Starting phenix.real_space_refine on Sat Feb 7 09:30:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uft_26480/02_2026/7uft_26480.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uft_26480/02_2026/7uft_26480.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7uft_26480/02_2026/7uft_26480.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uft_26480/02_2026/7uft_26480.map" model { file = "/net/cci-nas-00/data/ceres_data/7uft_26480/02_2026/7uft_26480.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uft_26480/02_2026/7uft_26480.cif" } resolution = 2.9 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= 0.003 sd= 1.032 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 4 6.06 5 S 176 5.16 5 C 20384 2.51 5 N 5592 2.21 5 O 6168 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 92 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32324 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 8080 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1032, 8080 Classifications: {'peptide': 1032} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 56, 'TRANS': 975} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Restraints were copied for chains: B, C, D Time building chain proxies: 9.77, per 1000 atoms: 0.30 Number of scatterers: 32324 At special positions: 0 Unit cell: (97.15, 144.05, 169.51, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 4 29.99 S 176 16.00 O 6168 8.00 N 5592 7.00 C 20384 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=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1101 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 272 " pdb="ZN ZN A1101 " - pdb=" NE2 HIS A 594 " pdb=" ZN B1101 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 272 " pdb="ZN ZN B1101 " - pdb=" NE2 HIS B 594 " pdb=" ZN C1101 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 272 " pdb="ZN ZN C1101 " - pdb=" NE2 HIS C 594 " pdb=" ZN D1101 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 272 " pdb="ZN ZN D1101 " - pdb=" NE2 HIS D 594 " 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7640 Finding SS restraints... Secondary structure from input PDB file: 88 helices and 48 sheets defined 29.1% alpha, 21.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 3 through 20 removed outlier: 3.552A pdb=" N ASP A 10 " --> pdb=" O ASN A 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG A 11 " --> pdb=" O ARG A 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL A 20 " --> pdb=" O MET A 16 " (cutoff:3.500A) Processing helix chain 'A' and resid 21 through 23 No H-bonds generated for 'chain 'A' and resid 21 through 23' Processing helix chain 'A' and resid 44 through 54 removed outlier: 3.574A pdb=" N THR A 50 " --> pdb=" O ALA A 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG A 51 " --> pdb=" O ALA A 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER A 54 " --> pdb=" O THR A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 194 through 211 removed outlier: 3.563A pdb=" N SER A 210 " --> pdb=" O VAL A 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU A 211 " --> pdb=" O VAL A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 233 removed outlier: 4.203A pdb=" N TRP A 222 " --> pdb=" O ASP A 218 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N ALA A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN A 229 " --> pdb=" O ALA A 225 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 250 removed outlier: 4.078A pdb=" N LEU A 245 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS A 248 " --> pdb=" O ALA A 244 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ALA A 249 " --> pdb=" O LEU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 297 removed outlier: 3.839A pdb=" N THR A 284 " --> pdb=" O PRO A 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU A 285 " --> pdb=" O VAL A 281 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG A 286 " --> pdb=" O ARG A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 311 through 322 removed outlier: 3.561A pdb=" N PHE A 315 " --> pdb=" O ALA A 311 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 336 removed outlier: 3.672A pdb=" N GLU A 327 " --> pdb=" O PRO A 323 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG A 328 " --> pdb=" O ASP A 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU A 335 " --> pdb=" O ALA A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 354 through 372 Processing helix chain 'A' and resid 391 through 399 Processing helix chain 'A' and resid 407 through 412 removed outlier: 3.980A pdb=" N ASN A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 447 through 458 Processing helix chain 'A' and resid 481 through 487 removed outlier: 3.676A pdb=" N THR A 485 " --> pdb=" O ILE A 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET A 486 " --> pdb=" O ARG A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 504 through 521 Processing helix chain 'A' and resid 536 through 541 removed outlier: 3.593A pdb=" N THR A 539 " --> pdb=" O HIS A 536 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU A 540 " --> pdb=" O ARG A 537 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 571 removed outlier: 3.536A pdb=" N LYS A 547 " --> pdb=" O GLN A 543 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG A 558 " --> pdb=" O GLU A 554 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N THR A 559 " --> pdb=" O SER A 555 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 591 removed outlier: 3.504A pdb=" N SER A 591 " --> pdb=" O THR A 587 " (cutoff:3.500A) Processing helix chain 'A' and resid 602 through 635 removed outlier: 3.587A pdb=" N HIS A 606 " --> pdb=" O ILE A 602 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP A 622 " --> pdb=" O LYS A 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG A 625 " --> pdb=" O SER A 621 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA A 630 " --> pdb=" O ASP A 626 " (cutoff:3.500A) Processing helix chain 'A' and resid 734 through 739 removed outlier: 3.558A pdb=" N CYS A 738 " --> pdb=" O ASP A 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA A 739 " --> pdb=" O ALA A 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 734 through 739' Processing helix chain 'A' and resid 831 through 836 removed outlier: 3.963A pdb=" N PHE A 836 " --> pdb=" O GLU A 833 " (cutoff:3.500A) Processing helix chain 'A' and resid 912 through 924 Processing helix chain 'B' and resid 4 through 20 removed outlier: 3.551A pdb=" N ASP B 10 " --> pdb=" O ASN B 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG B 11 " --> pdb=" O ARG B 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL B 20 " --> pdb=" O MET B 16 " (cutoff:3.500A) Processing helix chain 'B' and resid 21 through 23 No H-bonds generated for 'chain 'B' and resid 21 through 23' Processing helix chain 'B' and resid 44 through 54 removed outlier: 3.574A pdb=" N THR B 50 " --> pdb=" O ALA B 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG B 51 " --> pdb=" O ALA B 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER B 54 " --> pdb=" O THR B 50 " (cutoff:3.500A) Processing helix chain 'B' and resid 194 through 211 removed outlier: 3.564A pdb=" N SER B 210 " --> pdb=" O VAL B 206 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 211 " --> pdb=" O VAL B 207 " (cutoff:3.500A) Processing helix chain 'B' and resid 218 through 233 removed outlier: 4.204A pdb=" N TRP B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA B 227 " --> pdb=" O LYS B 223 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N GLN B 229 " --> pdb=" O ALA B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 250 removed outlier: 4.078A pdb=" N LEU B 245 " --> pdb=" O ASN B 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS B 248 " --> pdb=" O ALA B 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA B 249 " --> pdb=" O LEU B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 297 removed outlier: 3.838A pdb=" N THR B 284 " --> pdb=" O PRO B 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU B 285 " --> pdb=" O VAL B 281 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG B 286 " --> pdb=" O ARG B 282 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 322 removed outlier: 3.560A pdb=" N PHE B 315 " --> pdb=" O ALA B 311 " (cutoff:3.500A) Processing helix chain 'B' and resid 322 through 336 removed outlier: 3.673A pdb=" N GLU B 327 " --> pdb=" O PRO B 323 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG B 328 " --> pdb=" O ASP B 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL B 329 " --> pdb=" O LEU B 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU B 335 " --> pdb=" O ALA B 331 " (cutoff:3.500A) Processing helix chain 'B' and resid 354 through 372 Processing helix chain 'B' and resid 391 through 399 Processing helix chain 'B' and resid 407 through 412 removed outlier: 3.980A pdb=" N ASN B 412 " --> pdb=" O LEU B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 447 through 458 Processing helix chain 'B' and resid 481 through 487 removed outlier: 3.677A pdb=" N THR B 485 " --> pdb=" O ILE B 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET B 486 " --> pdb=" O ARG B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 521 Processing helix chain 'B' and resid 536 through 541 removed outlier: 3.592A pdb=" N THR B 539 " --> pdb=" O HIS B 536 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU B 540 " --> pdb=" O ARG B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 571 removed outlier: 3.535A pdb=" N LYS B 547 " --> pdb=" O GLN B 543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG B 558 " --> pdb=" O GLU B 554 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR B 559 " --> pdb=" O SER B 555 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 591 removed outlier: 3.503A pdb=" N SER B 591 " --> pdb=" O THR B 587 " (cutoff:3.500A) Processing helix chain 'B' and resid 602 through 635 removed outlier: 3.588A pdb=" N HIS B 606 " --> pdb=" O ILE B 602 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP B 622 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) removed outlier: 4.930A pdb=" N ARG B 625 " --> pdb=" O SER B 621 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA B 630 " --> pdb=" O ASP B 626 " (cutoff:3.500A) Processing helix chain 'B' and resid 734 through 739 removed outlier: 3.559A pdb=" N CYS B 738 " --> pdb=" O ASP B 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA B 739 " --> pdb=" O ALA B 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 734 through 739' Processing helix chain 'B' and resid 831 through 836 removed outlier: 3.964A pdb=" N PHE B 836 " --> pdb=" O GLU B 833 " (cutoff:3.500A) Processing helix chain 'B' and resid 912 through 924 Processing helix chain 'C' and resid 4 through 20 removed outlier: 3.551A pdb=" N ASP C 10 " --> pdb=" O ASN C 6 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ARG C 11 " --> pdb=" O ARG C 7 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 20 " --> pdb=" O MET C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 23 No H-bonds generated for 'chain 'C' and resid 21 through 23' Processing helix chain 'C' and resid 44 through 54 removed outlier: 3.573A pdb=" N THR C 50 " --> pdb=" O ALA C 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG C 51 " --> pdb=" O ALA C 47 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N SER C 54 " --> pdb=" O THR C 50 " (cutoff:3.500A) Processing helix chain 'C' and resid 194 through 211 removed outlier: 3.564A pdb=" N SER C 210 " --> pdb=" O VAL C 206 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU C 211 " --> pdb=" O VAL C 207 " (cutoff:3.500A) Processing helix chain 'C' and resid 218 through 233 removed outlier: 4.204A pdb=" N TRP C 222 " --> pdb=" O ASP C 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA