G1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.28 -116.28 1 2.00e+01 2.50e-03 3.46e+01 dihedral pdb=" C5' ADP B1000 " pdb=" O5' ADP B1000 " pdb=" PA ADP B1000 " pdb=" O2A ADP B1000 " ideal model delta sinusoidal sigma weight residual -60.00 56.27 -116.27 1 2.00e+01 2.50e-03 3.46e+01 ... (remaining 23083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 5227 0.058 - 0.115: 722 0.115 - 0.173: 99 0.173 - 0.230: 8 0.230 - 0.288: 4 Chirality restraints: 6060 Sorted by residual: chirality pdb=" CA ILE D 411 " pdb=" N ILE D 411 " pdb=" C ILE D 411 " pdb=" CB ILE D 411 " both_signs ideal model delta sigma weight residual False 2.43 2.72 -0.29 2.00e-01 2.50e+01 2.07e+00 chirality pdb=" CA VAL A 409 " pdb=" N VAL A 409 " pdb=" C VAL A 409 " pdb=" CB VAL A 409 " both_signs ideal model delta sigma weight residual False 2.44 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 chirality pdb=" CA ILE F 411 " pdb=" N ILE F 411 " pdb=" C ILE F 411 " pdb=" CB ILE F 411 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.36e+00 ... (remaining 6057 not shown) Planarity restraints: 6517 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 58 " 0.021 2.00e-02 2.50e+03 4.40e-02 1.94e+01 pdb=" C ASP B 58 " -0.076 2.00e-02 2.50e+03 pdb=" O ASP B 58 " 0.032 2.00e-02 2.50e+03 pdb=" N ALA B 59 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 402 " -0.009 2.00e-02 2.50e+03 1.71e-02 2.93e+00 pdb=" C LYS A 402 " 0.030 2.00e-02 2.50e+03 pdb=" O LYS A 402 " -0.011 2.00e-02 2.50e+03 pdb=" N SER A 403 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 251 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.45e+00 pdb=" C ILE B 251 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE B 251 " -0.010 2.00e-02 2.50e+03 pdb=" N SER B 252 " -0.009 2.00e-02 2.50e+03 ... (remaining 6514 not shown) Histogram of nonbonded interaction distances: 1.36 - 2.07: 28 2.07 - 2.78: 8377 2.78 - 3.48: 50960 3.48 - 4.19: 93008 4.19 - 4.90: 160259 Nonbonded interactions: 312632 Sorted by model distance: nonbonded pdb=" OG SER B 403 " pdb=" CD1 PHE C 273 " model vdw 1.362 3.340 nonbonded pdb=" OE1 GLU H 64 " pdb=" O ASN H 408 " model vdw 1.441 3.040 nonbonded pdb=" OE2 GLU C 64 " pdb=" NH1 ARG C 410 " model vdw 1.509 3.120 nonbonded pdb=" N ILE G 63 " pdb=" O GLY G 230 " model vdw 1.610 3.120 nonbonded pdb=" OG SER B 403 " pdb=" CG PHE C 273 " model vdw 1.708 3.260 ... (remaining 312627 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 17 through 279 or resid 385 through 1001)) selection = chain 'B' selection = (chain 'C' and (resid 17 through 279 or resid 385 through 1001)) selection = (chain 'D' and (resid 17 through 279 or resid 385 through 1001)) selection = (chain 'F' and (resid 17 through 279 or resid 385 through 1001)) selection = chain 'G' selection = (chain 'H' and (resid 17 through 279 or resid 385 through 1001)) } 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: 3.530 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 0.650 Check model and map are aligned: 0.120 Set scattering table: 0.110 Process input model: 32.330 Find NCS groups from input model: 0.990 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8172 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 : 0.007 0.458 37800 Z= 0.437 Angle : 0.692 11.195 51208 Z= 0.382 Chirality : 0.043 0.288 6060 Planarity : 0.003 0.044 6517 Dihedral : 11.054 116.386 14208 Min Nonbonded Distance : 1.362 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.08 % Allowed : 3.36 % Favored : 96.56 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.73 (0.10), residues: 4708 helix: -1.71 (0.09), residues: 2315 sheet: -0.85 (0.18), residues: 636 loop : -2.09 (0.12), residues: 1757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 262 TYR 0.010 0.001 TYR D 469 PHE 0.010 0.001 PHE H 604 TRP 0.005 0.001 TRP A 477 HIS 0.003 0.001 HIS F 710 Details of bonding type rmsd covalent geometry : bond 0.00622 (37797) covalent geometry : angle 0.69215 (51208) hydrogen bonds : bond 0.22723 ( 2100) hydrogen bonds : angle 8.16901 ( 6183) Misc. bond : bond 0.35454 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 740 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 740 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 255 TYR cc_start: 0.7933 (t80) cc_final: 0.7701 (t80) REVERT: B 718 TYR cc_start: 0.8439 (p90) cc_final: 0.8226 (p90) REVERT: H 718 TYR cc_start: 0.8551 (p90) cc_final: 0.8322 (p90) outliers start: 0 outliers final: 4 residues processed: 740 average time/residue: 0.6230 time to fit residues: 565.6621 Evaluate side-chains 498 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 494 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 ASP Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain D residue 136 ASP Chi-restraints excluded: chain H residue 164 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 432 optimal weight: 30.0000 chunk 197 optimal weight: 2.9990 chunk 388 optimal weight: 6.9990 chunk 455 optimal weight: 3.9990 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 2.9990 chunk 132 optimal weight: 0.0770 chunk 261 optimal weight: 0.7980 chunk 248 optimal weight: 8.9990 chunk 207 optimal weight: 40.0000 chunk 470 optimal weight: 1.9990 overall best weight: 1.7744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 29 HIS A 111 GLN A 173 GLN ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 206 GLN A 254 ASN A 275 ASN A 317 ASN A 518 HIS ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 576 HIS A 671 ASN B 29 HIS B 111 GLN B 173 GLN B 254 ASN B 259 ASN B 277 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 576 HIS B 671 ASN C 29 HIS C 111 GLN C 254 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 277 GLN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 576 HIS C 671 ASN D 29 HIS D 111 GLN D 175 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 254 ASN D 275 ASN D 396 GLN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 576 HIS E 29 HIS E 111 GLN E 173 GLN E 254 ASN E 518 HIS ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 576 HIS E 611 GLN E 671 ASN F 29 HIS F 111 GLN F 168 ASN F 173 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 254 ASN F 317 ASN F 321 GLN F 399 ASN F 571 HIS F 576 HIS F 671 ASN G 29 HIS G 111 GLN G 173 GLN G 246 HIS G 254 ASN G 263 GLN G 277 GLN ** G 395 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 576 HIS G 671 ASN H 111 GLN H 164 ASN H 168 ASN H 253 GLN H 277 GLN ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 576 HIS H 671 ASN Total number of N/Q/H flips: 66 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4004 r_free = 0.4004 target = 0.175166 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3453 r_free = 0.3453 target = 0.126152 restraints weight = 46342.721| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 2.49 r_work: 0.3051 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.2339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 37800 Z= 0.199 Angle : 0.673 8.403 51208 Z= 0.334 Chirality : 0.046 0.242 6060 Planarity : 0.004 0.045 6517 Dihedral : 5.746 65.144 5206 Min Nonbonded Distance : 1.835 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.80 % Favored : 96.16 % Rotamer: Outliers : 2.72 % Allowed : 11.83 % Favored : 85.