Starting phenix.real_space_refine on Sat Mar 7 05:48:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vnn_32043/03_2026/7vnn_32043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnn_32043/03_2026/7vnn_32043.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vnn_32043/03_2026/7vnn_32043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnn_32043/03_2026/7vnn_32043.map" model { file = "/net/cci-nas-00/data/ceres_data/7vnn_32043/03_2026/7vnn_32043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnn_32043/03_2026/7vnn_32043.cif" } resolution = 2.64 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 21 9.91 5 S 75 5.16 5 C 24325 2.51 5 N 6320 2.21 5 O 8082 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 72 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 38823 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "B" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "C" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Chain: "D" Number of atoms: 5134 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 641, 5066 Classifications: {'peptide': 641} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 613} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 641, 5066 Classifications: {'peptide': 641} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 613} Chain breaks: 1 bond proxies already assigned to first conformer: 5091 Chain: "E" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "F" Number of atoms: 5035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Chain: "G" Number of atoms: 5103 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 Conformer: "B" Number of residues, atoms: 638, 5035 Classifications: {'peptide': 638} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 610} Chain breaks: 1 bond proxies already assigned to first conformer: 5058 Chain: "H" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 394, 3186 Classifications: {'peptide': 394} Link IDs: {'PTRANS': 20, 'TRANS': 373} Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' CA': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 71 residue: pdb=" N AGLY A 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 488 " occ=0.50 residue: pdb=" N ATHR A 489 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BTHR A 489 " occ=0.50 residue: pdb=" N ALYS A 490 " occ=0.50 ... (16 atoms not shown) pdb=" NZ BLYS A 490 " occ=0.50 residue: pdb=" N AASN A 491 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 491 " occ=0.50 residue: pdb=" N ASER A 492 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 492 " occ=0.50 residue: pdb=" N ASER A 493 " occ=0.50 ... (10 atoms not shown) pdb=" OG BSER A 493 " occ=0.50 residue: pdb=" N AGLY A 494 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY A 494 " occ=0.50 residue: pdb=" N AGLN A 495 " occ=0.50 ... (16 atoms not shown) pdb=" NE2BGLN A 495 " occ=0.50 residue: pdb=" N AILE A 496 " occ=0.50 ... (14 atoms not shown) pdb=" CD1BILE A 496 " occ=0.50 residue: pdb=" N AVAL A 497 " occ=0.50 ... (12 atoms not shown) pdb=" CG2BVAL A 497 " occ=0.50 residue: pdb=" N THR A 498 " occ=0.50 ... (5 atoms not shown) pdb=" CG2 THR A 498 " occ=0.50 residue: pdb=" N AGLY B 488 " occ=0.50 ... (6 atoms not shown) pdb=" O BGLY B 488 " occ=0.50 ... (remaining 59 not shown) Time building chain proxies: 13.60, per 1000 atoms: 0.35 Number of scatterers: 38823 At special positions: 0 Unit cell: (180.4, 176.88, 201.52, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Ca 21 19.99 S 75 16.00 O 8082 8.00 N 6320 7.00 C 24325 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: 3.31 Conformation dependent library (CDL) restraints added in 2.7 seconds 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9232 Finding SS restraints... Secondary structure from input PDB file: 112 helices and 100 sheets defined 18.7% alpha, 36.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.96 Creating SS restraints... Processing helix chain 'A' and resid 227 through 234 Processing helix chain 'A' and resid 246 through 253 removed outlier: 3.598A pdb=" N GLU A 251 " --> pdb=" O SER A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 279 Processing helix chain 'A' and resid 286 through 290 Processing helix chain 'A' and resid 425 through 429 removed outlier: 3.686A pdb=" N ILE A 429 " --> pdb=" O GLU A 426 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 472 Processing helix chain 'A' and resid 503 through 513 removed outlier: 4.567A pdb=" N SER A 508 " --> pdb=" O SER A 504 " (cutoff:3.500A) removed outlier: 5.149A pdb=" N GLN A 509 " --> pdb=" O ASP A 505 