C 227 " --> pdb=" O LYS C 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN C 229 " --> pdb=" O ALA C 225 " (cutoff:3.500A) Processing helix chain 'C' and resid 241 through 250 removed outlier: 4.078A pdb=" N LEU C 245 " --> pdb=" O ASN C 241 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS C 248 " --> pdb=" O ALA C 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA C 249 " --> pdb=" O LEU C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 280 through 297 removed outlier: 3.839A pdb=" N THR C 284 " --> pdb=" O PRO C 280 " (cutoff:3.500A) removed outlier: 4.267A pdb=" N GLU C 285 " --> pdb=" O VAL C 281 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N ARG C 286 " --> pdb=" O ARG C 282 " (cutoff:3.500A) Processing helix chain 'C' and resid 311 through 322 removed outlier: 3.561A pdb=" N PHE C 315 " --> pdb=" O ALA C 311 " (cutoff:3.500A) Processing helix chain 'C' and resid 322 through 336 removed outlier: 3.672A pdb=" N GLU C 327 " --> pdb=" O PRO C 323 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ARG C 328 " --> pdb=" O ASP C 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL C 329 " --> pdb=" O LEU C 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU C 335 " --> pdb=" O ALA C 331 " (cutoff:3.500A) Processing helix chain 'C' and resid 354 through 372 Processing helix chain 'C' and resid 391 through 399 Processing helix chain 'C' and resid 407 through 412 removed outlier: 3.981A pdb=" N ASN C 412 " --> pdb=" O LEU C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 447 through 458 Processing helix chain 'C' and resid 481 through 487 removed outlier: 3.676A pdb=" N THR C 485 " --> pdb=" O ILE C 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET C 486 " --> pdb=" O ARG C 482 " (cutoff:3.500A) Processing helix chain 'C' and resid 504 through 521 Processing helix chain 'C' and resid 536 through 541 removed outlier: 3.592A pdb=" N THR C 539 " --> pdb=" O HIS C 536 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU C 540 " --> pdb=" O ARG C 537 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 571 removed outlier: 3.535A pdb=" N LYS C 547 " --> pdb=" O GLN C 543 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ARG C 558 " --> pdb=" O GLU C 554 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR C 559 " --> pdb=" O SER C 555 " (cutoff:3.500A) Processing helix chain 'C' and resid 577 through 591 removed outlier: 3.503A pdb=" N SER C 591 " --> pdb=" O THR C 587 " (cutoff:3.500A) Processing helix chain 'C' and resid 602 through 635 removed outlier: 3.587A pdb=" N HIS C 606 " --> pdb=" O ILE C 602 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ASP C 622 " --> pdb=" O LYS C 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N ARG C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ALA C 630 " --> pdb=" O ASP C 626 " (cutoff:3.500A) Processing helix chain 'C' and resid 734 through 739 removed outlier: 3.558A pdb=" N CYS C 738 " --> pdb=" O ASP C 734 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N ALA C 739 " --> pdb=" O ALA C 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 734 through 739' Processing helix chain 'C' and resid 831 through 836 removed outlier: 3.964A pdb=" N PHE C 836 " --> pdb=" O GLU C 833 " (cutoff:3.500A) Processing helix chain 'C' and resid 912 through 924 Processing helix chain 'D' and resid 4 through 20 removed outlier: 3.552A pdb=" N ASP D 10 " --> pdb=" O ASN D 6 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ARG D 11 " --> pdb=" O ARG D 7 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL D 20 " --> pdb=" O MET D 16 " (cutoff:3.500A) Processing helix chain 'D' and resid 21 through 23 No H-bonds generated for 'chain 'D' and resid 21 through 23' Processing helix chain 'D' and resid 44 through 54 removed outlier: 3.573A pdb=" N THR D 50 " --> pdb=" O ALA D 46 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N ARG D 51 " --> pdb=" O ALA D 47 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER D 54 " --> pdb=" O THR D 50 " (cutoff:3.500A) Processing helix chain 'D' and resid 194 through 211 removed outlier: 3.565A pdb=" N SER D 210 " --> pdb=" O VAL D 206 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N LEU D 211 " --> pdb=" O VAL D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 218 through 233 removed outlier: 4.204A pdb=" N TRP D 222 " --> pdb=" O ASP D 218 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ALA D 227 " --> pdb=" O LYS D 223 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN D 229 " --> pdb=" O ALA D 225 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 250 removed outlier: 4.077A pdb=" N LEU D 245 " --> pdb=" O ASN D 241 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N LYS D 248 " --> pdb=" O ALA D 244 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ALA D 249 " --> pdb=" O LEU D 245 " (cutoff:3.500A) Processing helix chain 'D' and resid 280 through 297 removed outlier: 3.839A pdb=" N THR D 284 " --> pdb=" O PRO D 280 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N GLU D 285 " --> pdb=" O VAL D 281 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG D 286 " --> pdb=" O ARG D 282 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 322 removed outlier: 3.560A pdb=" N PHE D 315 " --> pdb=" O ALA D 311 " (cutoff:3.500A) Processing helix chain 'D' and resid 322 through 336 removed outlier: 3.672A pdb=" N GLU D 327 " --> pdb=" O PRO D 323 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N ARG D 328 " --> pdb=" O ASP D 324 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N VAL D 329 " --> pdb=" O LEU D 325 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 354 through 372 Processing helix chain 'D' and resid 391 through 399 Processing helix chain 'D' and resid 407 through 412 removed outlier: 3.980A pdb=" N ASN D 412 " --> pdb=" O LEU D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 447 through 458 Processing helix chain 'D' and resid 481 through 487 removed outlier: 3.676A pdb=" N THR D 485 " --> pdb=" O ILE D 481 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N MET D 486 " --> pdb=" O ARG D 482 " (cutoff:3.500A) Processing helix chain 'D' and resid 504 through 521 Processing helix chain 'D' and resid 536 through 541 removed outlier: 3.592A pdb=" N THR D 539 " --> pdb=" O HIS D 536 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LEU D 540 " --> pdb=" O ARG D 537 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 571 removed outlier: 3.535A pdb=" N LYS D 547 " --> pdb=" O GLN D 543 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ARG D 558 " --> pdb=" O GLU D 554 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N THR D 559 " --> pdb=" O SER D 555 " (cutoff:3.500A) Processing helix chain 'D' and resid 577 through 591 removed outlier: 3.504A pdb=" N SER D 591 " --> pdb=" O THR D 587 " (cutoff:3.500A) Processing helix chain 'D' and resid 602 through 635 removed outlier: 3.589A pdb=" N HIS D 606 " --> pdb=" O ILE D 602 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N ASP D 622 " --> pdb=" O LYS D 618 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N ARG D 625 " --> pdb=" O SER D 621 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ALA D 630 " --> pdb=" O ASP D 626 " (cutoff:3.500A) Processing helix chain 'D' and resid 734 through 739 removed outlier: 3.559A pdb=" N CYS D 738 " --> pdb=" O ASP D 734 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ALA D 739 " --> pdb=" O ALA D 735 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 734 through 739' Processing helix chain 'D' and resid 831 through 836 removed outlier: 3.963A pdb=" N PHE D 836 " --> pdb=" O GLU D 833 " (cutoff:3.500A) Processing helix chain 'D' and resid 912 through 924 Processing sheet with id=AA1, first strand: chain 'A' and resid 25 through 30 removed outlier: 6.963A pdb=" N ILE A 190 " --> pdb=" O LEU A 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA A 92 " --> pdb=" O LEU A 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU A 95 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY A 81 " --> pdb=" O PHE A 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE A 151 " --> pdb=" O GLY A 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA A 112 " --> pdb=" O ALA A 124 " (cutoff:3.500A) removed outlier: 5.091A pdb=" N ALA A 124 " --> pdb=" O ALA A 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA A 114 " --> pdb=" O ILE A 122 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 467 through 471 removed outlier: 6.341A pdb=" N THR A 264 " --> pdb=" O GLY A 467 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N LEU A 469 " --> pdb=" O THR A 264 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR A 266 " --> pdb=" O LEU A 469 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE A 471 " --> pdb=" O THR A 266 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET A 268 " --> pdb=" O PHE A 471 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 307 through 309 removed outlier: 6.453A pdb=" N TYR A 307 " --> pdb=" O ILE A 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 379 through 381 removed outlier: 6.682A pdb=" N ILE A 380 " --> pdb=" O LEU A 405 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 644 through 646 removed outlier: 3.662A pdb=" N ALA A 658 " --> pdb=" O ARG A 645 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 668 through 669 removed outlier: 3.763A pdb=" N SER A 696 " --> pdb=" O HIS A 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG A 704 " --> pdb=" O ASP A 699 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 740 through 741 removed outlier: 3.632A pdb=" N THR A 740 " --> pdb=" O ILE A 718 " (cutoff:3.500A) removed outlier: 7.048A pdb=" N LYS A 797 " --> pdb=" O ALA A 886 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA A 886 " --> pdb=" O LYS A 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU A 799 " --> pdb=" O LEU A 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY A 862 " --> pdb=" O SER A 883 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 746 through 752 removed outlier: 3.749A pdb=" N HIS A 746 " --> pdb=" O LYS A 763 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL A 761 " --> pdb=" O VAL A 748 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ILE A 750 " --> pdb=" O VAL A 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL A 759 " --> pdb=" O ILE A 750 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP A 769 " --> pdb=" O TYR A 766 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE A 843 " --> pdb=" O GLU A 815 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU A 815 " --> pdb=" O PHE A 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS A 847 " --> pdb=" O ARG A 811 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG A 811 " --> pdb=" O HIS A 847 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 937 through 943 removed outlier: 3.615A pdb=" N MET A 976 " --> pdb=" O GLU A 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS A 974 " --> pdb=" O ILE A 942 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 946 through 948 Processing sheet with id=AB3, first strand: chain 'A' and resid 946 through 948 Processing sheet with id=AB4, first strand: chain 'B' and resid 25 through 30 removed outlier: 6.963A pdb=" N ILE B 190 " --> pdb=" O LEU B 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA B 92 " --> pdb=" O LEU B 193 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU B 95 " --> pdb=" O PRO B 133 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY B 81 " --> pdb=" O PHE B 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE B 151 " --> pdb=" O GLY B 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA B 112 " --> pdb=" O ALA B 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA B 124 " --> pdb=" O ALA B 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA B 114 " --> pdb=" O ILE B 122 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 467 through 471 removed outlier: 6.341A pdb=" N THR B 264 " --> pdb=" O GLY B 467 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU B 469 " --> pdb=" O THR B 264 " (cutoff:3.500A) removed outlier: 5.784A pdb=" N THR B 266 " --> pdb=" O LEU B 469 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE B 471 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET B 268 " --> pdb=" O PHE B 471 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 307 through 309 removed outlier: 6.452A pdb=" N TYR B 307 " --> pdb=" O ILE B 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'B' and resid 379 through 381 removed outlier: 6.681A pdb=" N ILE B 380 " --> pdb=" O LEU B 405 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 644 through 646 removed outlier: 3.661A pdb=" N ALA B 658 " --> pdb=" O ARG B 645 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 668 through 669 removed outlier: 3.762A pdb=" N SER B 696 " --> pdb=" O HIS B 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG B 704 " --> pdb=" O ASP B 699 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 740 through 741 removed outlier: 3.631A pdb=" N THR B 740 " --> pdb=" O ILE B 718 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS B 797 " --> pdb=" O ALA B 886 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N ALA B 886 " --> pdb=" O LYS B 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU B 799 " --> pdb=" O LEU B 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY B 862 " --> pdb=" O SER B 883 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 746 through 752 removed outlier: 3.749A pdb=" N HIS B 746 " --> pdb=" O LYS B 763 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL B 761 " --> pdb=" O VAL B 748 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE B 750 " --> pdb=" O VAL B 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL B 759 " --> pdb=" O ILE B 750 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP B 769 " --> pdb=" O TYR B 766 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE B 843 " --> pdb=" O GLU B 815 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU B 815 " --> pdb=" O PHE B 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS B 847 " --> pdb=" O ARG B 811 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG B 811 " --> pdb=" O HIS B 847 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 937 through 943 removed outlier: 3.615A pdb=" N MET B 976 " --> pdb=" O GLU B 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS B 974 " --> pdb=" O ILE B 942 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 946 through 948 Processing sheet with id=AC6, first strand: chain 'B' and resid 946 through 948 Processing sheet with id=AC7, first strand: chain 'C' and resid 25 through 30 removed outlier: 6.963A pdb=" N ILE C 190 " --> pdb=" O LEU C 28 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ALA C 92 " --> pdb=" O LEU C 193 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LEU C 95 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'C' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY C 81 " --> pdb=" O PHE C 151 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N PHE C 151 " --> pdb=" O GLY C 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA C 112 " --> pdb=" O ALA C 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA C 124 " --> pdb=" O ALA C 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA C 114 " --> pdb=" O ILE C 122 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 467 through 471 removed outlier: 6.340A pdb=" N THR C 264 " --> pdb=" O GLY C 467 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU C 469 " --> pdb=" O THR C 264 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR C 266 " --> pdb=" O LEU C 469 " (cutoff:3.500A) removed outlier: 7.504A pdb=" N PHE C 471 " --> pdb=" O THR C 266 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N MET C 268 " --> pdb=" O PHE C 471 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 307 through 309 removed outlier: 6.452A pdb=" N TYR C 307 " --> pdb=" O ILE C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AD1 Processing sheet with id=AD2, first strand: chain 'C' and resid 379 through 381 removed outlier: 6.681A pdb=" N ILE C 380 " --> pdb=" O LEU C 405 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 644 through 646 removed outlier: 3.661A pdb=" N ALA C 658 " --> pdb=" O ARG C 645 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 668 through 669 removed outlier: 3.762A pdb=" N SER C 696 " --> pdb=" O HIS C 687 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ARG C 704 " --> pdb=" O ASP C 699 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 740 through 741 removed outlier: 3.631A pdb=" N THR C 740 " --> pdb=" O ILE C 718 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N LYS C 797 " --> pdb=" O ALA C 886 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA C 886 " --> pdb=" O LYS C 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU C 799 " --> pdb=" O LEU C 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY C 862 " --> pdb=" O SER C 883 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 746 through 752 removed outlier: 3.750A pdb=" N HIS C 746 " --> pdb=" O LYS C 763 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL C 761 " --> pdb=" O VAL C 748 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N ILE C 750 " --> pdb=" O VAL C 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL C 759 " --> pdb=" O ILE C 750 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ASP C 769 " --> pdb=" O TYR C 766 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N PHE C 843 " --> pdb=" O GLU C 815 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N GLU C 815 " --> pdb=" O PHE C 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS C 847 " --> pdb=" O ARG C 811 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ARG C 811 " --> pdb=" O HIS C 847 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 937 through 943 removed outlier: 3.616A pdb=" N MET C 976 " --> pdb=" O GLU C 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS C 974 " --> pdb=" O ILE C 942 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 946 through 948 Processing sheet with id=AD9, first strand: chain 'C' and resid 946 through 948 Processing sheet with id=AE1, first strand: chain 'D' and resid 25 through 30 removed outlier: 6.964A pdb=" N ILE D 190 " --> pdb=" O LEU D 28 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ALA D 92 " --> pdb=" O LEU D 193 " (cutoff:3.500A) removed outlier: 6.087A pdb=" N LEU D 95 " --> pdb=" O PRO D 133 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 32 through 38 removed outlier: 3.656A pdb=" N GLY D 81 " --> pdb=" O PHE D 151 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE D 151 " --> pdb=" O GLY D 81 " (cutoff:3.500A) removed outlier: 6.916A pdb=" N ALA D 112 " --> pdb=" O ALA D 124 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N ALA D 124 " --> pdb=" O ALA D 112 " (cutoff:3.500A) removed outlier: 7.123A pdb=" N ALA D 114 " --> pdb=" O ILE D 122 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 467 through 471 removed outlier: 6.341A pdb=" N THR D 264 " --> pdb=" O GLY D 467 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N LEU D 469 " --> pdb=" O THR D 264 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N THR D 266 " --> pdb=" O LEU D 469 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N PHE D 471 " --> pdb=" O THR D 266 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N MET D 268 " --> pdb=" O PHE D 471 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 307 through 309 removed outlier: 6.452A pdb=" N TYR D 307 " --> pdb=" O ILE D 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AE4 Processing sheet with id=AE5, first strand: chain 'D' and resid 379 through 381 removed outlier: 6.681A pdb=" N ILE D 380 " --> pdb=" O LEU D 405 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 644 through 646 removed outlier: 3.661A pdb=" N ALA D 658 " --> pdb=" O ARG D 645 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 668 through 669 removed outlier: 3.763A pdb=" N SER D 696 " --> pdb=" O HIS D 687 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ARG D 704 " --> pdb=" O ASP D 699 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 740 through 741 removed outlier: 3.631A pdb=" N THR D 740 " --> pdb=" O ILE D 718 " (cutoff:3.500A) removed outlier: 7.049A pdb=" N LYS D 797 " --> pdb=" O ALA D 886 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA D 886 " --> pdb=" O LYS D 797 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU D 799 " --> pdb=" O LEU D 884 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N GLY D 862 " --> pdb=" O SER D 883 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 746 through 752 removed outlier: 3.749A pdb=" N HIS D 746 " --> pdb=" O LYS D 763 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N VAL D 761 " --> pdb=" O VAL D 748 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE D 750 " --> pdb=" O VAL D 759 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N VAL D 759 " --> pdb=" O ILE D 750 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ASP D 769 " --> pdb=" O TYR D 766 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N PHE D 843 " --> pdb=" O GLU D 815 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N GLU D 815 " --> pdb=" O PHE D 843 " (cutoff:3.500A) removed outlier: 5.233A pdb=" N HIS D 847 " --> pdb=" O ARG D 811 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N ARG D 811 " --> pdb=" O HIS D 847 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 937 through 943 removed outlier: 3.615A pdb=" N MET D 976 " --> pdb=" O GLU D 940 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N LYS D 974 " --> pdb=" O ILE D 942 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 946 through 948 Processing sheet with id=AF3, first strand: chain 'D' and resid 946 through 948 1265 hydrogen bonds defined for protein. 3555 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: 8.87 Time building geometry restraints manager: 3.