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: -0.76 (0.11), residues: 4708 helix: 0.29 (0.10), residues: 2392 sheet: -0.24 (0.18), residues: 616 loop : -1.68 (0.13), residues: 1700 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG F 139 TYR 0.013 0.001 TYR D 141 PHE 0.014 0.002 PHE G 220 TRP 0.006 0.001 TRP H 477 HIS 0.007 0.001 HIS E 518 Details of bonding type rmsd covalent geometry : bond 0.00455 (37797) covalent geometry : angle 0.67349 (51208) hydrogen bonds : bond 0.04835 ( 2100) hydrogen bonds : angle 5.01278 ( 6183) Misc. bond : bond 0.00269 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 668 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 557 time to evaluate : 1.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8181 (mt-10) cc_final: 0.7904 (mt-10) REVERT: A 139 ARG cc_start: 0.8115 (tpt-90) cc_final: 0.7909 (tpt170) REVERT: A 195 ASP cc_start: 0.8071 (t0) cc_final: 0.7812 (t0) REVERT: A 215 ASP cc_start: 0.8307 (m-30) cc_final: 0.8105 (m-30) REVERT: A 667 ARG cc_start: 0.9166 (OUTLIER) cc_final: 0.8953 (tpt90) REVERT: B 63 ILE cc_start: 0.8485 (OUTLIER) cc_final: 0.8208 (mm) REVERT: B 231 MET cc_start: 0.7835 (mmp) cc_final: 0.7568 (mmp) REVERT: C 164 ASN cc_start: 0.8418 (p0) cc_final: 0.8178 (p0) REVERT: C 213 ILE cc_start: 0.9010 (mt) cc_final: 0.8618 (mp) REVERT: C 456 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7653 (mt-10) REVERT: C 462 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7955 (mt-10) REVERT: C 667 ARG cc_start: 0.8980 (OUTLIER) cc_final: 0.8648 (tpt-90) REVERT: D 109 GLN cc_start: 0.8372 (OUTLIER) cc_final: 0.8138 (pt0) REVERT: D 136 ASP cc_start: 0.7950 (t70) cc_final: 0.7507 (t0) REVERT: D 410 ARG cc_start: 0.7888 (ttp80) cc_final: 0.7569 (ttp80) REVERT: D 476 GLU cc_start: 0.8380 (OUTLIER) cc_final: 0.8024 (mm-30) REVERT: E 109 GLN cc_start: 0.8477 (OUTLIER) cc_final: 0.7570 (pm20) REVERT: E 684 GLU cc_start: 0.8397 (OUTLIER) cc_final: 0.7863 (mp0) REVERT: G 111 GLN cc_start: 0.8165 (tt0) cc_final: 0.7892 (tt0) REVERT: G 165 TYR cc_start: 0.7886 (p90) cc_final: 0.7663 (p90) REVERT: G 274 LEU cc_start: 0.8139 (OUTLIER) cc_final: 0.7844 (tm) REVERT: H 243 ARG cc_start: 0.8057 (ttt90) cc_final: 0.7826 (ttp-170) REVERT: H 425 LYS cc_start: 0.7501 (mttt) cc_final: 0.7209 (mtmm) REVERT: H 594 MET cc_start: 0.8132 (mtp) cc_final: 0.7919 (ptm) outliers start: 111 outliers final: 19 residues processed: 621 average time/residue: 0.6078 time to fit residues: 465.1960 Evaluate side-chains 480 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 452 time to evaluate : 1.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain B residue 63 ILE Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 667 ARG Chi-restraints excluded: chain C residue 680 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 109 GLN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain G residue 221 SER Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 95 SER Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 409 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 247 optimal weight: 2.9990 chunk 424 optimal weight: 1.9990 chunk 305 optimal weight: 8.9990 chunk 53 optimal weight: 9.9990 chunk 405 optimal weight: 6.9990 chunk 89 optimal weight: 30.0000 chunk 292 optimal weight: 0.5980 chunk 389 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 134 optimal weight: 7.9990 chunk 131 optimal weight: 0.0670 overall best weight: 1.3324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 150 ASN ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 263 GLN A 275 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 635 ASN B 259 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 399 ASN ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 94 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 173 GLN ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 396 GLN ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 671 ASN H 253 GLN H 258 GLN ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4005 r_free = 0.4005 target = 0.175201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.124882 restraints weight = 46180.695| |-----------------------------------------------------------------------------| r_work (start): 0.3408 rms_B_bonded: 1.91 r_work: 0.3130 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3016 rms_B_bonded: 3.91 restraints_weight: 0.2500 r_work (final): 0.3016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8693 moved from start: 0.2826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 37800 Z= 0.161 Angle : 0.625 9.386 51208 Z= 0.307 Chirality : 0.045 0.403 6060 Planarity : 0.004 0.068 6517 Dihedral : 5.478 59.595 5198 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.84 % Favored : 96.11 % Rotamer: Outliers : 2.92 % Allowed : 13.79 % Favored : 83.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.14 (0.12), residues: 4708 helix: 1.20 (0.11), residues: 2380 sheet: 0.11 (0.19), residues: 586 loop : -1.48 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.023 0.000 ARG H 410 TYR 0.019 0.001 TYR D 141 PHE 0.014 0.001 PHE C 273 TRP 0.004 0.001 TRP E 477 HIS 0.003 0.001 HIS F 710 Details of bonding type rmsd covalent geometry : bond 0.00367 (37797) covalent geometry : angle 0.62544 (51208) hydrogen bonds : bond 0.04210 ( 2100) hydrogen bonds : angle 4.57007 ( 6183) Misc. bond : bond 0.00505 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 509 time to evaluate : 1.364 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 130 GLU cc_start: 0.8201 (mt-10) cc_final: 0.7968 (mt-10) REVERT: A 190 LEU cc_start: 0.8349 (tp) cc_final: 0.8073 (tm) REVERT: A 233 THR cc_start: 0.8285 (m) cc_final: 0.8057 (t) REVERT: B 231 MET cc_start: 0.8028 (mmp) cc_final: 0.7745 (mmp) REVERT: B 707 ARG cc_start: 0.8530 (OUTLIER) cc_final: 0.8166 (ttt-90) REVERT: C 164 ASN cc_start: 0.8315 (OUTLIER) cc_final: 0.8097 (p0) REVERT: C 439 ILE cc_start: 0.8660 (pp) cc_final: 0.8437 (mt) REVERT: C 456 GLU cc_start: 0.8165 (mm-30) cc_final: 0.7722 (mt-10) REVERT: C 462 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.7969 (mt-10) REVERT: D 347 MET cc_start: 0.8913 (OUTLIER) cc_final: 0.8712 (mpt) REVERT: D 476 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8050 (mm-30) REVERT: E 200 ASP cc_start: 0.8548 (OUTLIER) cc_final: 0.8121 (OUTLIER) REVERT: E 462 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8084 (mm-30) REVERT: E 626 GLU cc_start: 0.8454 (OUTLIER) cc_final: 0.8119 (tt0) REVERT: E 684 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.7919 (mp0) REVERT: E 707 ARG cc_start: 0.8708 (OUTLIER) cc_final: 0.8449 (ttt-90) REVERT: F 21 ARG cc_start: 0.8121 (OUTLIER) cc_final: 0.7771 (mmm160) REVERT: F 139 ARG cc_start: 0.8707 (tpt170) cc_final: 0.8507 (tpt170) REVERT: F 580 LYS cc_start: 0.7539 (mptt) cc_final: 0.7072 (mttp) REVERT: G 111 GLN cc_start: 0.8321 (tt0) cc_final: 0.8036 (tt0) REVERT: G 164 ASN cc_start: 0.8982 (p0) cc_final: 0.8561 (p0) REVERT: G 165 TYR cc_start: 0.7809 (p90) cc_final: 0.7444 (p90) REVERT: G 274 LEU cc_start: 0.8089 (OUTLIER) cc_final: 0.7803 (tm) REVERT: G 420 ASN cc_start: 0.8513 (m-40) cc_final: 0.8235 (m-40) REVERT: H 243 ARG cc_start: 0.8078 (ttt90) cc_final: 0.7863 (ttp-170) REVERT: H 425 LYS cc_start: 0.7771 (mttt) cc_final: 0.7437 (mtmt) REVERT: H 580 LYS cc_start: 0.7982 (mmtt) cc_final: 0.7549 (mmpt) outliers start: 119 outliers final: 26 residues processed: 573 average time/residue: 0.6325 time to fit residues: 443.9642 Evaluate side-chains 484 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 447 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 626 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 684 GLU Chi-restraints excluded: chain G residue 263 GLN Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 410 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 387 optimal weight: 20.0000 chunk 110 optimal weight: 1.9990 chunk 437 optimal weight: 7.9990 chunk 223 optimal weight: 0.9990 chunk 124 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 156 optimal weight: 0.5980 chunk 127 optimal weight: 8.9990 chunk 338 optimal weight: 4.9990 chunk 358 optimal weight: 0.6980 chunk 352 optimal weight: 2.9990 overall best weight: 1.