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE A 513 " --> pdb=" O GLN A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 556 Processing helix chain 'A' and resid 581 through 595 removed outlier: 3.784A pdb=" N LYS A 593 " --> pdb=" O LYS A 589 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N THR A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 599 through 603 Processing helix chain 'A' and resid 757 through 765 removed outlier: 3.612A pdb=" N HIS A 765 " --> pdb=" O ILE A 761 " (cutoff:3.500A) Processing helix chain 'A' and resid 794 through 800 Processing helix chain 'A' and resid 829 through 831 No H-bonds generated for 'chain 'A' and resid 829 through 831' Processing helix chain 'A' and resid 843 through 845 No H-bonds generated for 'chain 'A' and resid 843 through 845' Processing helix chain 'B' and resid 227 through 234 Processing helix chain 'B' and resid 248 through 253 removed outlier: 4.306A pdb=" N GLN B 252 " --> pdb=" O SER B 248 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLY B 253 " --> pdb=" O PHE B 249 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 248 through 253' Processing helix chain 'B' and resid 272 through 279 Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.059A pdb=" N ASP B 291 " --> pdb=" O GLU B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 429 removed outlier: 3.726A pdb=" N ILE B 429 " --> pdb=" O GLU B 426 " (cutoff:3.500A) Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 503 through 513 removed outlier: 4.750A pdb=" N SER B 508 " --> pdb=" O SER B 504 " (cutoff:3.500A) removed outlier: 5.413A pdb=" N GLN B 509 " --> pdb=" O ASP B 505 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ILE B 513 " --> pdb=" O GLN B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 556 Processing helix chain 'B' and resid 581 through 594 removed outlier: 3.691A pdb=" N LYS B 593 " --> pdb=" O LYS B 589 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR B 594 " --> pdb=" O ASP B 590 " (cutoff:3.500A) Processing helix chain 'B' and resid 599 through 603 Processing helix chain 'B' and resid 757 through 765 removed outlier: 3.691A pdb=" N HIS B 765 " --> pdb=" O ILE B 761 " (cutoff:3.500A) Processing helix chain 'B' and resid 794 through 799 Processing helix chain 'B' and resid 829 through 831 No H-bonds generated for 'chain 'B' and resid 829 through 831' Processing helix chain 'B' and resid 843 through 845 No H-bonds generated for 'chain 'B' and resid 843 through 845' Processing helix chain 'C' and resid 227 through 234 Processing helix chain 'C' and resid 246 through 253 removed outlier: 3.786A pdb=" N GLU C 251 " --> pdb=" O SER C 248 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY C 253 " --> pdb=" O ALA C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 272 through 279 Processing helix chain 'C' and resid 286 through 291 removed outlier: 3.816A pdb=" N ASP C 291 " --> pdb=" O GLU C 288 " (cutoff:3.500A) Processing helix chain 'C' and resid 425 through 429 removed outlier: 3.726A pdb=" N ILE C 429 " --> pdb=" O GLU C 426 " (cutoff:3.500A) Processing helix chain 'C' and resid 463 through 472 Processing helix chain 'C' and resid 503 through 513 removed outlier: 4.611A pdb=" N SER C 508 " --> pdb=" O SER C 504 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N GLN C 509 " --> pdb=" O ASP C 505 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ILE C 513 " --> pdb=" O GLN C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 546 through 556 Processing helix chain 'C' and resid 581 through 593 Processing helix chain 'C' and resid 599 through 603 Processing helix chain 'C' and resid 757 through 765 Processing helix chain 'C' and resid 794 through 800 Processing helix chain 'C' and resid 829 through 831 No H-bonds generated for 'chain 'C' and resid 829 through 831' Processing helix chain 'C' and resid 843 through 845 No H-bonds generated for 'chain 'C' and resid 843 through 845' Processing helix chain 'D' and resid 227 through 234 Processing helix chain 'D' and resid 246 through 253 removed outlier: 3.628A pdb=" N GLU D 251 " --> pdb=" O SER D 248 " (cutoff:3.500A) Processing helix chain 'D' and resid 272 through 279 Processing helix chain 'D' and resid 286 through 291 removed outlier: 3.751A pdb=" N ASP D 291 " --> pdb=" O GLU D 288 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 429 removed outlier: 3.745A pdb=" N ILE D 429 " --> pdb=" O GLU D 426 " (cutoff:3.500A) Processing helix chain 'D' and resid 463 through 472 Processing helix chain 'D' and resid 503 through 513 removed