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 10872 1.34 - 1.46: 7494 1.46 - 1.58: 14446 1.58 - 1.70: 0 1.70 - 1.82: 308 Bond restraints: 33120 Sorted by residual: bond pdb=" C SER D 621 " pdb=" N ASP D 622 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.52e+00 bond pdb=" C SER A 621 " pdb=" N ASP A 622 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.48e+00 bond pdb=" C SER C 621 " pdb=" N ASP C 622 " ideal model delta sigma weight residual 1.332 1.303 0.030 1.40e-02 5.10e+03 4.48e+00 bond pdb=" C SER B 621 " pdb=" N ASP B 622 " ideal model delta sigma weight residual 1.332 1.303 0.029 1.40e-02 5.10e+03 4.44e+00 bond pdb=" C ASP A 216 " pdb=" N ALA A 217 " ideal model delta sigma weight residual 1.332 1.307 0.026 1.40e-02 5.10e+03 3.42e+00 ... (remaining 33115 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.49: 42412 1.49 - 2.98: 2273 2.98 - 4.46: 285 4.46 - 5.95: 30 5.95 - 7.44: 20 Bond angle restraints: 45020 Sorted by residual: angle pdb=" N ILE A 24 " pdb=" CA ILE A 24 " pdb=" C ILE A 24 " ideal model delta sigma weight residual 111.62 108.33 3.29 7.90e-01 1.60e+00 1.73e+01 angle pdb=" N ILE B 24 " pdb=" CA ILE B 24 " pdb=" C ILE B 24 " ideal model delta sigma weight residual 111.62 108.35 3.27 7.90e-01 1.60e+00 1.71e+01 angle pdb=" N ILE C 24 " pdb=" CA ILE C 24 " pdb=" C ILE C 24 " ideal model delta sigma weight residual 111.62 108.37 3.25 7.90e-01 1.60e+00 1.69e+01 angle pdb=" N ILE D 24 " pdb=" CA ILE D 24 " pdb=" C ILE D 24 " ideal model delta sigma weight residual 111.62 108.37 3.25 7.90e-01 1.60e+00 1.69e+01 angle pdb=" N ASP C 475 " pdb=" CA ASP C 475 " pdb=" CB ASP C 475 " ideal model delta sigma weight residual 114.17 109.77 4.40 1.14e+00 7.69e-01 1.49e+01 ... (remaining 45015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.69: 17703 17.69 - 35.38: 1701 35.38 - 53.07: 276 53.07 - 70.75: 56 70.75 - 88.44: 20 Dihedral angle restraints: 19756 sinusoidal: 7872 harmonic: 11884 Sorted by residual: dihedral pdb=" CA SER C 186 " pdb=" C SER C 186 " pdb=" N SER C 187 " pdb=" CA SER C 187 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA SER A 186 " pdb=" C SER A 186 " pdb=" N SER A 187 " pdb=" CA SER A 187 " ideal model delta harmonic sigma weight residual 180.00 151.07 28.93 0 5.00e+00 4.00e-02 3.35e+01 dihedral pdb=" CA SER D 186 " pdb=" C SER D 186 " pdb=" N SER D 187 " pdb=" CA SER D 187 " ideal model delta harmonic sigma weight residual 180.00 151.13 28.87 0 5.00e+00 4.00e-02 3.33e+01 ... (remaining 19753 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 2444 0.031 - 0.062: 1493 0.062 - 0.093: 544 0.093 - 0.124: 297 0.124 - 0.155: 78 Chirality restraints: 4856 Sorted by residual: chirality pdb=" CA ILE A 750 " pdb=" N ILE A 750 " pdb=" C ILE A 750 " pdb=" CB ILE A 750 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE B 190 " pdb=" N ILE B 190 " pdb=" C ILE B 190 " pdb=" CB ILE B 190 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.83e-01 chirality pdb=" CA ASP A 465 " pdb=" N ASP A 465 " pdb=" C ASP A 465 " pdb=" CB ASP A 465 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.76e-01 ... (remaining 4853 not shown) Planarity restraints: 5900 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 198 " 0.023 2.00e-02 2.50e+03 2.14e-02 7.98e+00 pdb=" CG PHE A 198 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE A 198 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE A 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 198 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE A 198 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE C 198 " -0.022 2.00e-02 2.50e+03 2.12e-02 7.84e+00 pdb=" CG PHE C 198 " 0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE C 198 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 PHE C 198 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE C 198 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE C 198 " -0.013 2.00e-02 2.50e+03 pdb=" CZ PHE C 198 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 198 " 0.023 2.00e-02 2.50e+03 2.11e-02 7.80e+00 pdb=" CG PHE B 198 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 PHE B 198 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE B 198 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 198 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 198 " 0.013 2.00e-02 2.50e+03 pdb=" CZ PHE B 198 " -0.000 2.00e-02 2.50e+03 ... (remaining 5897 not shown) Histogram of nonbonded interaction distances: 1.91 - 2.51: 192 2.51 - 3.11: 23752 3.11 - 3.70: 46810 3.70 - 4.30: 70104 4.30 - 4.90: 121105 Nonbonded interactions: 261963 Sorted by model distance: nonbonded pdb=" OD1 ASP C 274 " pdb="ZN ZN C1101 " model vdw 1.910 2.230 nonbonded pdb=" OD1 ASP D 274 " pdb="ZN ZN D1101 " model vdw 1.911 2.230 nonbonded pdb=" OD1 ASP B 274 " pdb="ZN ZN B1101 " model vdw 1.911 2.230 nonbonded pdb=" OD2 ASP C 384 " pdb="ZN ZN C1101 " model vdw 1.911 2.230 nonbonded pdb=" OD2 ASP A 384 " pdb="ZN ZN A1101 " model vdw 1.911 2.230 ... (remaining 261958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.09 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' } 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: 18.670 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: 0.680 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 38.240 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:9.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 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 : 0.008 0.230 33128 Z= 0.335 Angle : 0.744 7.438 45020 Z= 0.442 Chirality : 0.049 0.155 4856 Planarity : 0.005 0.055 5900 Dihedral : 13.891 88.443 12116 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.94 % Allowed : 5.81 % Favored : 93.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.81 (0.11), residues: 4120 helix: -1.99 (0.13), residues: 1088 sheet: -1.95 (0.15), residues: 1000 loop : -3.17 (0.10), residues: 2032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 367 TYR 0.020 0.002 TYR D 388 PHE 0.048 0.003 PHE A 198 TRP 0.014 0.002 TRP B 904 HIS 0.007 0.001 HIS B 899 Details of bonding type rmsd covalent geometry : bond 0.00696 (33120) covalent geometry : angle 0.74378 (45020) hydrogen bonds : bond 0.22888 ( 1257) hydrogen bonds : angle 7.63039 ( 3555) metal coordination : bond 0.21379 ( 8) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 640 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 608 time to evaluate : 1.584 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 212 GLU cc_start: 0.8423 (mp0) cc_final: 0.8167 (mp0) REVERT: A 252 LYS cc_start: 0.8799 (mttt) cc_final: 0.8497 (mmmt) REVERT: A 1002 ASP cc_start: 0.8240 (p0) cc_final: 0.7891 (p0) REVERT: B 212 GLU cc_start: 0.8405 (mp0) cc_final: 0.8152 (mp0) REVERT: B 252 LYS cc_start: 0.8817 (mttt) cc_final: 0.8517 (mmmt) REVERT: B 1002 ASP cc_start: 0.8255 (p0) cc_final: 0.7899 (p0) REVERT: C 212 GLU cc_start: 0.8424 (mp0) cc_final: 0.8168 (mp0) REVERT: C 252 LYS cc_start: 0.8791 (mttt) cc_final: 0.8488 (mmmt) REVERT: C 1002 ASP cc_start: 0.8239 (p0) cc_final: 0.7886 (p0) REVERT: D 212 GLU cc_start: 0.8409 (mp0) cc_final: 0.8145 (mp0) REVERT: D 252 LYS cc_start: 0.8819 (mttt) cc_final: 0.8523 (mmmt) REVERT: D 1002 ASP cc_start: 0.8254 (p0) cc_final: 0.7900 (p0) outliers start: 32 outliers final: 8 residues processed: 628 average time/residue: 0.7370 time to fit residues: 542.8704 Evaluate side-chains 401 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 393 time to evaluate : 1.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 734 ASP Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 734 ASP Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 734 ASP Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 734 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 197 optimal weight: 6.9990 chunk 388 optimal weight: 1.9990 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 0.9980 chunk 132 optimal weight: 0.9980 chunk 261 optimal weight: 0.9980 chunk 248 optimal weight: 0.9990 chunk 207 optimal weight: 0.7980 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 0.0670 chunk 244 optimal weight: 7.9990 overall best weight: 0.7718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 6 ASN A 543 GLN A 544 GLN A 929 ASN B 543 GLN B 544 GLN B 857 ASN B 929 ASN C 543 GLN C 544 GLN C 929 ASN D 543 GLN D 544 GLN D 857 ASN D 929 ASN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.113688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.098843 restraints weight = 53624.411| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.77 r_work: 0.3071 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33128 Z= 0.117 Angle : 0.584 6.674 45020 Z= 0.310 Chirality : 0.045 0.153 4856 Planarity : 0.005 0.045 5900 Dihedral : 4.954 26.264 4512 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.58 % Allowed : 13.03 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.35 (0.12), residues: 4120 helix: -0.02 (0.16), residues: 1112 sheet: -1.34 (0.15), residues: 1016 loop : -2.62 (0.12), residues: 1992 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 487 TYR 0.016 0.001 TYR C 388 PHE 0.021 0.001 PHE A 198 TRP 0.013 0.001 TRP B 904 HIS 0.004 0.001 HIS B 594 Details of bonding type rmsd covalent geometry : bond 0.00253 (33120) covalent geometry : angle 0.58439 (45020) hydrogen bonds : bond 0.04518 ( 1257) hydrogen bonds : angle 4.85408 ( 3555) metal coordination : bond 0.00442 ( 8) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 605 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 517 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 252 LYS cc_start: 0.9026 (mttt) cc_final: 0.8594 (mmmt) REVERT: A 354 CYS cc_start: 0.6984 (OUTLIER) cc_final: 0.6649 (p) REVERT: A 554 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7845 (tt0) REVERT: A 770 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7548 (mm-30) REVERT: A 899 HIS cc_start: 0.7924 (t70) cc_final: 0.7565 (t70) REVERT: A 1002 ASP cc_start: 0.8581 (p0) cc_final: 0.8266 (p0) REVERT: B 252 LYS cc_start: 0.9046 (mttt) cc_final: 0.8591 (mmmt) REVERT: B 354 CYS cc_start: 0.6952 (OUTLIER) cc_final: 0.6617 (p) REVERT: B 554 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7835 (tt0) REVERT: B 570 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7951 (mp0) REVERT: B 770 GLU cc_start: 0.8560 (OUTLIER) cc_final: 0.7365 (mm-30) REVERT: B 1002 ASP cc_start: 0.8582 (p0) cc_final: 0.8253 (p0) REVERT: C 252 LYS cc_start: 0.9012 (mttt) cc_final: 0.8592 (mmmt) REVERT: C 354 CYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6627 (p) REVERT: C 554 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7840 (tt0) REVERT: C 770 GLU cc_start: 0.8682 (OUTLIER) cc_final: 0.7522 (mm-30) REVERT: C 899 HIS cc_start: 0.7918 (t70) cc_final: 0.7556 (t70) REVERT: C 1002 ASP cc_start: 0.8572 (p0) cc_final: 0.8255 (p0) REVERT: D 252 LYS cc_start: 0.9059 (mttt) cc_final: 0.8607 (mmmt) REVERT: D 354 CYS cc_start: 0.6954 (OUTLIER) cc_final: 0.6627 (p) REVERT: D 554 GLU cc_start: 0.8672 (OUTLIER) cc_final: 0.7853 (tt0) REVERT: D 570 GLU cc_start: 0.8169 (OUTLIER) cc_final: 0.7959 (mp0) REVERT: D 770 GLU cc_start: 0.8555 (OUTLIER) cc_final: 0.7359 (mm-30) REVERT: D 899 HIS cc_start: 0.7924 (t70) cc_final: 0.7566 (t70) REVERT: D 1002 ASP cc_start: 0.8593 (p0) cc_final: 0.8267 (p0) outliers start: 88 outliers final: 32 residues processed: 581 average time/residue: 0.6789 time to fit residues: 467.6532 Evaluate side-chains 460 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 414 time to evaluate : 1.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 838 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 838 SER Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 939 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 67 optimal weight: 2.9990 chunk 204 optimal weight: 9.9990 chunk 359 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 156 optimal weight: 9.9990 chunk 61 optimal weight: 0.7980 chunk 186 optimal weight: 8.9990 chunk 113 optimal weight: 0.2980 chunk 123 optimal weight: 0.9990 chunk 276 optimal weight: 8.9990 chunk 333 optimal weight: 5.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS A 213 ASN A 857 ASN B 213 ASN B 457 ASN B 857 ASN C 126 HIS C 213 ASN C 457 ASN C 857 ASN D 213 ASN D 457 ASN D 857 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.114691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.100102 restraints weight = 53278.479| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.65 r_work: 0.3116 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work (final): 0.3116 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33128 Z= 0.113 Angle : 0.552 7.592 45020 Z= 0.289 Chirality : 0.044 0.146 4856 Planarity : 0.004 0.045 5900 Dihedral : 4.650 25.483 4504 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 3.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 2.99 % Allowed : 14.55 % Favored : 82.