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 164 ASN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 266 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4006 r_free = 0.4006 target = 0.175341 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.126375 restraints weight = 46251.466| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 2.35 r_work: 0.3094 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2974 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 37800 Z= 0.141 Angle : 0.608 11.647 51208 Z= 0.294 Chirality : 0.044 0.360 6060 Planarity : 0.003 0.043 6517 Dihedral : 5.308 56.983 5198 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.39 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.70 % Favored : 96.26 % Rotamer: Outliers : 3.04 % Allowed : 14.53 % Favored : 82.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.54 (0.12), residues: 4708 helix: 1.58 (0.11), residues: 2377 sheet: 0.33 (0.19), residues: 586 loop : -1.38 (0.13), residues: 1745 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 410 TYR 0.019 0.001 TYR D 141 PHE 0.015 0.001 PHE C 273 TRP 0.003 0.001 TRP E 477 HIS 0.003 0.001 HIS F 710 Details of bonding type rmsd covalent geometry : bond 0.00321 (37797) covalent geometry : angle 0.60761 (51208) hydrogen bonds : bond 0.03811 ( 2100) hydrogen bonds : angle 4.38189 ( 6183) Misc. bond : bond 0.00343 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 626 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 502 time to evaluate : 1.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8818 (mp) REVERT: A 190 LEU cc_start: 0.8299 (tp) cc_final: 0.7982 (tm) REVERT: A 195 ASP cc_start: 0.8092 (t0) cc_final: 0.7735 (t0) REVERT: A 233 THR cc_start: 0.8499 (m) cc_final: 0.8293 (t) REVERT: A 667 ARG cc_start: 0.9146 (OUTLIER) cc_final: 0.8923 (tpt90) REVERT: B 231 MET cc_start: 0.8023 (mmp) cc_final: 0.7796 (mmp) REVERT: B 249 ASP cc_start: 0.8419 (m-30) cc_final: 0.8091 (m-30) REVERT: B 667 ARG cc_start: 0.9079 (OUTLIER) cc_final: 0.8598 (tpt170) REVERT: B 707 ARG cc_start: 0.8575 (OUTLIER) cc_final: 0.8225 (ttt-90) REVERT: C 164 ASN cc_start: 0.8255 (OUTLIER) cc_final: 0.8029 (p0) REVERT: C 456 GLU cc_start: 0.8289 (mm-30) cc_final: 0.7780 (mt-10) REVERT: C 462 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7976 (mt-10) REVERT: D 347 MET cc_start: 0.8939 (OUTLIER) cc_final: 0.8729 (mpt) REVERT: D 410 ARG cc_start: 0.7976 (ttp80) cc_final: 0.7025 (ttp-170) REVERT: E 200 ASP cc_start: 0.8469 (OUTLIER) cc_final: 0.7979 (OUTLIER) REVERT: E 231 MET cc_start: 0.8602 (mmt) cc_final: 0.8390 (mmp) REVERT: E 462 GLU cc_start: 0.8576 (OUTLIER) cc_final: 0.8138 (mm-30) REVERT: E 525 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.8383 (ptpt) REVERT: E 626 GLU cc_start: 0.8566 (OUTLIER) cc_final: 0.8205 (tt0) REVERT: E 684 GLU cc_start: 0.8568 (OUTLIER) cc_final: 0.8089 (mp0) REVERT: F 21 ARG cc_start: 0.8193 (OUTLIER) cc_final: 0.7751 (mmm160) REVERT: F 182 LEU cc_start: 0.8039 (mm) cc_final: 0.7684 (tp) REVERT: F 185 LYS cc_start: 0.8227 (mmmm) cc_final: 0.7900 (tptp) REVERT: F 347 MET cc_start: 0.8731 (pmm) cc_final: 0.8414 (pmm) REVERT: F 580 LYS cc_start: 0.7555 (mptt) cc_final: 0.6995 (mttm) REVERT: G 111 GLN cc_start: 0.8424 (tt0) cc_final: 0.8178 (tt0) REVERT: G 164 ASN cc_start: 0.8917 (p0) cc_final: 0.8506 (p0) REVERT: G 165 TYR cc_start: 0.7776 (p90) cc_final: 0.7172 (p90) REVERT: G 274 LEU cc_start: 0.8066 (OUTLIER) cc_final: 0.7782 (tm) REVERT: G 420 ASN cc_start: 0.8598 (m-40) cc_final: 0.8309 (m-40) REVERT: H 31 LYS cc_start: 0.8414 (mttt) cc_final: 0.8116 (mmtt) REVERT: H 122 ARG cc_start: 0.7734 (tmt90) cc_final: 0.7482 (ttt-90) REVERT: H 165 TYR cc_start: 0.8668 (p90) cc_final: 0.8430 (p90) REVERT: H 243 ARG cc_start: 0.8176 (ttt90) cc_final: 0.7910 (ttp-170) REVERT: H 425 LYS cc_start: 0.7923 (mttt) cc_final: 0.7562 (mtmt) REVERT: H 523 GLU cc_start: 0.8258 (mp0) cc_final: 0.7981 (mp0) REVERT: H 580 LYS cc_start: 0.7927 (mmtt) cc_final: 0.7442 (mmpt) REVERT: H 594 MET cc_start: 0.8359 (mtp) cc_final: 0.8115 (ptm) REVERT: H 667 ARG cc_start: 0.9054 (OUTLIER) cc_final: 0.8594 (tpt90) outliers start: 124 outliers final: 40 residues processed: 571 average time/residue: 0.6220 time to fit residues: 436.6832 Evaluate side-chains 513 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 459 time to evaluate : 0.940 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 409 VAL Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain A residue 667 ARG Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 56 GLU Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 164 ASN Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 525 LYS Chi-restraints excluded: chain E residue 626 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 195 ASP Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 189 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 525 LYS Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 162 optimal weight: 5.9990 chunk 308 optimal weight: 5.9990 chunk 119 optimal weight: 0.8980 chunk 125 optimal weight: 0.9990 chunk 149 optimal weight: 0.9990 chunk 267 optimal weight: 5.9990 chunk 291 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 420 optimal weight: 0.7980 chunk 439 optimal weight: 3.9990 chunk 246 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 399 ASN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 173 GLN E 201 GLN E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS G 571 HIS ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.175598 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.125116 restraints weight = 46219.642| |-----------------------------------------------------------------------------| r_work (start): 0.3410 rms_B_bonded: 1.95 r_work: 0.3138 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 37800 Z= 0.129 Angle : 0.601 10.487 51208 Z= 0.287 Chirality : 0.044 0.327 6060 Planarity : 0.003 0.043 6517 Dihedral : 5.193 56.184 5198 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.65 % Favored : 96.30 % Rotamer: Outliers : 2.80 % Allowed : 15.58 % Favored : 81.