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.81 (0.12), residues: 4120 helix: 0.51 (0.16), residues: 1132 sheet: -1.09 (0.15), residues: 1020 loop : -2.34 (0.12), residues: 1968 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 894 TYR 0.013 0.001 TYR C 388 PHE 0.016 0.001 PHE C 198 TRP 0.012 0.001 TRP C 904 HIS 0.003 0.001 HIS A 109 Details of bonding type rmsd covalent geometry : bond 0.00255 (33120) covalent geometry : angle 0.55219 (45020) hydrogen bonds : bond 0.03963 ( 1257) hydrogen bonds : angle 4.51137 ( 3555) metal coordination : bond 0.00080 ( 8) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 565 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 463 time to evaluate : 1.434 Fit side-chains REVERT: A 56 GLN cc_start: 0.8075 (mm110) cc_final: 0.7404 (mp10) REVERT: A 252 LYS cc_start: 0.8993 (mttt) cc_final: 0.8600 (mmmt) REVERT: A 354 CYS cc_start: 0.7056 (OUTLIER) cc_final: 0.6703 (p) REVERT: A 554 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7881 (tt0) REVERT: A 570 GLU cc_start: 0.8103 (mp0) cc_final: 0.7893 (mp0) REVERT: A 691 ASP cc_start: 0.8277 (p0) cc_final: 0.7928 (p0) REVERT: A 770 GLU cc_start: 0.8694 (OUTLIER) cc_final: 0.8382 (mp0) REVERT: A 802 ASP cc_start: 0.8586 (p0) cc_final: 0.8176 (p0) REVERT: A 899 HIS cc_start: 0.7936 (t70) cc_final: 0.7614 (t70) REVERT: A 1002 ASP cc_start: 0.8534 (p0) cc_final: 0.8289 (p0) REVERT: B 56 GLN cc_start: 0.8051 (mm110) cc_final: 0.7418 (mp10) REVERT: B 252 LYS cc_start: 0.9043 (mttt) cc_final: 0.8615 (mmmt) REVERT: B 354 CYS cc_start: 0.7019 (OUTLIER) cc_final: 0.6663 (p) REVERT: B 554 GLU cc_start: 0.8637 (OUTLIER) cc_final: 0.7857 (tt0) REVERT: B 570 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7792 (tp30) REVERT: B 691 ASP cc_start: 0.8285 (p0) cc_final: 0.7932 (p0) REVERT: B 770 GLU cc_start: 0.8500 (OUTLIER) cc_final: 0.8250 (mp0) REVERT: B 802 ASP cc_start: 0.8636 (p0) cc_final: 0.8204 (OUTLIER) REVERT: B 1002 ASP cc_start: 0.8543 (p0) cc_final: 0.8291 (p0) REVERT: C 56 GLN cc_start: 0.8057 (mm110) cc_final: 0.7428 (mp10) REVERT: C 252 LYS cc_start: 0.9014 (mttt) cc_final: 0.8606 (mmmt) REVERT: C 354 CYS cc_start: 0.7068 (OUTLIER) cc_final: 0.6720 (p) REVERT: C 554 GLU cc_start: 0.8652 (OUTLIER) cc_final: 0.7883 (tt0) REVERT: C 570 GLU cc_start: 0.8129 (mp0) cc_final: 0.7925 (mp0) REVERT: C 691 ASP cc_start: 0.8272 (p0) cc_final: 0.7927 (p0) REVERT: C 770 GLU cc_start: 0.8693 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: C 802 ASP cc_start: 0.8629 (p0) cc_final: 0.8224 (OUTLIER) REVERT: C 899 HIS cc_start: 0.7941 (t70) cc_final: 0.7621 (t70) REVERT: C 1002 ASP cc_start: 0.8545 (p0) cc_final: 0.8303 (p0) REVERT: D 56 GLN cc_start: 0.8074 (mm110) cc_final: 0.7408 (mp10) REVERT: D 252 LYS cc_start: 0.9019 (mttt) cc_final: 0.8604 (mmmt) REVERT: D 354 CYS cc_start: 0.7024 (OUTLIER) cc_final: 0.6682 (p) REVERT: D 554 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7886 (tt0) REVERT: D 570 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7809 (tp30) REVERT: D 691 ASP cc_start: 0.8246 (p0) cc_final: 0.7891 (p0) REVERT: D 770 GLU cc_start: 0.8476 (OUTLIER) cc_final: 0.8238 (mp0) REVERT: D 802 ASP cc_start: 0.8636 (p0) cc_final: 0.8203 (OUTLIER) REVERT: D 899 HIS cc_start: 0.7955 (t70) cc_final: 0.7679 (t70) REVERT: D 1002 ASP cc_start: 0.8542 (p0) cc_final: 0.8295 (p0) outliers start: 102 outliers final: 47 residues processed: 529 average time/residue: 0.6519 time to fit residues: 412.4855 Evaluate side-chains 461 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 403 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 335 optimal weight: 8.9990 chunk 327 optimal weight: 4.9990 chunk 206 optimal weight: 10.0000 chunk 61 optimal weight: 0.8980 chunk 116 optimal weight: 4.9990 chunk 404 optimal weight: 3.9990 chunk 231 optimal weight: 0.7980 chunk 266 optimal weight: 7.9990 chunk 72 optimal weight: 6.9990 chunk 308 optimal weight: 5.9990 chunk 71 optimal weight: 0.9990 overall best weight: 2.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN A 857 ASN A 900 HIS ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN C 857 ASN C 900 HIS D 213 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN D 900 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.110752 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.096725 restraints weight = 52670.188| |-----------------------------------------------------------------------------| r_work (start): 0.3197 rms_B_bonded: 2.52 r_work: 0.3075 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2944 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 33128 Z= 0.181 Angle : 0.604 7.746 45020 Z= 0.315 Chirality : 0.047 0.151 4856 Planarity : 0.004 0.046 5900 Dihedral : 4.825 26.631 4504 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.25 % Favored : 91.75 % Rotamer: Outliers : 3.46 % Allowed : 16.17 % Favored : 80.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.62 (0.13), residues: 4120 helix: 0.68 (0.16), residues: 1128 sheet: -1.04 (0.15), residues: 1032 loop : -2.18 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 894 TYR 0.012 0.001 TYR D 388 PHE 0.021 0.002 PHE A 843 TRP 0.010 0.001 TRP C 222 HIS 0.005 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00427 (33120) covalent geometry : angle 0.60401 (45020) hydrogen bonds : bond 0.04547 ( 1257) hydrogen bonds : angle 4.50654 ( 3555) metal coordination : bond 0.00206 ( 8) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 543 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 425 time to evaluate : 1.376 Fit side-chains REVERT: A 56 GLN cc_start: 0.8139 (mm110) cc_final: 0.7442 (mp10) REVERT: A 178 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7500 (mppt) REVERT: A 252 LYS cc_start: 0.9085 (mttt) cc_final: 0.8633 (mmmt) REVERT: A 354 CYS cc_start: 0.7684 (OUTLIER) cc_final: 0.7358 (p) REVERT: A 554 GLU cc_start: 0.8837 (OUTLIER) cc_final: 0.8177 (tt0) REVERT: A 570 GLU cc_start: 0.8298 (OUTLIER) cc_final: 0.7858 (tp30) REVERT: A 691 ASP cc_start: 0.8446 (p0) cc_final: 0.7952 (p0) REVERT: A 699 ASP cc_start: 0.9040 (t0) cc_final: 0.8719 (t0) REVERT: A 770 GLU cc_start: 0.8847 (OUTLIER) cc_final: 0.8569 (mp0) REVERT: A 1002 ASP cc_start: 0.8699 (p0) cc_final: 0.8435 (p0) REVERT: B 178 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7488 (mppt) REVERT: B 252 LYS cc_start: 0.9118 (mttt) cc_final: 0.8643 (mmmt) REVERT: B 354 CYS cc_start: 0.7658 (OUTLIER) cc_final: 0.7329 (p) REVERT: B 554 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8089 (tt0) REVERT: B 570 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7943 (tp30) REVERT: B 691 ASP cc_start: 0.8448 (p0) cc_final: 0.7954 (p0) REVERT: B 699 ASP cc_start: 0.8999 (t0) cc_final: 0.8693 (t0) REVERT: B 770 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8454 (mp0) REVERT: B 1002 ASP cc_start: 0.8690 (p0) cc_final: 0.8419 (p0) REVERT: C 178 LYS cc_start: 0.8017 (mmmt) cc_final: 0.7505 (mppt) REVERT: C 252 LYS cc_start: 0.9100 (mttt) cc_final: 0.8645 (mmmt) REVERT: C 354 CYS cc_start: 0.7690 (OUTLIER) cc_final: 0.7364 (p) REVERT: C 554 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8169 (tt0) REVERT: C 570 GLU cc_start: 0.8306 (OUTLIER) cc_final: 0.7863 (tp30) REVERT: C 691 ASP cc_start: 0.8446 (p0) cc_final: 0.7957 (p0) REVERT: C 699 ASP cc_start: 0.9017 (t0) cc_final: 0.8697 (t0) REVERT: C 770 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8580 (mp0) REVERT: C 1002 ASP cc_start: 0.8684 (p0) cc_final: 0.8422 (p0) REVERT: D 178 LYS cc_start: 0.7990 (mmmt) cc_final: 0.7478 (mppt) REVERT: D 252 LYS cc_start: 0.9115 (mttt) cc_final: 0.8652 (mmmt) REVERT: D 354 CYS cc_start: 0.7639 (OUTLIER) cc_final: 0.7320 (p) REVERT: D 554 GLU cc_start: 0.8821 (OUTLIER) cc_final: 0.8157 (tt0) REVERT: D 570 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: D 691 ASP cc_start: 0.8428 (p0) cc_final: 0.7933 (p0) REVERT: D 699 ASP cc_start: 0.9023 (t0) cc_final: 0.8712 (t0) REVERT: D 770 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.8444 (mp0) REVERT: D 1002 ASP cc_start: 0.8690 (p0) cc_final: 0.8416 (p0) outliers start: 118 outliers final: 57 residues processed: 498 average time/residue: 0.6555 time to fit residues: 390.2108 Evaluate side-chains 475 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 402 time to evaluate : 1.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 808 SER Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 976 MET Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 808 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 808 SER Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 294 optimal weight: 0.8980 chunk 310 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 211 optimal weight: 7.9990 chunk 63 optimal weight: 8.9990 chunk 341 optimal weight: 2.9990 chunk 363 optimal weight: 2.9990 chunk 263 optimal weight: 1.9990 chunk 232 optimal weight: 7.9990 chunk 408 optimal weight: 0.9990 chunk 44 optimal weight: 7.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 126 HIS ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN B 900 HIS C 126 HIS ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.109537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.095151 restraints weight = 51951.003| |-----------------------------------------------------------------------------| r_work (start): 0.3210 rms_B_bonded: 2.54 r_work: 0.3088 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 33128 Z= 0.148 Angle : 0.587 8.342 45020 Z= 0.306 Chirality : 0.046 0.150 4856 Planarity : 0.004 0.046 5900 Dihedral : 4.733 25.656 4504 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 4.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.72 % Favored : 92.28 % Rotamer: Outliers : 4.02 % Allowed : 17.08 % Favored : 78.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.44 (0.13), residues: 4120 helix: 0.85 (0.16), residues: 1132 sheet: -0.93 (0.15), residues: 1028 loop : -2.10 (0.13), residues: 1960 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 894 TYR 0.013 0.001 TYR D 388 PHE 0.019 0.002 PHE D 843 TRP 0.011 0.001 TRP B 904 HIS 0.004 0.001 HIS C 594 Details of bonding type rmsd covalent geometry : bond 0.00347 (33120) covalent geometry : angle 0.58731 (45020) hydrogen bonds : bond 0.04155 ( 1257) hydrogen bonds : angle 4.41107 ( 3555) metal coordination : bond 0.00129 ( 8) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 137 poor density : 429 time to evaluate : 1.450 Fit side-chains REVERT: A 56 GLN cc_start: 0.8090 (mm110) cc_final: 0.7318 (mp10) REVERT: A 60 GLN cc_start: 0.7484 (pt0) cc_final: 0.7258 (mm110) REVERT: A 178 LYS cc_start: 0.8008 (mmmt) cc_final: 0.7527 (mmmt) REVERT: A 252 LYS cc_start: 0.9047 (mttt) cc_final: 0.8630 (mmmt) REVERT: A 354 CYS cc_start: 0.7584 (OUTLIER) cc_final: 0.7264 (p) REVERT: A 554 GLU cc_start: 0.8813 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: A 570 GLU cc_start: 0.8321 (OUTLIER) cc_final: 0.7877 (tp30) REVERT: A 622 ASP cc_start: 0.8254 (t70) cc_final: 0.7879 (m-30) REVERT: A 699 ASP cc_start: 0.9048 (t0) cc_final: 0.8733 (t0) REVERT: A 770 GLU cc_start: 0.8835 (OUTLIER) cc_final: 0.8491 (mp0) REVERT: A 1002 ASP cc_start: 0.8720 (p0) cc_final: 0.8462 (p0) REVERT: B 56 GLN cc_start: 0.8141 (mm110) cc_final: 0.7381 (mp10) REVERT: B 60 GLN cc_start: 0.7478 (pt0) cc_final: 0.7262 (mm110) REVERT: B 178 LYS cc_start: 0.8009 (mmmt) cc_final: 0.7522 (mmmt) REVERT: B 252 LYS cc_start: 0.9089 (mttt) cc_final: 0.8647 (mmmt) REVERT: B 354 CYS cc_start: 0.7561 (OUTLIER) cc_final: 0.7233 (p) REVERT: B 554 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8124 (tt0) REVERT: B 570 GLU cc_start: 0.8358 (OUTLIER) cc_final: 0.7942 (tp30) REVERT: B 622 ASP cc_start: 0.8255 (t70) cc_final: 0.7883 (m-30) REVERT: B 699 ASP cc_start: 0.9038 (t0) cc_final: 0.8730 (t0) REVERT: B 770 GLU cc_start: 0.8675 (OUTLIER) cc_final: 0.8394 (mp0) REVERT: B 1002 ASP cc_start: 0.8720 (p0) cc_final: 0.8459 (p0) REVERT: C 56 GLN cc_start: 0.8148 (mm110) cc_final: 0.7399 (mp10) REVERT: C 178 LYS cc_start: 0.7999 (mmmt) cc_final: 0.7504 (mmmt) REVERT: C 252 LYS cc_start: 0.9066 (mttt) cc_final: 0.8633 (mmmt) REVERT: C 354 CYS cc_start: 0.7590 (OUTLIER) cc_final: 0.7274 (p) REVERT: C 554 GLU cc_start: 0.8825 (OUTLIER) cc_final: 0.8195 (tt0) REVERT: C 570 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7883 (tp30) REVERT: C 622 ASP cc_start: 0.8245 (t70) cc_final: 0.7880 (m-30) REVERT: C 699 ASP cc_start: 0.9033 (t0) cc_final: 0.8723 (t0) REVERT: C 770 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8502 (mp0) REVERT: C 1002 ASP cc_start: 0.8720 (p0) cc_final: 0.8460 (p0) REVERT: D 56 GLN cc_start: 0.8141 (mm110) cc_final: 0.7388 (mp10) REVERT: D 60 GLN cc_start: 0.7464 (pt0) cc_final: 0.7255 (mm110) REVERT: D 178 LYS cc_start: 0.8004 (mmmt) cc_final: 0.7521 (mmmt) REVERT: D 252 LYS cc_start: 0.9059 (mttt) cc_final: 0.8638 (mmmt) REVERT: D 354 CYS cc_start: 0.7525 (OUTLIER) cc_final: 0.7213 (p) REVERT: D 554 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8173 (tt0) REVERT: D 570 GLU cc_start: 0.8375 (OUTLIER) cc_final: 0.7959 (tp30) REVERT: D 622 ASP cc_start: 0.8253 (t70) cc_final: 0.7887 (m-30) REVERT: D 699 ASP cc_start: 0.9039 (t0) cc_final: 0.8725 (t0) REVERT: D 770 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8389 (mp0) REVERT: D 1002 ASP cc_start: 0.8721 (p0) cc_final: 0.8451 (p0) outliers start: 137 outliers final: 71 residues processed: 516 average time/residue: 0.6270 time to fit residues: 388.1155 Evaluate side-chains 481 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 394 time to evaluate : 1.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 838 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 830 GLU Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 895 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 762 THR Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 830 GLU Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 133 optimal weight: 2.9990 chunk 251 optimal weight: 3.9990 chunk 316 optimal weight: 0.7980 chunk 271 optimal weight: 1.9990 chunk 241 optimal weight: 2.9990 chunk 124 optimal weight: 4.9990 chunk 323 optimal weight: 0.9980 chunk 16 optimal weight: 3.9990 chunk 200 optimal weight: 9.9990 chunk 126 optimal weight: 9.9990 chunk 10 optimal weight: 0.1980 overall best weight: 1.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 ASN ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN D 213 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.111918 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.097181 restraints weight = 52709.597| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.58 r_work: 0.3101 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8629 moved from start: 0.2131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33128 Z= 0.130 Angle : 0.576 8.506 45020 Z= 0.299 Chirality : 0.045 0.147 4856 Planarity : 0.004 0.045 5900 Dihedral : 4.635 25.009 4504 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.69 % Favored : 92.31 % Rotamer: Outliers : 3.96 % Allowed : 17.58 % Favored : 78.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.35 (0.13), residues: 4120 helix: 0.88 (0.16), residues: 1156 sheet: -0.82 (0.15), residues: 1068 loop : -2.10 (0.13), residues: 1896 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 11 TYR 0.013 0.001 TYR B 388 PHE 0.019 0.001 PHE D 843 TRP 0.011 0.001 TRP D 904 HIS 0.004 0.001 HIS C 594 Details of bonding type rmsd covalent geometry : bond 0.00300 (33120) covalent geometry : angle 0.57589 (45020) hydrogen bonds : bond 0.03880 ( 1257) hydrogen bonds : angle 4.34030 ( 3555) metal coordination : bond 0.00096 ( 8) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 415 time to evaluate : 1.338 Fit side-chains REVERT: A 56 GLN cc_start: 0.8023 (mm110) cc_final: 0.7373 (mp10) REVERT: A 87 LEU cc_start: 0.7536 (OUTLIER) cc_final: 0.7190 (pp) REVERT: A 178 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7533 (mmmt) REVERT: A 354 CYS cc_start: 0.7266 (OUTLIER) cc_final: 0.6956 (p) REVERT: A 524 MET cc_start: 0.8789 (OUTLIER) cc_final: 0.8561 (tpt) REVERT: A 554 GLU cc_start: 0.8598 (OUTLIER) cc_final: 0.7900 (tt0) REVERT: A 570 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7838 (tp30) REVERT: A 699 ASP cc_start: 0.8958 (t0) cc_final: 0.8700 (t0) REVERT: A 705 GLU cc_start: 0.7831 (OUTLIER) cc_final: 0.7426 (tp30) REVERT: A 770 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8271 (mp0) REVERT: A 1002 ASP cc_start: 0.8618 (p0) cc_final: 0.8412 (p0) REVERT: B 56 GLN cc_start: 0.8070 (mm110) cc_final: 0.7406 (mp10) REVERT: B 87 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7165 (pp) REVERT: B 178 LYS cc_start: 0.7975 (mmmt) cc_final: 0.7514 (mmmt) REVERT: B 354 CYS cc_start: 0.7253 (OUTLIER) cc_final: 0.6939 (p) REVERT: B 524 MET cc_start: 0.8802 (OUTLIER) cc_final: 0.8591 (tpt) REVERT: B 554 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.7879 (tt0) REVERT: B 570 GLU cc_start: 0.8199 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: B 699 ASP cc_start: 0.8958 (t0) cc_final: 0.8717 (t0) REVERT: B 705 GLU cc_start: 0.7848 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: B 770 GLU cc_start: 0.8438 (OUTLIER) cc_final: 0.8180 (mp0) REVERT: B 1002 ASP cc_start: 0.8608 (p0) cc_final: 0.8400 (p0) REVERT: C 56 GLN cc_start: 0.8076 (mm110) cc_final: 0.7407 (mp10) REVERT: C 87 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.7173 (pp) REVERT: C 178 LYS cc_start: 0.7986 (mmmt) cc_final: 0.7536 (mmmt) REVERT: C 354 CYS cc_start: 0.7286 (OUTLIER) cc_final: 0.6986 (p) REVERT: C 524 MET cc_start: 0.8791 (OUTLIER) cc_final: 0.8564 (tpt) REVERT: C 554 GLU cc_start: 0.8609 (OUTLIER) cc_final: 0.7916 (tt0) REVERT: C 570 GLU cc_start: 0.8149 (OUTLIER) cc_final: 0.7840 (tp30) REVERT: C 699 ASP cc_start: 0.8958 (t0) cc_final: 0.8706 (t0) REVERT: C 705 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7570 (tp30) REVERT: C 770 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.8275 (mp0) REVERT: C 1002 ASP cc_start: 0.8622 (p0) cc_final: 0.8413 (p0) REVERT: D 56 GLN cc_start: 0.8052 (mm110) cc_final: 0.7402 (mp10) REVERT: D 178 LYS cc_start: 0.7973 (mmmt) cc_final: 0.7525 (mmmt) REVERT: D 354 CYS cc_start: 0.7241 (OUTLIER) cc_final: 0.6939 (p) REVERT: D 554 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.7928 (tt0) REVERT: D 570 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7904 (tp30) REVERT: D 699 ASP cc_start: 0.8950 (t0) cc_final: 0.8694 (t0) REVERT: D 705 GLU cc_start: 0.7857 (OUTLIER) cc_final: 0.7465 (tp30) REVERT: D 770 GLU cc_start: 0.8408 (OUTLIER) cc_final: 0.8160 (mp0) REVERT: D 1002 ASP cc_start: 0.8624 (p0) cc_final: 0.8411 (p0) outliers start: 135 outliers final: 82 residues processed: 506 average time/residue: 0.6139 time to fit residues: 374.3157 Evaluate side-chains 500 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 108 poor density : 392 time to evaluate : 1.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 524 MET Chi-restraints excluded: chain A residue 554 GLU Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 830 GLU Chi-restraints excluded: chain A residue 838 SER Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 895 THR Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 524 MET Chi-restraints excluded: chain B residue 554 GLU Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 808 SER Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 838 SER Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 895 THR Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 524 MET Chi-restraints excluded: chain C residue 554 GLU Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 808 SER Chi-restraints excluded: chain C residue 810 SER Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 830 GLU Chi-restraints excluded: chain C residue 838 SER Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 895 THR Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 554 GLU Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 762 THR Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 808 SER Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 838 SER Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 895 THR Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 943 GLU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 64 optimal weight: 10.0000 chunk 126 optimal weight: 9.9990 chunk 225 optimal weight: 0.9980 chunk 200 optimal weight: 9.9990 chunk 184 optimal weight: 6.9990 chunk 161 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 286 optimal weight: 0.9980 chunk 171 optimal weight: 7.9990 chunk 127 optimal weight: 0.3980 chunk 72 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN B 213 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 60 GLN C 213 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN D 60 GLN D 213 ASN D 457 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.113347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098629 restraints weight = 52599.950| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.59 r_work: 0.3126 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3126 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33128 Z= 0.114 Angle : 0.564 8.684 45020 Z= 0.292 Chirality : 0.044 0.149 4856 Planarity : 0.004 0.045 5900 Dihedral : 4.491 23.982 4504 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 4.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.45 % Favored : 92.55 % Rotamer: Outliers : 3.84 % Allowed : 18.02 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.20 (0.13), residues: 4120 helix: 1.05 (0.16), residues: 1156 sheet: -0.74 (0.15), residues: 1088 loop : -2.05 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 11 TYR 0.013 0.001 TYR B 388 PHE 0.017 0.001 PHE B 843 TRP 0.012 0.001 TRP B 904 HIS 0.004 0.001 HIS C 594 Details of bonding type rmsd covalent geometry : bond 0.00261 (33120) covalent geometry : angle 0.56395 (45020) hydrogen bonds : bond 0.03539 ( 1257) hydrogen bonds : angle 4.23418 ( 3555) metal coordination : bond 0.00070 ( 8) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 131 poor density : 439 time to evaluate : 1.097 Fit side-chains REVERT: A 56 GLN cc_start: 0.7988 (mm110) cc_final: 0.7377 (mp10) REVERT: A 87 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7176 (pp) REVERT: A 178 LYS cc_start: 0.7960 (mmmt) cc_final: 0.7528 (mmmt) REVERT: A 354 CYS cc_start: 0.7087 (OUTLIER) cc_final: 0.6705 (p) REVERT: A 554 GLU cc_start: 0.8616 (tt0) cc_final: 0.7890 (tt0) REVERT: A 570 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7879 (tp30) REVERT: A 622 ASP cc_start: 0.7945 (t70) cc_final: 0.7580 (m-30) REVERT: A 699 ASP cc_start: 0.8950 (t0) cc_final: 0.8679 (t0) REVERT: A 705 GLU cc_start: 0.7776 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: A 770 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8179 (mp0) REVERT: B 56 GLN cc_start: 0.7990 (mm110) cc_final: 0.7359 (mp10) REVERT: B 87 LEU cc_start: 0.7490 (OUTLIER) cc_final: 0.7158 (pp) REVERT: B 178 LYS cc_start: 0.7938 (mmmt) cc_final: 0.7492 (mmmt) REVERT: B 354 CYS cc_start: 0.7064 (OUTLIER) cc_final: 0.6688 (p) REVERT: B 554 GLU cc_start: 0.8592 (tt0) cc_final: 0.7869 (tt0) REVERT: B 570 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7949 (tp30) REVERT: B 622 ASP cc_start: 0.7933 (t70) cc_final: 0.7560 (m-30) REVERT: B 699 ASP cc_start: 0.8941 (t0) cc_final: 0.8709 (t0) REVERT: B 705 GLU cc_start: 0.7788 (OUTLIER) cc_final: 0.7431 (tp30) REVERT: B 770 GLU cc_start: 0.8339 (OUTLIER) cc_final: 0.8104 (mp0) REVERT: B 1002 ASP cc_start: 0.8594 (p0) cc_final: 0.8380 (p0) REVERT: C 56 GLN cc_start: 0.7995 (mm110) cc_final: 0.7363 (mp10) REVERT: C 87 LEU cc_start: 0.7507 (OUTLIER) cc_final: 0.7173 (pp) REVERT: C 178 LYS cc_start: 0.7939 (mmmt) cc_final: 0.7496 (mmmt) REVERT: C 354 CYS cc_start: 0.7109 (OUTLIER) cc_final: 0.6755 (p) REVERT: C 554 GLU cc_start: 0.8615 (tt0) cc_final: 0.7920 (tt0) REVERT: C 570 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7882 (tp30) REVERT: C 622 ASP cc_start: 0.7952 (t70) cc_final: 0.7596 (m-30) REVERT: C 699 ASP cc_start: 0.8957 (t0) cc_final: 0.8717 (t0) REVERT: C 705 GLU cc_start: 0.7787 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: C 717 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 770 GLU cc_start: 0.8487 (OUTLIER) cc_final: 0.8188 (mp0) REVERT: C 1002 ASP cc_start: 0.8601 (p0) cc_final: 0.8399 (p0) REVERT: D 56 GLN cc_start: 0.7983 (mm110) cc_final: 0.7359 (mp10) REVERT: D 87 LEU cc_start: 0.7479 (OUTLIER) cc_final: 0.7143 (pp) REVERT: D 178 LYS cc_start: 0.7942 (mmmt) cc_final: 0.7508 (mmmt) REVERT: D 354 CYS cc_start: 0.7045 (OUTLIER) cc_final: 0.6677 (p) REVERT: D 554 GLU cc_start: 0.8632 (tt0) cc_final: 0.7925 (tt0) REVERT: D 570 GLU cc_start: 0.8196 (OUTLIER) cc_final: 0.7948 (tp30) REVERT: D 622 ASP cc_start: 0.7926 (t70) cc_final: 0.7561 (m-30) REVERT: D 699 ASP cc_start: 0.8958 (t0) cc_final: 0.8721 (t0) REVERT: D 705 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: D 770 GLU cc_start: 0.8312 (OUTLIER) cc_final: 0.8086 (mp0) REVERT: D 1002 ASP cc_start: 0.8603 (p0) cc_final: 0.8390 (p0) outliers start: 131 outliers final: 69 residues processed: 523 average time/residue: 0.5989 time to fit residues: 376.0426 Evaluate side-chains 485 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 90 poor density : 395 time to evaluate : 1.264 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 595 ASP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 810 SER Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 762 THR Chi-restraints excluded: chain B residue 770 GLU Chi-restraints excluded: chain B residue 810 SER Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 595 ASP Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 717 GLU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 762 THR Chi-restraints excluded: chain D residue 770 GLU Chi-restraints excluded: chain D residue 810 SER Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 943 GLU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 192 optimal weight: 6.9990 chunk 208 optimal weight: 0.7980 chunk 197 optimal weight: 4.9990 chunk 239 optimal weight: 0.2980 chunk 159 optimal weight: 3.9990 chunk 248 optimal weight: 0.8980 chunk 396 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 241 optimal weight: 0.0570 chunk 389 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 overall best weight: 0.6098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 457 ASN B 457 ASN C 457 ASN D 457 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.115575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.100850 restraints weight = 52592.453| |-----------------------------------------------------------------------------| r_work (start): 0.3282 rms_B_bonded: 2.61 r_work: 0.3162 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work (final): 0.3162 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2557 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 33128 Z= 0.099 Angle : 0.557 8.705 45020 Z= 0.286 Chirality : 0.044 0.155 4856 Planarity : 0.004 0.044 5900 Dihedral : 4.344 22.812 4504 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.48 % Favored : 92.52 % Rotamer: Outliers : 2.85 % Allowed : 19.57 % Favored : 77.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.13), residues: 4120 helix: 1.15 (0.16), residues: 1156 sheet: -0.66 (0.15), residues: 1092 loop : -1.92 (0.13), residues: 1872 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 894 TYR 0.012 0.001 TYR B 388 PHE 0.014 0.001 PHE D 843 TRP 0.013 0.001 TRP A 904 HIS 0.004 0.001 HIS D 109 Details of bonding type rmsd covalent geometry : bond 0.00225 (33120) covalent geometry : angle 0.55672 (45020) hydrogen bonds : bond 0.03145 ( 1257) hydrogen bonds : angle 4.14021 ( 3555) metal coordination : bond 0.00036 ( 8) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 532 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 435 time to evaluate : 1.275 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 GLN cc_start: 0.7981 (mm110) cc_final: 0.7343 (mp10) REVERT: A 87 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7134 (pp) REVERT: A 178 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7500 (mmmt) REVERT: A 354 CYS cc_start: 0.6773 (OUTLIER) cc_final: 0.6494 (p) REVERT: A 570 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7907 (tp30) REVERT: A 699 ASP cc_start: 0.8937 (t0) cc_final: 0.8696 (t0) REVERT: A 705 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7390 (tp30) REVERT: A 717 GLU cc_start: 0.7616 (OUTLIER) cc_final: 0.7345 (mp0) REVERT: A 770 GLU cc_start: 0.8371 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: B 56 GLN cc_start: 0.7938 (mm110) cc_final: 0.7324 (mp10) REVERT: B 87 LEU cc_start: 0.7419 (OUTLIER) cc_final: 0.7086 (pp) REVERT: B 178 LYS cc_start: 0.7921 (mmmt) cc_final: 0.7477 (mmmt) REVERT: B 354 CYS cc_start: 0.6750 (OUTLIER) cc_final: 0.6384 (p) REVERT: B 554 GLU cc_start: 0.8591 (tt0) cc_final: 0.7842 (tt0) REVERT: B 570 GLU cc_start: 0.8134 (OUTLIER) cc_final: 0.7927 (tp30) REVERT: B 699 ASP cc_start: 0.8893 (t0) cc_final: 0.8653 (t0) REVERT: B 705 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7382 (tp30) REVERT: B 717 GLU cc_start: 0.7612 (OUTLIER) cc_final: 0.7277 (mp0) REVERT: C 56 GLN cc_start: 0.7942 (mm110) cc_final: 0.7317 (mp10) REVERT: C 87 LEU cc_start: 0.7426 (OUTLIER) cc_final: 0.7087 (pp) REVERT: C 178 LYS cc_start: 0.7933 (mmmt) cc_final: 0.7492 (mmmt) REVERT: C 354 CYS cc_start: 0.6782 (OUTLIER) cc_final: 0.6504 (p) REVERT: C 570 GLU cc_start: 0.8125 (OUTLIER) cc_final: 0.7901 (tp30) REVERT: C 699 ASP cc_start: 0.8910 (t0) cc_final: 0.8662 (t0) REVERT: C 705 GLU cc_start: 0.7749 (OUTLIER) cc_final: 0.7400 (tp30) REVERT: C 717 GLU cc_start: 0.7574 (OUTLIER) cc_final: 0.7314 (mp0) REVERT: C 770 GLU cc_start: 0.8356 (OUTLIER) cc_final: 0.8062 (mp0) REVERT: D 56 GLN cc_start: 0.7915 (mm110) cc_final: 0.7308 (mp10) REVERT: D 87 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7078 (pp) REVERT: D 178 LYS cc_start: 0.7911 (mmmt) cc_final: 0.7476 (mmmt) REVERT: D 354 CYS cc_start: 0.6716 (OUTLIER) cc_final: 0.6425 (p) REVERT: D 516 MET cc_start: 0.8249 (ttt) cc_final: 0.7895 (ttt) REVERT: D 570 GLU cc_start: 0.8138 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: D 699 ASP cc_start: 0.8926 (t0) cc_final: 0.8680 (t0) REVERT: D 705 GLU cc_start: 0.7733 (OUTLIER) cc_final: 0.7363 (tp30) REVERT: D 717 GLU cc_start: 0.7588 (OUTLIER) cc_final: 0.7297 (mp0) outliers start: 97 outliers final: 60 residues processed: 502 average time/residue: 0.5949 time to fit residues: 360.7496 Evaluate side-chains 500 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 418 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 570 GLU Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 293 SER Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 570 GLU Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 570 GLU Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 717 GLU Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 943 GLU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 293 SER Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 570 GLU Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 717 GLU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 282 optimal weight: 1.9990 chunk 372 optimal weight: 3.9990 chunk 311 optimal weight: 0.5980 chunk 281 optimal weight: 5.9990 chunk 233 optimal weight: 7.9990 chunk 250 optimal weight: 6.9990 chunk 389 optimal weight: 0.9990 chunk 339 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 144 optimal weight: 0.0770 overall best weight: 0.9142 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.113256 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098893 restraints weight = 51818.347| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 2.57 r_work: 0.3150 rms_B_bonded: 2.99 restraints_weight: 0.5000 r_work (final): 0.3150 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 33128 Z= 0.111 Angle : 0.572 8.898 45020 Z= 0.294 Chirality : 0.044 0.148 4856 Planarity : 0.004 0.044 5900 Dihedral : 4.364 22.775 4504 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.55 % Favored : 92.45 % Rotamer: Outliers : 2.93 % Allowed : 19.81 % Favored : 77.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4120 helix: 1.24 (0.16), residues: 1156 sheet: -0.59 (0.15), residues: 1088 loop : -1.90 (0.13), residues: 1876 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 894 TYR 0.012 0.001 TYR D 388 PHE 0.016 0.001 PHE A 843 TRP 0.010 0.001 TRP C 904 HIS 0.004 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00256 (33120) covalent geometry : angle 0.57151 (45020) hydrogen bonds : bond 0.03308 ( 1257) hydrogen bonds : angle 4.11615 ( 3555) metal coordination : bond 0.00067 ( 8) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 535 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 435 time to evaluate : 1.034 Fit side-chains REVERT: A 56 GLN cc_start: 0.7984 (mm110) cc_final: 0.7316 (mp10) REVERT: A 87 LEU cc_start: 0.7462 (OUTLIER) cc_final: 0.7124 (pp) REVERT: A 174 LYS cc_start: 0.8573 (OUTLIER) cc_final: 0.8211 (pmtt) REVERT: A 178 LYS cc_start: 0.7952 (mmmt) cc_final: 0.7526 (mmmt) REVERT: A 354 CYS cc_start: 0.6913 (OUTLIER) cc_final: 0.6511 (p) REVERT: A 554 GLU cc_start: 0.8562 (tt0) cc_final: 0.7827 (tt0) REVERT: A 622 ASP cc_start: 0.7944 (t70) cc_final: 0.7552 (m-30) REVERT: A 699 ASP cc_start: 0.8918 (t0) cc_final: 0.8681 (t0) REVERT: A 705 GLU cc_start: 0.7752 (OUTLIER) cc_final: 0.7428 (tp30) REVERT: A 717 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7465 (mp0) REVERT: A 770 GLU cc_start: 0.8308 (OUTLIER) cc_final: 0.8019 (mp0) REVERT: B 56 GLN cc_start: 0.8013 (mm110) cc_final: 0.7366 (mp10) REVERT: B 87 LEU cc_start: 0.7394 (OUTLIER) cc_final: 0.7055 (pp) REVERT: B 178 LYS cc_start: 0.7922 (mmmt) cc_final: 0.7482 (mmmt) REVERT: B 354 CYS cc_start: 0.6904 (OUTLIER) cc_final: 0.6505 (p) REVERT: B 554 GLU cc_start: 0.8569 (tt0) cc_final: 0.7819 (tt0) REVERT: B 622 ASP cc_start: 0.7900 (t70) cc_final: 0.7505 (m-30) REVERT: B 699 ASP cc_start: 0.8904 (t0) cc_final: 0.8670 (t0) REVERT: B 705 GLU cc_start: 0.7755 (OUTLIER) cc_final: 0.7398 (tp30) REVERT: B 717 GLU cc_start: 0.7625 (OUTLIER) cc_final: 0.7290 (mp0) REVERT: C 56 GLN cc_start: 0.7982 (mm110) cc_final: 0.7331 (mp10) REVERT: C 87 LEU cc_start: 0.7412 (OUTLIER) cc_final: 0.7068 (pp) REVERT: C 178 LYS cc_start: 0.7928 (mmmt) cc_final: 0.7491 (mmmt) REVERT: C 354 CYS cc_start: 0.6987 (OUTLIER) cc_final: 0.6611 (p) REVERT: C 554 GLU cc_start: 0.8589 (tt0) cc_final: 0.7869 (tt0) REVERT: C 622 ASP cc_start: 0.7940 (t70) cc_final: 0.7557 (m-30) REVERT: C 699 ASP cc_start: 0.8910 (t0) cc_final: 0.8676 (t0) REVERT: C 705 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.7420 (tp30) REVERT: C 717 GLU cc_start: 0.7611 (OUTLIER) cc_final: 0.7309 (mp0) REVERT: C 770 GLU cc_start: 0.8303 (OUTLIER) cc_final: 0.8020 (mp0) REVERT: D 56 GLN cc_start: 0.7980 (mm110) cc_final: 0.7337 (mp10) REVERT: D 87 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.7077 (pp) REVERT: D 178 LYS cc_start: 0.7931 (mmmt) cc_final: 0.7497 (mmmt) REVERT: D 354 CYS cc_start: 0.6873 (OUTLIER) cc_final: 0.6470 (p) REVERT: D 554 GLU cc_start: 0.8600 (tt0) cc_final: 0.7860 (tt0) REVERT: D 622 ASP cc_start: 0.7920 (t70) cc_final: 0.7514 (m-30) REVERT: D 699 ASP cc_start: 0.8916 (t0) cc_final: 0.8685 (t0) REVERT: D 705 GLU cc_start: 0.7762 (OUTLIER) cc_final: 0.7433 (tp30) REVERT: D 717 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.7293 (mp0) outliers start: 100 outliers final: 62 residues processed: 505 average time/residue: 0.5769 time to fit residues: 352.0959 Evaluate side-chains 497 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 416 time to evaluate : 1.