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.77 (0.12), residues: 4708 helix: 1.79 (0.11), residues: 2386 sheet: 0.45 (0.20), residues: 590 loop : -1.33 (0.13), residues: 1732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 243 TYR 0.021 0.001 TYR D 141 PHE 0.019 0.001 PHE C 273 TRP 0.003 0.001 TRP G 631 HIS 0.002 0.001 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00290 (37797) covalent geometry : angle 0.60102 (51208) hydrogen bonds : bond 0.03632 ( 2100) hydrogen bonds : angle 4.27943 ( 6183) Misc. bond : bond 0.00291 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 491 time to evaluate : 1.090 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8735 (mp) REVERT: A 190 LEU cc_start: 0.8233 (tp) cc_final: 0.7928 (tm) REVERT: A 195 ASP cc_start: 0.8099 (t0) cc_final: 0.7706 (t0) REVERT: B 114 GLN cc_start: 0.7803 (OUTLIER) cc_final: 0.7588 (tp40) REVERT: B 137 ILE cc_start: 0.8749 (mm) cc_final: 0.8514 (mp) REVERT: B 231 MET cc_start: 0.8069 (mmp) cc_final: 0.7785 (mmp) REVERT: B 249 ASP cc_start: 0.8308 (m-30) cc_final: 0.7974 (m-30) REVERT: B 495 THR cc_start: 0.8261 (p) cc_final: 0.7781 (t) REVERT: B 667 ARG cc_start: 0.9027 (OUTLIER) cc_final: 0.8552 (tpt170) REVERT: B 707 ARG cc_start: 0.8501 (OUTLIER) cc_final: 0.8142 (ttt-90) REVERT: C 189 LEU cc_start: 0.8558 (tp) cc_final: 0.8283 (tt) REVERT: C 213 ILE cc_start: 0.9053 (mt) cc_final: 0.8829 (mp) REVERT: C 243 ARG cc_start: 0.8216 (OUTLIER) cc_final: 0.7913 (ttm-80) REVERT: C 456 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7720 (mt-10) REVERT: C 462 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7906 (mt-10) REVERT: D 347 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8727 (mpt) REVERT: D 410 ARG cc_start: 0.8070 (ttp80) cc_final: 0.7223 (ttp-170) REVERT: D 476 GLU cc_start: 0.8390 (OUTLIER) cc_final: 0.7966 (mm-30) REVERT: E 114 GLN cc_start: 0.8411 (OUTLIER) cc_final: 0.8188 (mm-40) REVERT: E 462 GLU cc_start: 0.8508 (OUTLIER) cc_final: 0.8117 (mm-30) REVERT: E 684 GLU cc_start: 0.8448 (OUTLIER) cc_final: 0.7970 (mp0) REVERT: E 707 ARG cc_start: 0.8602 (OUTLIER) cc_final: 0.8177 (ttp80) REVERT: F 21 ARG cc_start: 0.8150 (OUTLIER) cc_final: 0.7738 (mmm160) REVERT: F 182 LEU cc_start: 0.8071 (mm) cc_final: 0.7582 (tt) REVERT: F 185 LYS cc_start: 0.8287 (mmmm) cc_final: 0.8022 (tptp) REVERT: F 347 MET cc_start: 0.8685 (pmm) cc_final: 0.8449 (pmm) REVERT: F 518 HIS cc_start: 0.8349 (t-90) cc_final: 0.8086 (t70) REVERT: F 580 LYS cc_start: 0.7491 (mptt) cc_final: 0.7212 (mptm) REVERT: G 164 ASN cc_start: 0.8882 (p0) cc_final: 0.8423 (p0) REVERT: G 165 TYR cc_start: 0.7682 (p90) cc_final: 0.7280 (p90) REVERT: G 274 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7832 (tm) REVERT: G 420 ASN cc_start: 0.8543 (m-40) cc_final: 0.8284 (m-40) REVERT: H 31 LYS cc_start: 0.8330 (mttt) cc_final: 0.8095 (mmtt) REVERT: H 122 ARG cc_start: 0.7739 (tmt90) cc_final: 0.7491 (ttt-90) REVERT: H 165 TYR cc_start: 0.8582 (p90) cc_final: 0.8306 (p90) REVERT: H 243 ARG cc_start: 0.8121 (ttt90) cc_final: 0.7878 (ttp-170) REVERT: H 425 LYS cc_start: 0.8005 (mttt) cc_final: 0.7663 (mtmt) REVERT: H 523 GLU cc_start: 0.8085 (mp0) cc_final: 0.7868 (mp0) REVERT: H 580 LYS cc_start: 0.7848 (mmtt) cc_final: 0.7343 (mmpt) REVERT: H 594 MET cc_start: 0.8257 (mtp) cc_final: 0.8009 (ptm) REVERT: H 667 ARG cc_start: 0.9043 (OUTLIER) cc_final: 0.8579 (tpt90) outliers start: 114 outliers final: 40 residues processed: 561 average time/residue: 0.6131 time to fit residues: 422.7838 Evaluate side-chains 510 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 455 time to evaluate : 1.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 260 ILE Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 417 THR Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 243 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 114 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain E residue 707 ARG Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 235 THR Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Chi-restraints excluded: chain H residue 680 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 384 optimal weight: 1.9990 chunk 377 optimal weight: 3.9990 chunk 80 optimal weight: 40.0000 chunk 262 optimal weight: 2.9990 chunk 348 optimal weight: 1.9990 chunk 158 optimal weight: 4.9990 chunk 69 optimal weight: 5.9990 chunk 41 optimal weight: 0.6980 chunk 283 optimal weight: 7.9990 chunk 147 optimal weight: 50.0000 chunk 406 optimal weight: 2.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 390 GLN ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 671 ASN ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN ** D 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN H 168 ASN H 254 ASN H 258 GLN ** H 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 671 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3980 r_free = 0.3980 target = 0.173046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3418 r_free = 0.3418 target = 0.123270 restraints weight = 46170.086| |-----------------------------------------------------------------------------| r_work (start): 0.3397 rms_B_bonded: 2.31 r_work: 0.3058 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 37800 Z= 0.214 Angle : 0.661 10.803 51208 Z= 0.319 Chirality : 0.046 0.274 6060 Planarity : 0.004 0.091 6517 Dihedral : 5.729 66.782 5198 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.93 % Favored : 96.03 % Rotamer: Outliers : 3.09 % Allowed : 15.90 % Favored : 81.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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 (0.12), residues: 4708 helix: 1.70 (0.11), residues: 2385 sheet: 0.46 (0.20), residues: 581 loop : -1.25 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 410 TYR 0.020 0.002 TYR D 141 PHE 0.017 0.002 PHE C 273 TRP 0.005 0.001 TRP H 477 HIS 0.004 0.001 HIS G 622 Details of bonding type rmsd covalent geometry : bond 0.00502 (37797) covalent geometry : angle 0.66080 (51208) hydrogen bonds : bond 0.03973 ( 2100) hydrogen bonds : angle 4.41853 ( 6183) Misc. bond : bond 0.00464 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 488 time to evaluate : 1.428 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.9057 (OUTLIER) cc_final: 0.8789 (mp) REVERT: A 139 ARG cc_start: 0.8663 (tpt170) cc_final: 0.8438 (tpt170) REVERT: A 190 LEU cc_start: 0.8345 (tp) cc_final: 0.7997 (tm) REVERT: A 195 ASP cc_start: 0.8141 (t0) cc_final: 0.7812 (t0) REVERT: A 218 LYS cc_start: 0.8888 (ttpt) cc_final: 0.8683 (mtmm) REVERT: B 122 ARG cc_start: 0.8703 (OUTLIER) cc_final: 0.7328 (ttp80) REVERT: B 137 ILE cc_start: 0.8749 (mm) cc_final: 0.8521 (mp) REVERT: B 231 MET cc_start: 0.8121 (mmp) cc_final: 0.7891 (mmp) REVERT: B 540 MET cc_start: 0.9275 (OUTLIER) cc_final: 0.8878 (mtp) REVERT: B 667 ARG cc_start: 0.9113 (OUTLIER) cc_final: 0.8605 (tpt170) REVERT: C 122 ARG cc_start: 0.8720 (OUTLIER) cc_final: 0.7764 (tpt-90) REVERT: C 189 LEU cc_start: 0.8594 (tp) cc_final: 0.8284 (tt) REVERT: C 456 GLU cc_start: 0.8376 (mm-30) cc_final: 0.7848 (mt-10) REVERT: C 462 GLU cc_start: 0.8720 (OUTLIER) cc_final: 0.8046 (mt-10) REVERT: D 63 ILE cc_start: 0.6256 (OUTLIER) cc_final: 0.6033 (tp) REVERT: D 103 ILE cc_start: 0.8914 (OUTLIER) cc_final: 0.8489 (mp) REVERT: D 347 MET cc_start: 0.8963 (OUTLIER) cc_final: 0.8756 (mpt) REVERT: D 476 GLU cc_start: 0.8527 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: D 598 LYS cc_start: 0.8932 (OUTLIER) cc_final: 0.8379 (mtpp) REVERT: D 680 MET cc_start: 0.9210 (OUTLIER) cc_final: 0.8928 (mmm) REVERT: E 109 GLN cc_start: 0.8523 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: E 201 GLN cc_start: 0.7729 (mm-40) cc_final: 0.7338 (mm-40) REVERT: E 525 LYS cc_start: 0.8694 (OUTLIER) cc_final: 