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 LEU Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 166 PHE Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 174 LYS Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 626 ASP Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 717 GLU Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 717 GLU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 943 GLU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 166 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 717 GLU Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 943 GLU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 717 GLU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 943 GLU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 401 optimal weight: 0.9980 chunk 274 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 203 optimal weight: 3.9990 chunk 341 optimal weight: 0.6980 chunk 223 optimal weight: 8.9990 chunk 101 optimal weight: 5.9990 chunk 386 optimal weight: 0.9980 chunk 306 optimal weight: 4.9990 chunk 131 optimal weight: 5.9990 chunk 64 optimal weight: 9.9990 overall best weight: 1.9384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** A 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 126 HIS B 294 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN ** B 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 126 HIS C 294 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** C 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 126 HIS D 294 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN ** D 606 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.111378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.096735 restraints weight = 52783.710| |-----------------------------------------------------------------------------| r_work (start): 0.3242 rms_B_bonded: 2.57 r_work: 0.3134 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work (final): 0.3134 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2361 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 33128 Z= 0.160 Angle : 0.614 9.044 45020 Z= 0.317 Chirality : 0.046 0.150 4856 Planarity : 0.004 0.044 5900 Dihedral : 4.629 24.015 4504 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.28 % Favored : 91.72 % Rotamer: Outliers : 2.73 % Allowed : 19.98 % Favored : 77.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.96 (0.13), residues: 4120 helix: 1.44 (0.16), residues: 1104 sheet: -0.69 (0.15), residues: 1068 loop : -1.87 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG D 645 TYR 0.012 0.001 TYR C 388 PHE 0.021 0.002 PHE D 843 TRP 0.008 0.001 TRP C 222 HIS 0.004 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00379 (33120) covalent geometry : angle 0.61380 (45020) hydrogen bonds : bond 0.04080 ( 1257) hydrogen bonds : angle 4.24224 ( 3555) metal coordination : bond 0.00159 ( 8) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8240 Ramachandran restraints generated. 4120 Oldfield, 0 Emsley, 4120 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 513 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 93 poor density : 420 time to evaluate : 1.239 Fit side-chains REVERT: A 56 GLN cc_start: 0.8079 (mm110) cc_final: 0.7356 (mp10) REVERT: A 178 LYS cc_start: 0.7989 (mmmt) cc_final: 0.7560 (mmmt) REVERT: A 354 CYS cc_start: 0.7449 (OUTLIER) cc_final: 0.7055 (p) REVERT: A 554 GLU cc_start: 0.8585 (tt0) cc_final: 0.7894 (tt0) REVERT: A 622 ASP cc_start: 0.8000 (t70) cc_final: 0.7680 (m-30) REVERT: A 699 ASP cc_start: 0.8981 (t0) cc_final: 0.8734 (t0) REVERT: A 705 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7427 (tp30) REVERT: A 770 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8219 (mp0) REVERT: B 56 GLN cc_start: 0.8076 (mm110) cc_final: 0.7343 (mp10) REVERT: B 87 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7148 (pp) REVERT: B 178 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7531 (mmmt) REVERT: B 354 CYS cc_start: 0.7441 (OUTLIER) cc_final: 0.7038 (p) REVERT: B 554 GLU cc_start: 0.8581 (tt0) cc_final: 0.7882 (tt0) REVERT: B 622 ASP cc_start: 0.7999 (t70) cc_final: 0.7679 (m-30) REVERT: B 699 ASP cc_start: 0.8965 (t0) cc_final: 0.8721 (t0) REVERT: B 705 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7439 (tp30) REVERT: C 56 GLN cc_start: 0.8066 (mm110) cc_final: 0.7286 (mp10) REVERT: C 87 LEU cc_start: 0.7503 (OUTLIER) cc_final: 0.7158 (pp) REVERT: C 178 LYS cc_start: 0.7976 (mmmt) cc_final: 0.7545 (mmmt) REVERT: C 354 CYS cc_start: 0.7530 (OUTLIER) cc_final: 0.7141 (p) REVERT: C 554 GLU cc_start: 0.8589 (tt0) cc_final: 0.7894 (tt0) REVERT: C 622 ASP cc_start: 0.8002 (t70) cc_final: 0.7681 (m-30) REVERT: C 699 ASP cc_start: 0.8981 (t0) cc_final: 0.8734 (t0) REVERT: C 705 GLU cc_start: 0.7809 (OUTLIER) cc_final: 0.7467 (tp30) REVERT: C 717 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7451 (mp0) REVERT: C 770 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8218 (mp0) REVERT: D 56 GLN cc_start: 0.8069 (mm110) cc_final: 0.7341 (mp10) REVERT: D 87 LEU cc_start: 0.7509 (OUTLIER) cc_final: 0.7174 (pp) REVERT: D 178 LYS cc_start: 0.7967 (mmmt) cc_final: 0.7541 (mmmt) REVERT: D 354 CYS cc_start: 0.7440 (OUTLIER) cc_final: 0.7039 (p) REVERT: D 554 GLU cc_start: 0.8602 (tt0) cc_final: 0.7901 (tt0) REVERT: D 622 ASP cc_start: 0.8002 (t70) cc_final: 0.7683 (m-30) REVERT: D 699 ASP cc_start: 0.8978 (t0) cc_final: 0.8734 (t0) REVERT: D 705 GLU cc_start: 0.7825 (OUTLIER) cc_final: 0.7477 (tp30) outliers start: 93 outliers final: 67 residues processed: 491 average time/residue: 0.6208 time to fit residues: 365.6173 Evaluate side-chains 482 residues out of total 3408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 401 time to evaluate : 1.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 VAL Chi-restraints excluded: chain A residue 152 VAL Chi-restraints excluded: chain A residue 168 VAL Chi-restraints excluded: chain A residue 176 THR Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 354 CYS Chi-restraints excluded: chain A residue 389 THR Chi-restraints excluded: chain A residue 522 SER Chi-restraints excluded: chain A residue 647 SER Chi-restraints excluded: chain A residue 652 VAL Chi-restraints excluded: chain A residue 705 GLU Chi-restraints excluded: chain A residue 762 THR Chi-restraints excluded: chain A residue 770 GLU Chi-restraints excluded: chain A residue 821 ILE Chi-restraints excluded: chain A residue 855 VAL Chi-restraints excluded: chain A residue 859 SER Chi-restraints excluded: chain A residue 939 LEU Chi-restraints excluded: chain A residue 943 GLU Chi-restraints excluded: chain A residue 1019 LEU Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 140 VAL Chi-restraints excluded: chain B residue 152 VAL Chi-restraints excluded: chain B residue 166 PHE Chi-restraints excluded: chain B residue 168 VAL Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 198 PHE Chi-restraints excluded: chain B residue 294 ASN Chi-restraints excluded: chain B residue 354 CYS Chi-restraints excluded: chain B residue 389 THR Chi-restraints excluded: chain B residue 522 SER Chi-restraints excluded: chain B residue 595 ASP Chi-restraints excluded: chain B residue 647 SER Chi-restraints excluded: chain B residue 652 VAL Chi-restraints excluded: chain B residue 705 GLU Chi-restraints excluded: chain B residue 821 ILE Chi-restraints excluded: chain B residue 855 VAL Chi-restraints excluded: chain B residue 859 SER Chi-restraints excluded: chain B residue 939 LEU Chi-restraints excluded: chain B residue 1019 LEU Chi-restraints excluded: chain C residue 87 LEU Chi-restraints excluded: chain C residue 140 VAL Chi-restraints excluded: chain C residue 152 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 176 THR Chi-restraints excluded: chain C residue 198 PHE Chi-restraints excluded: chain C residue 293 SER Chi-restraints excluded: chain C residue 294 ASN Chi-restraints excluded: chain C residue 354 CYS Chi-restraints excluded: chain C residue 389 THR Chi-restraints excluded: chain C residue 522 SER Chi-restraints excluded: chain C residue 647 SER Chi-restraints excluded: chain C residue 652 VAL Chi-restraints excluded: chain C residue 705 GLU Chi-restraints excluded: chain C residue 717 GLU Chi-restraints excluded: chain C residue 762 THR Chi-restraints excluded: chain C residue 770 GLU Chi-restraints excluded: chain C residue 821 ILE Chi-restraints excluded: chain C residue 855 VAL Chi-restraints excluded: chain C residue 859 SER Chi-restraints excluded: chain C residue 939 LEU Chi-restraints excluded: chain C residue 1019 LEU Chi-restraints excluded: chain D residue 87 LEU Chi-restraints excluded: chain D residue 140 VAL Chi-restraints excluded: chain D residue 152 VAL Chi-restraints excluded: chain D residue 166 PHE Chi-restraints excluded: chain D residue 168 VAL Chi-restraints excluded: chain D residue 176 THR Chi-restraints excluded: chain D residue 198 PHE Chi-restraints excluded: chain D residue 294 ASN Chi-restraints excluded: chain D residue 354 CYS Chi-restraints excluded: chain D residue 389 THR Chi-restraints excluded: chain D residue 522 SER Chi-restraints excluded: chain D residue 595 ASP Chi-restraints excluded: chain D residue 647 SER Chi-restraints excluded: chain D residue 652 VAL Chi-restraints excluded: chain D residue 705 GLU Chi-restraints excluded: chain D residue 821 ILE Chi-restraints excluded: chain D residue 855 VAL Chi-restraints excluded: chain D residue 859 SER Chi-restraints excluded: chain D residue 939 LEU Chi-restraints excluded: chain D residue 1019 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 412 random chunks: chunk 340 optimal weight: 1.9990 chunk 303 optimal weight: 9.9990 chunk 380 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 400 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 305 optimal weight: 0.7980 chunk 130 optimal weight: 6.9990 chunk 112 optimal weight: 2.9990 chunk 160 optimal weight: 0.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 457 ASN ** B 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 457 ASN C 294 ASN ** C 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 457 ASN ** D 420 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 457 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.111921 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3236 r_free = 0.3236 target = 0.097201 restraints weight = 52839.680| |-----------------------------------------------------------------------------| r_work (start): 0.3225 rms_B_bonded: 2.59 r_work: 0.3103 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8617 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 33128 Z= 0.141 Angle : 0.608 8.855 45020 Z= 0.314 Chirality : 0.046 0.154 4856 Planarity : 0.004 0.044 5900 Dihedral : 4.612 24.003 4504 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 5.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 2.79 % Allowed : 20.72 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.13), residues: 4120 helix: 1.46 (0.16), residues: 1104 sheet: -0.69 (0.15), residues: 1068 loop : -1.85 (0.13), residues: 1948 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 811 TYR 0.013 0.001 TYR B 388 PHE 0.020 0.001 PHE C 843 TRP 0.009 0.001 TRP B 904 HIS 0.004 0.001 HIS D 594 Details of bonding type rmsd covalent geometry : bond 0.00331 (33120) covalent geometry : angle 0.60824 (45020) hydrogen bonds : bond 0.03868 ( 1257) hydrogen bonds : angle 4.22633 ( 3555) metal coordination : bond 0.00104 ( 8) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9194.64 seconds wall clock time: 158 minutes 8.59 seconds (9488.59 seconds total)