0.8412 (ttpt) REVERT: E 684 GLU cc_start: 0.8564 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: F 21 ARG cc_start: 0.8208 (OUTLIER) cc_final: 0.7800 (mmm160) REVERT: F 174 LEU cc_start: 0.8437 (mm) cc_final: 0.8092 (mp) REVERT: F 182 LEU cc_start: 0.8026 (mm) cc_final: 0.7592 (tt) REVERT: F 185 LYS cc_start: 0.8320 (mmmm) cc_final: 0.7901 (tptp) REVERT: F 224 ASP cc_start: 0.7325 (t0) cc_final: 0.7111 (t70) REVERT: F 452 ARG cc_start: 0.8651 (OUTLIER) cc_final: 0.7537 (ptt-90) REVERT: F 580 LYS cc_start: 0.7782 (mptt) cc_final: 0.7374 (mptm) REVERT: G 122 ARG cc_start: 0.8361 (OUTLIER) cc_final: 0.7321 (ttp-170) REVERT: G 164 ASN cc_start: 0.8720 (p0) cc_final: 0.8354 (p0) REVERT: G 165 TYR cc_start: 0.7705 (p90) cc_final: 0.7266 (p90) REVERT: G 218 LYS cc_start: 0.9013 (mtpp) cc_final: 0.8593 (mmtt) REVERT: G 274 LEU cc_start: 0.8158 (OUTLIER) cc_final: 0.7862 (tm) REVERT: G 420 ASN cc_start: 0.8609 (m-40) cc_final: 0.8377 (m-40) REVERT: H 31 LYS cc_start: 0.8430 (mttt) cc_final: 0.8082 (mmtt) REVERT: H 122 ARG cc_start: 0.7865 (tmt90) cc_final: 0.7607 (ttt-90) REVERT: H 165 TYR cc_start: 0.8595 (p90) cc_final: 0.8349 (p90) REVERT: H 214 SER cc_start: 0.8761 (t) cc_final: 0.8343 (p) REVERT: H 243 ARG cc_start: 0.8225 (ttt90) cc_final: 0.7916 (ttp-170) REVERT: H 425 LYS cc_start: 0.8093 (mttt) cc_final: 0.7713 (mtmt) REVERT: H 523 GLU cc_start: 0.8268 (mp0) cc_final: 0.7907 (mp0) REVERT: H 657 ARG cc_start: 0.8466 (mmm160) cc_final: 0.8190 (mmm-85) REVERT: H 667 ARG cc_start: 0.9126 (OUTLIER) cc_final: 0.8767 (tpt90) REVERT: H 669 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.7545 (mp0) outliers start: 126 outliers final: 53 residues processed: 555 average time/residue: 0.6453 time to fit residues: 439.2183 Evaluate side-chains 538 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 464 time to evaluate : 1.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 114 GLN Chi-restraints excluded: chain B residue 119 VAL Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 446 LEU Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 103 ILE Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 191 VAL Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 347 MET Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 598 LYS Chi-restraints excluded: chain D residue 680 MET Chi-restraints excluded: chain E residue 46 LEU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 235 THR Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 525 LYS Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 21 ARG Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain F residue 452 ARG Chi-restraints excluded: chain F residue 540 MET Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 135 ILE Chi-restraints excluded: chain G residue 195 ASP Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 61 ILE Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 474 ILE Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 522 MET Chi-restraints excluded: chain H residue 525 LYS Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Chi-restraints excluded: chain H residue 669 GLU Chi-restraints excluded: chain H residue 707 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 112 optimal weight: 0.2980 chunk 185 optimal weight: 0.8980 chunk 33 optimal weight: 6.9990 chunk 435 optimal weight: 0.7980 chunk 119 optimal weight: 0.7980 chunk 198 optimal weight: 1.9990 chunk 82 optimal weight: 0.4980 chunk 398 optimal weight: 0.6980 chunk 259 optimal weight: 5.9990 chunk 442 optimal weight: 20.0000 chunk 327 optimal weight: 5.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 390 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 671 ASN D 183 ASN D 275 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 671 ASN ** H 571 HIS ** 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 = 0.4011 r_free = 0.4011 target = 0.175793 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3463 r_free = 0.3463 target = 0.126440 restraints weight = 46239.406| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 2.02 r_work: 0.3138 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8678 moved from start: 0.3685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 37800 Z= 0.121 Angle : 0.615 10.952 51208 Z= 0.294 Chirality : 0.044 0.218 6060 Planarity : 0.004 0.112 6517 Dihedral : 5.161 54.982 5198 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 2.06 % Allowed : 17.33 % Favored : 80.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.94 (0.12), residues: 4708 helix: 1.93 (0.11), residues: 2384 sheet: 0.59 (0.20), residues: 583 loop : -1.26 (0.13), residues: 1741 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG H 410 TYR 0.016 0.001 TYR D 141 PHE 0.017 0.001 PHE C 273 TRP 0.004 0.001 TRP E 631 HIS 0.002 0.000 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00267 (37797) covalent geometry : angle 0.61467 (51208) hydrogen bonds : bond 0.03482 ( 2100) hydrogen bonds : angle 4.23931 ( 6183) Misc. bond : bond 0.00315 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 572 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 488 time to evaluate : 1.448 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8977 (OUTLIER) cc_final: 0.8649 (mp) REVERT: A 139 ARG cc_start: 0.8691 (tpt170) cc_final: 0.8439 (tpt170) REVERT: A 190 LEU cc_start: 0.8220 (tp) cc_final: 0.7864 (tm) REVERT: A 218 LYS cc_start: 0.8852 (ttpt) cc_final: 0.8649 (mtmm) REVERT: B 231 MET cc_start: 0.8085 (mmp) cc_final: 0.7858 (mmp) REVERT: B 249 ASP cc_start: 0.8218 (m-30) cc_final: 0.7858 (m-30) REVERT: B 495 THR cc_start: 0.8307 (p) cc_final: 0.7776 (t) REVERT: B 540 MET cc_start: 0.9127 (OUTLIER) cc_final: 0.8745 (mtp) REVERT: B 667 ARG cc_start: 0.9049 (OUTLIER) cc_final: 0.8546 (tpt170) REVERT: B 707 ARG cc_start: 0.8514 (OUTLIER) cc_final: 0.8149 (ttt-90) REVERT: C 122 ARG cc_start: 0.8662 (OUTLIER) cc_final: 0.7700 (tpt-90) REVERT: C 189 LEU cc_start: 0.8556 (tp) cc_final: 0.8337 (tt) REVERT: C 456 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7703 (mt-10) REVERT: C 462 GLU cc_start: 0.8631 (OUTLIER) cc_final: 0.7856 (mt-10) REVERT: D 397 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7702 (mp0) REVERT: D 476 GLU cc_start: 0.8384 (OUTLIER) cc_final: 0.7905 (mm-30) REVERT: E 109 GLN cc_start: 0.8452 (OUTLIER) cc_final: 0.7626 (pm20) REVERT: E 200 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.8148 (m-30) REVERT: E 201 GLN cc_start: 0.7631 (mm-40) cc_final: 0.7360 (mm-40) REVERT: E 231 MET cc_start: 0.8562 (mmt) cc_final: 0.7952 (mmt) REVERT: E 462 GLU cc_start: 0.8504 (OUTLIER) cc_final: 0.8099 (mm-30) REVERT: E 684 GLU cc_start: 0.8430 (OUTLIER) cc_final: 0.7948 (mp0) REVERT: E 707 ARG cc_start: 0.8595 (ttt180) cc_final: 0.8152 (ttp80) REVERT: F 174 LEU cc_start: 0.8349 (mm) cc_final: 0.8002 (mp) REVERT: F 182 LEU cc_start: 0.7987 (mm) cc_final: 0.7579 (tt) REVERT: F 185 LYS cc_start: 0.8293 (mmmm) cc_final: 0.7944 (tptp) REVERT: F 224 ASP cc_start: 0.7276 (t0) cc_final: 0.7032 (t70) REVERT: F 580 LYS cc_start: 0.7518 (mptt) cc_final: 0.7218 (mptm) REVERT: F 621 MET cc_start: 0.9084 (mtp) cc_final: 0.8859 (mtm) REVERT: G 164 ASN cc_start: 0.8749 (p0) cc_final: 0.8397 (p0) REVERT: G 165 TYR cc_start: 0.7615 (p90) cc_final: 0.7184 (p90) REVERT: G 274 LEU cc_start: 0.8199 (OUTLIER) cc_final: 0.7916 (tm) REVERT: H 122 ARG cc_start: 0.7786 (tmt90) cc_final: 0.7511 (ttt-90) REVERT: H 214 SER cc_start: 0.8714 (t) cc_final: 0.8316 (p) REVERT: H 243 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7825 (ttp-170) REVERT: H 425 LYS cc_start: 0.8025 (mttt) cc_final: 0.7677 (mtmt) REVERT: H 523 GLU cc_start: 0.8176 (mp0) cc_final: 0.7937 (mp0) REVERT: H 580 LYS cc_start: 0.7796 (mmtt) cc_final: 0.7289 (mmpt) REVERT: H 657 ARG cc_start: 0.8400 (mmm160) cc_final: 0.8131 (mmm-85) REVERT: H 667 ARG cc_start: 0.9074 (OUTLIER) cc_final: 0.8591 (tpt90) outliers start: 84 outliers final: 32 residues processed: 532 average time/residue: 0.6295 time to fit residues: 412.0152 Evaluate side-chains 503 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 457 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 411 ILE Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 136 ASP Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 200 ASP Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 167 ILE Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 268 optimal weight: 6.9990 chunk 418 optimal weight: 6.9990 chunk 253 optimal weight: 6.9990 chunk 187 optimal weight: 1.9990 chunk 111 optimal weight: 1.9990 chunk 385 optimal weight: 30.0000 chunk 118 optimal weight: 0.6980 chunk 382 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 99 optimal weight: 0.5980 chunk 471 optimal weight: 6.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 246 HIS H 168 ASN ** H 571 HIS ** 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 = 0.3989 r_free = 0.3989 target = 0.174905 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.124749 restraints weight = 45397.278| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.25 r_work: 0.3065 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.3758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 37800 Z= 0.152 Angle : 0.645 11.024 51208 Z= 0.308 Chirality : 0.045 0.356 6060 Planarity : 0.003 0.045 6517 Dihedral : 5.312 58.094 5198 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.61 % Favored : 96.35 % Rotamer: Outliers : 2.11 % Allowed : 17.84 % Favored : 80.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % 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: 0.98 (0.12), residues: 4708 helix: 1.95 (0.11), residues: 2380 sheet: 0.63 (0.20), residues: 586 loop : -1.23 (0.13), residues: 1742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 243 TYR 0.014 0.001 TYR D 141 PHE 0.016 0.001 PHE C 273 TRP 0.004 0.001 TRP H 477 HIS 0.002 0.001 HIS F 710 Details of bonding type rmsd covalent geometry : bond 0.00350 (37797) covalent geometry : angle 0.64503 (51208) hydrogen bonds : bond 0.03639 ( 2100) hydrogen bonds : angle 4.28544 ( 6183) Misc. bond : bond 0.00282 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 474 time to evaluate : 1.365 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8983 (OUTLIER) cc_final: 0.8679 (mp) REVERT: A 139 ARG cc_start: 0.8661 (tpt170) cc_final: 0.8347 (tpt170) REVERT: A 190 LEU cc_start: 0.8260 (tp) cc_final: 0.7869 (tm) REVERT: A 218 LYS cc_start: 0.8965 (ttpt) cc_final: 0.8756 (mtmm) REVERT: B 231 MET cc_start: 0.8077 (mmp) cc_final: 0.7793 (mmp) REVERT: B 249 ASP cc_start: 0.8257 (m-30) cc_final: 0.7866 (m-30) REVERT: B 495 THR cc_start: 0.8286 (p) cc_final: 0.7725 (t) REVERT: B 540 MET cc_start: 0.9203 (OUTLIER) cc_final: 0.8825 (mtp) REVERT: B 667 ARG cc_start: 0.9117 (OUTLIER) cc_final: 0.8644 (tpt170) REVERT: B 707 ARG cc_start: 0.8512 (OUTLIER) cc_final: 0.8145 (ttt-90) REVERT: C 122 ARG cc_start: 0.8687 (OUTLIER) cc_final: 0.7922 (tpt-90) REVERT: C 189 LEU cc_start: 0.8572 (tp) cc_final: 0.8307 (tt) REVERT: C 456 GLU cc_start: 0.8298 (mm-30) cc_final: 0.7916 (mt-10) REVERT: C 462 GLU cc_start: 0.8651 (OUTLIER) cc_final: 0.7876 (mt-10) REVERT: D 63 ILE cc_start: 0.6100 (OUTLIER) cc_final: 0.5810 (tp) REVERT: D 163 GLU cc_start: 0.8130 (pp20) cc_final: 0.7737 (pp20) REVERT: D 164 ASN cc_start: 0.7998 (p0) cc_final: 0.7676 (p0) REVERT: D 397 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7842 (mp0) REVERT: D 476 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: D 684 GLU cc_start: 0.8735 (OUTLIER) cc_final: 0.8032 (mp0) REVERT: E 109 GLN cc_start: 0.8487 (OUTLIER) cc_final: 0.7691 (pm20) REVERT: E 200 ASP cc_start: 0.8484 (m-30) cc_final: 0.8235 (m-30) REVERT: E 201 GLN cc_start: 0.7576 (mm-40) cc_final: 0.7367 (mm-40) REVERT: E 231 MET cc_start: 0.8552 (mmt) cc_final: 0.7901 (mmt) REVERT: E 462 GLU cc_start: 0.8573 (OUTLIER) cc_final: 0.8105 (mm-30) REVERT: E 626 GLU cc_start: 0.8544 (OUTLIER) cc_final: 0.8307 (tt0) REVERT: E 684 GLU cc_start: 0.8559 (OUTLIER) cc_final: 0.8079 (mp0) REVERT: E 707 ARG cc_start: 0.8666 (ttt180) cc_final: 0.8255 (ttp80) REVERT: F 174 LEU cc_start: 0.8332 (mm) cc_final: 0.7967 (mp) REVERT: F 182 LEU cc_start: 0.8001 (mm) cc_final: 0.7570 (tt) REVERT: F 185 LYS cc_start: 0.8311 (mmmm) cc_final: 0.7951 (tptp) REVERT: F 224 ASP cc_start: 0.7375 (t0) cc_final: 0.7057 (t70) REVERT: F 580 LYS cc_start: 0.7541 (mptt) cc_final: 0.7191 (mptm) REVERT: F 621 MET cc_start: 0.9100 (mtp) cc_final: 0.8858 (mtm) REVERT: G 164 ASN cc_start: 0.8795 (p0) cc_final: 0.8384 (p0) REVERT: G 165 TYR cc_start: 0.7637 (p90) cc_final: 0.7295 (p90) REVERT: G 218 LYS cc_start: 0.8999 (mtpp) cc_final: 0.8551 (mmtt) REVERT: G 274 LEU cc_start: 0.8265 (OUTLIER) cc_final: 0.7974 (tm) REVERT: H 31 LYS cc_start: 0.8404 (mttt) cc_final: 0.8002 (mmtt) REVERT: H 122 ARG cc_start: 0.7686 (tmt90) cc_final: 0.7396 (ttt180) REVERT: H 214 SER cc_start: 0.8726 (t) cc_final: 0.8335 (p) REVERT: H 243 ARG cc_start: 0.8077 (ttt90) cc_final: 0.7786 (ttp-170) REVERT: H 425 LYS cc_start: 0.7971 (mttt) cc_final: 0.7574 (mtmt) REVERT: H 523 GLU cc_start: 0.8331 (mp0) cc_final: 0.8005 (mp0) REVERT: H 580 LYS cc_start: 0.7822 (mmtt) cc_final: 0.7245 (mmpt) REVERT: H 657 ARG cc_start: 0.8470 (mmm160) cc_final: 0.8165 (mmm-85) REVERT: H 667 ARG cc_start: 0.9094 (OUTLIER) cc_final: 0.8692 (tpt90) REVERT: H 669 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.7322 (mp0) outliers start: 86 outliers final: 38 residues processed: 520 average time/residue: 0.6359 time to fit residues: 407.0213 Evaluate side-chains 514 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 459 time to evaluate : 1.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 119 VAL Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain C residue 540 MET Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 89 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 119 VAL Chi-restraints excluded: chain E residue 124 LEU Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 626 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 156 ILE Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain G residue 93 LEU Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 395 GLN Chi-restraints excluded: chain H residue 39 VAL Chi-restraints excluded: chain H residue 92 LEU Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Chi-restraints excluded: chain H residue 669 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 84 optimal weight: 3.9990 chunk 392 optimal weight: 0.0870 chunk 287 optimal weight: 0.9980 chunk 265 optimal weight: 0.7980 chunk 342 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 312 optimal weight: 2.9990 chunk 188 optimal weight: 0.8980 chunk 127 optimal weight: 8.9990 chunk 224 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 571 HIS ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 571 HIS ** 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 = 0.4004 r_free = 0.4004 target = 0.176201 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.126408 restraints weight = 45901.085| |-----------------------------------------------------------------------------| r_work (start): 0.3423 rms_B_bonded: 2.32 r_work: 0.3086 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.3880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 37800 Z= 0.126 Angle : 0.637 16.406 51208 Z= 0.304 Chirality : 0.044 0.348 6060 Planarity : 0.003 0.043 6517 Dihedral : 5.108 55.114 5198 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.55 % Favored : 96.41 % Rotamer: Outliers : 1.64 % Allowed : 18.43 % Favored : 79.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.07 (0.12), residues: 4708 helix: 2.02 (0.11), residues: 2385 sheet: 0.75 (0.20), residues: 584 loop : -1.22 (0.13), residues: 1739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 243 TYR 0.013 0.001 TYR H 165 PHE 0.016 0.001 PHE C 273 TRP 0.004 0.001 TRP E 631 HIS 0.002 0.001 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00282 (37797) covalent geometry : angle 0.63741 (51208) hydrogen bonds : bond 0.03465 ( 2100) hydrogen bonds : angle 4.21604 ( 6183) Misc. bond : bond 0.00233 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 468 time to evaluate : 1.458 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 139 ARG cc_start: 0.8637 (tpt170) cc_final: 0.8308 (tpt170) REVERT: A 190 LEU cc_start: 0.8242 (tp) cc_final: 0.7856 (tm) REVERT: A 218 LYS cc_start: 0.8983 (ttpt) cc_final: 0.8781 (mtmm) REVERT: B 231 MET cc_start: 0.8101 (mmp) cc_final: 0.7806 (mmp) REVERT: B 249 ASP cc_start: 0.8218 (m-30) cc_final: 0.7843 (m-30) REVERT: B 495 THR cc_start: 0.8291 (p) cc_final: 0.7695 (t) REVERT: B 540 MET cc_start: 0.9138 (OUTLIER) cc_final: 0.8758 (mtp) REVERT: B 667 ARG cc_start: 0.9099 (OUTLIER) cc_final: 0.8630 (tpt170) REVERT: B 707 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8172 (ttt-90) REVERT: C 122 ARG cc_start: 0.8668 (OUTLIER) cc_final: 0.8062 (tpt-90) REVERT: C 165 TYR cc_start: 0.8658 (p90) cc_final: 0.8315 (p90) REVERT: C 189 LEU cc_start: 0.8500 (tp) cc_final: 0.8294 (tt) REVERT: C 462 GLU cc_start: 0.8623 (OUTLIER) cc_final: 0.7809 (mt-10) REVERT: D 63 ILE cc_start: 0.5951 (OUTLIER) cc_final: 0.5710 (tp) REVERT: D 165 TYR cc_start: 0.8476 (p90) cc_final: 0.8068 (OUTLIER) REVERT: D 367 MET cc_start: 0.8004 (pmm) cc_final: 0.5780 (tpt) REVERT: D 397 GLU cc_start: 0.8353 (OUTLIER) cc_final: 0.7868 (mp0) REVERT: D 476 GLU cc_start: 0.8562 (OUTLIER) cc_final: 0.8062 (mm-30) REVERT: D 684 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7960 (mp0) REVERT: E 109 GLN cc_start: 0.8475 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: E 200 ASP cc_start: 0.8442 (m-30) cc_final: 0.8183 (m-30) REVERT: E 201 GLN cc_start: 0.7475 (mm-40) cc_final: 0.7272 (mm-40) REVERT: E 462 GLU cc_start: 0.8518 (OUTLIER) cc_final: 0.8121 (mm-30) REVERT: E 684 GLU cc_start: 0.8541 (OUTLIER) cc_final: 0.8095 (mp0) REVERT: E 707 ARG cc_start: 0.8639 (ttt180) cc_final: 0.8261 (ttp80) REVERT: F 134 ASN cc_start: 0.8852 (p0) cc_final: 0.8633 (p0) REVERT: F 174 LEU cc_start: 0.8287 (mm) cc_final: 0.7917 (mp) REVERT: F 182 LEU cc_start: 0.7990 (mm) cc_final: 0.7561 (tt) REVERT: F 185 LYS cc_start: 0.8341 (mmmm) cc_final: 0.7981 (tptp) REVERT: F 224 ASP cc_start: 0.7417 (t0) cc_final: 0.7104 (t70) REVERT: F 580 LYS cc_start: 0.7454 (mptt) cc_final: 0.6913 (mttm) REVERT: F 621 MET cc_start: 0.9119 (mtp) cc_final: 0.8908 (mtm) REVERT: G 122 ARG cc_start: 0.8302 (OUTLIER) cc_final: 0.7193 (ttp-170) REVERT: G 164 ASN cc_start: 0.8681 (p0) cc_final: 0.8290 (p0) REVERT: G 165 TYR cc_start: 0.7236 (p90) cc_final: 0.6849 (p90) REVERT: G 218 LYS cc_start: 0.9031 (mtpp) cc_final: 0.8583 (mmtt) REVERT: G 274 LEU cc_start: 0.8323 (OUTLIER) cc_final: 0.8018 (tm) REVERT: H 122 ARG cc_start: 0.7690 (tmt90) cc_final: 0.7402 (ttt180) REVERT: H 214 SER cc_start: 0.8734 (t) cc_final: 0.8338 (p) REVERT: H 243 ARG cc_start: 0.8105 (ttt90) cc_final: 0.7813 (ttp-170) REVERT: H 425 LYS cc_start: 0.7988 (mttt) cc_final: 0.7585 (mtmt) REVERT: H 523 GLU cc_start: 0.8348 (mp0) cc_final: 0.8057 (mp0) REVERT: H 580 LYS cc_start: 0.7758 (mmtt) cc_final: 0.7163 (mmpt) REVERT: H 594 MET cc_start: 0.8405 (mtp) cc_final: 0.8153 (ptm) REVERT: H 657 ARG cc_start: 0.8443 (mmm160) cc_final: 0.8141 (mmm-85) REVERT: H 667 ARG cc_start: 0.9082 (OUTLIER) cc_final: 0.8634 (tpt90) outliers start: 67 outliers final: 29 residues processed: 506 average time/residue: 0.6252 time to fit residues: 389.2638 Evaluate side-chains 494 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 451 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 136 ASP Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 113 GLU Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 221 SER Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 540 MET Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 203 VAL Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 476 GLU Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 395 GLN Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 415 optimal weight: 0.5980 chunk 36 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 396 optimal weight: 0.6980 chunk 241 optimal weight: 0.6980 chunk 50 optimal weight: 2.9990 chunk 456 optimal weight: 0.5980 chunk 138 optimal weight: 3.9990 chunk 367 optimal weight: 0.7980 chunk 355 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 611 GLN ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 168 ASN ** H 571 HIS ** 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 = 0.4009 r_free = 0.4009 target = 0.176719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.127254 restraints weight = 45600.517| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 2.31 r_work: 0.3104 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2982 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 37800 Z= 0.124 Angle : 0.643 13.656 51208 Z= 0.306 Chirality : 0.044 0.337 6060 Planarity : 0.003 0.044 6517 Dihedral : 5.008 54.043 5198 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.36 % Favored : 96.60 % Rotamer: Outliers : 1.42 % Allowed : 18.80 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.15 (0.12), residues: 4708 helix: 2.08 (0.11), residues: 2386 sheet: 0.72 (0.20), residues: 592 loop : -1.16 (0.13), residues: 1730 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 243 TYR 0.018 0.001 TYR D 165 PHE 0.015 0.001 PHE C 273 TRP 0.004 0.000 TRP E 631 HIS 0.002 0.000 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00277 (37797) covalent geometry : angle 0.64284 (51208) hydrogen bonds : bond 0.03454 ( 2100) hydrogen bonds : angle 4.19783 ( 6183) Misc. bond : bond 0.00218 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9416 Ramachandran restraints generated. 4708 Oldfield, 0 Emsley, 4708 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 469 time to evaluate : 1.482 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 ILE cc_start: 0.8848 (OUTLIER) cc_final: 0.8312 (mp) REVERT: A 190 LEU cc_start: 0.8230 (tp) cc_final: 0.7904 (tm) REVERT: A 218 LYS cc_start: 0.8962 (ttpt) cc_final: 0.8721 (mtmm) REVERT: A 367 MET cc_start: 0.6787 (pmm) cc_final: 0.3966 (tpt) REVERT: B 122 ARG cc_start: 0.8655 (OUTLIER) cc_final: 0.7338 (ttp80) REVERT: B 249 ASP cc_start: 0.8195 (m-30) cc_final: 0.7842 (m-30) REVERT: B 495 THR cc_start: 0.8289 (p) cc_final: 0.7661 (t) REVERT: B 667 ARG cc_start: 0.9098 (OUTLIER) cc_final: 0.8650 (tpt170) REVERT: B 707 ARG cc_start: 0.8519 (OUTLIER) cc_final: 0.8163 (ttt-90) REVERT: C 122 ARG cc_start: 0.8636 (OUTLIER) cc_final: 0.8161 (tpt-90) REVERT: C 164 ASN cc_start: 0.7970 (t0) cc_final: 0.7607 (t0) REVERT: C 189 LEU cc_start: 0.8528 (tp) cc_final: 0.8291 (tt) REVERT: C 462 GLU cc_start: 0.8602 (OUTLIER) cc_final: 0.8349 (mt-10) REVERT: D 89 GLU cc_start: 0.8186 (mm-30) cc_final: 0.7969 (mm-30) REVERT: D 367 MET cc_start: 0.8025 (pmm) cc_final: 0.5923 (tpt) REVERT: D 397 GLU cc_start: 0.8355 (OUTLIER) cc_final: 0.7892 (mp0) REVERT: D 684 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7910 (mp0) REVERT: E 109 GLN cc_start: 0.8468 (OUTLIER) cc_final: 0.7678 (pm20) REVERT: E 231 MET cc_start: 0.8566 (mmt) cc_final: 0.7992 (mmt) REVERT: E 462 GLU cc_start: 0.8475 (OUTLIER) cc_final: 0.8139 (mm-30) REVERT: E 684 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.8087 (mp0) REVERT: E 707 ARG cc_start: 0.8608 (ttt180) cc_final: 0.8250 (ttp80) REVERT: F 134 ASN cc_start: 0.8795 (p0) cc_final: 0.8581 (p0) REVERT: F 174 LEU cc_start: 0.8263 (mm) cc_final: 0.7916 (mp) REVERT: F 182 LEU cc_start: 0.7983 (mm) cc_final: 0.7605 (tt) REVERT: F 224 ASP cc_start: 0.7408 (t0) cc_final: 0.7115 (t70) REVERT: F 580 LYS cc_start: 0.7442 (mptt) cc_final: 0.6926 (mttm) REVERT: F 621 MET cc_start: 0.9125 (mtp) cc_final: 0.8921 (mtm) REVERT: G 122 ARG cc_start: 0.8286 (OUTLIER) cc_final: 0.7107 (ttp-170) REVERT: G 164 ASN cc_start: 0.8656 (p0) cc_final: 0.8235 (p0) REVERT: G 165 TYR cc_start: 0.7434 (p90) cc_final: 0.6924 (p90) REVERT: G 218 LYS cc_start: 0.9006 (mtpp) cc_final: 0.8585 (mmtt) REVERT: G 274 LEU cc_start: 0.8349 (OUTLIER) cc_final: 0.8053 (tm) REVERT: H 122 ARG cc_start: 0.7731 (tmt90) cc_final: 0.7433 (ttt180) REVERT: H 214 SER cc_start: 0.8715 (t) cc_final: 0.8343 (p) REVERT: H 243 ARG cc_start: 0.8081 (ttt90) cc_final: 0.7817 (ttp-170) REVERT: H 425 LYS cc_start: 0.8012 (mttt) cc_final: 0.7631 (mtmt) REVERT: H 523 GLU cc_start: 0.8308 (mp0) cc_final: 0.8078 (mp0) REVERT: H 580 LYS cc_start: 0.7715 (mmtt) cc_final: 0.7225 (mmpt) REVERT: H 594 MET cc_start: 0.8366 (mtp) cc_final: 0.8113 (ptm) REVERT: H 667 ARG cc_start: 0.9085 (OUTLIER) cc_final: 0.8627 (tpt90) outliers start: 58 outliers final: 32 residues processed: 501 average time/residue: 0.6306 time to fit residues: 389.4277 Evaluate side-chains 492 residues out of total 4075 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 446 time to evaluate : 1.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 LEU Chi-restraints excluded: chain A residue 103 ILE Chi-restraints excluded: chain A residue 157 LEU Chi-restraints excluded: chain A residue 164 ASN Chi-restraints excluded: chain A residue 189 LEU Chi-restraints excluded: chain A residue 214 SER Chi-restraints excluded: chain A residue 397 GLU Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 680 MET Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 120 ILE Chi-restraints excluded: chain B residue 122 ARG Chi-restraints excluded: chain B residue 191 VAL Chi-restraints excluded: chain B residue 216 LEU Chi-restraints excluded: chain B residue 274 LEU Chi-restraints excluded: chain B residue 667 ARG Chi-restraints excluded: chain B residue 707 ARG Chi-restraints excluded: chain B residue 716 SER Chi-restraints excluded: chain C residue 92 LEU Chi-restraints excluded: chain C residue 122 ARG Chi-restraints excluded: chain C residue 245 SER Chi-restraints excluded: chain C residue 432 ILE Chi-restraints excluded: chain C residue 462 GLU Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 63 ILE Chi-restraints excluded: chain D residue 165 TYR Chi-restraints excluded: chain D residue 183 ASN Chi-restraints excluded: chain D residue 397 GLU Chi-restraints excluded: chain D residue 428 ILE Chi-restraints excluded: chain D residue 684 GLU Chi-restraints excluded: chain E residue 109 GLN Chi-restraints excluded: chain E residue 164 ASN Chi-restraints excluded: chain E residue 462 GLU Chi-restraints excluded: chain E residue 684 GLU Chi-restraints excluded: chain F residue 38 SER Chi-restraints excluded: chain F residue 403 SER Chi-restraints excluded: chain G residue 122 ARG Chi-restraints excluded: chain G residue 237 THR Chi-restraints excluded: chain G residue 274 LEU Chi-restraints excluded: chain G residue 395 GLN Chi-restraints excluded: chain H residue 235 THR Chi-restraints excluded: chain H residue 432 ILE Chi-restraints excluded: chain H residue 464 ILE Chi-restraints excluded: chain H residue 505 LEU Chi-restraints excluded: chain H residue 543 ILE Chi-restraints excluded: chain H residue 667 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 474 random chunks: chunk 0 optimal weight: 10.0000 chunk 187 optimal weight: 0.9980 chunk 146 optimal weight: 0.4980 chunk 283 optimal weight: 0.0270 chunk 90 optimal weight: 6.9990 chunk 413 optimal weight: 2.9990 chunk 47 optimal weight: 0.8980 chunk 375 optimal weight: 0.8980 chunk 100 optimal weight: 0.0770 chunk 13 optimal weight: 9.9990 chunk 453 optimal weight: 0.8980 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 396 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 183 ASN ** D 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 164 ASN E 206 GLN ** E 571 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 259 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 173 GLN H 175 ASN H 671 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4017 r_free = 0.4017 target = 0.177457 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.129028 restraints weight = 45635.815| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 2.21 r_work: 0.3129 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3005 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.3005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8664 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 37800 Z= 0.116 Angle : 0.640 15.924 51208 Z= 0.304 Chirality : 0.044 0.336 6060 Planarity : 0.003 0.046 6517 Dihedral : 4.892 52.337 5198 Min Nonbonded Distance : 2.022 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.04 % Allowed : 3.38 % Favored : 96.58 % Rotamer: Outliers : 1.37 % Allowed : 19.02 % Favored : 79.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.23 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.20 (0.12), residues: 4708 helix: 2.14 (0.11), residues: 2390 sheet: 0.76 (0.20), residues: 591 loop : -1.19 (0.13), residues: 1727 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 243 TYR 0.023 0.001 TYR D 141 PHE 0.015 0.001 PHE C 273 TRP 0.004 0.000 TRP E 631 HIS 0.002 0.000 HIS H 710 Details of bonding type rmsd covalent geometry : bond 0.00256 (37797) covalent geometry : angle 0.64035 (51208) hydrogen bonds : bond 0.03360 ( 2100) hydrogen bonds : angle 4.15329 ( 6183) Misc. bond : bond 0.00205 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15413.02 seconds wall clock time: 262 minutes 16.42 seconds (15736.42 seconds total)