outlier: 4.552A pdb=" N SER D 508 " --> pdb=" O SER D 504 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N GLN D 509 " --> pdb=" O ASP D 505 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE D 513 " --> pdb=" O GLN D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 556 Processing helix chain 'D' and resid 581 through 595 removed outlier: 3.825A pdb=" N LYS D 593 " --> pdb=" O LYS D 589 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N THR D 594 " --> pdb=" O ASP D 590 " (cutoff:3.500A) Processing helix chain 'D' and resid 599 through 603 Processing helix chain 'D' and resid 757 through 765 removed outlier: 3.590A pdb=" N HIS D 765 " --> pdb=" O ILE D 761 " (cutoff:3.500A) Processing helix chain 'D' and resid 794 through 800 Processing helix chain 'D' and resid 829 through 831 No H-bonds generated for 'chain 'D' and resid 829 through 831' Processing helix chain 'D' and resid 843 through 845 No H-bonds generated for 'chain 'D' and resid 843 through 845' Processing helix chain 'E' and resid 227 through 234 Processing helix chain 'E' and resid 246 through 253 removed outlier: 3.506A pdb=" N ALA E 250 " --> pdb=" O ASP E 247 " (cutoff:3.500A) Processing helix chain 'E' and resid 272 through 279 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.004A pdb=" N ASP E 291 " --> pdb=" O GLU E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 425 through 429 removed outlier: 3.719A pdb=" N ILE E 429 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing helix chain 'E' and resid 463 through 472 Processing helix chain 'E' and resid 503 through 513 removed outlier: 4.540A pdb=" N SER E 508 " --> pdb=" O SER E 504 " (cutoff:3.500A) removed outlier: 5.103A pdb=" N GLN E 509 " --> pdb=" O ASP E 505 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE E 513 " --> pdb=" O GLN E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 556 Processing helix chain 'E' and resid 581 through 593 removed outlier: 3.834A pdb=" N LYS E 593 " --> pdb=" O LYS E 589 " (cutoff:3.500A) Processing helix chain 'E' and resid 599 through 603 Processing helix chain 'E' and resid 757 through 765 removed outlier: 3.712A pdb=" N HIS E 765 " --> pdb=" O ILE E 761 " (cutoff:3.500A) Processing helix chain 'E' and resid 794 through 800 Processing helix chain 'E' and resid 829 through 831 No H-bonds generated for 'chain 'E' and resid 829 through 831' Processing helix chain 'E' and resid 843 through 845 No H-bonds generated for 'chain 'E' and resid 843 through 845' Processing helix chain 'F' and resid 227 through 234 Processing helix chain 'F' and resid 246 through 253 Processing helix chain 'F' and resid 272 through 279 Processing helix chain 'F' and resid 286 through 291 removed outlier: 4.188A pdb=" N ASP F 291 " --> pdb=" O GLU F 288 " (cutoff:3.500A) Processing helix chain 'F' and resid 425 through 429 removed outlier: 3.820A pdb=" N ILE F 429 " --> pdb=" O GLU F 426 " (cutoff:3.500A) Processing helix chain 'F' and resid 463 through 472 Processing helix chain 'F' and resid 503 through 513 removed outlier: 4.592A pdb=" N SER F 508 " --> pdb=" O SER F 504 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N GLN F 509 " --> pdb=" O ASP F 505 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE F 513 " --> pdb=" O GLN F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 556 Processing helix chain 'F' and resid 581 through 594 removed outlier: 3.849A pdb=" N LYS F 593 " --> pdb=" O LYS F 589 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N THR F 594 " --> pdb=" O ASP F 590 " (cutoff:3.500A) Processing helix chain 'F' and resid 599 through 603 Processing helix chain 'F' and resid 757 through 765 removed outlier: 3.795A pdb=" N HIS F 765 " --> pdb=" O ILE F 761 " (cutoff:3.500A) Processing helix chain 'F' and resid 794 through 801 Processing helix chain 'F' and resid 829 through 831 No H-bonds generated for 'chain 'F' and resid 829 through 831' Processing helix chain 'G' and resid 227 through 234 Processing helix chain 'G' and resid 246 through 250 Processing helix chain 'G' and resid 272 through 279 Processing helix chain 'G' and resid 286 through 291 removed outlier: 4.107A pdb=" N ASP G 291 " --> pdb=" O GLU G 288 " (cutoff:3.500A) Processing helix chain 'G' and resid 425 through 429 removed outlier: 3.648A pdb=" N ILE G 429 " --> pdb=" O GLU G 426 " (cutoff:3.500A) Processing helix chain 'G' and resid 463 through 471 Processing helix chain 'G' and resid 503 through 513 removed outlier: 4.665A pdb=" N SER G 508 " --> pdb=" O SER G 504 " (cutoff:3.500A) removed outlier: 5.353A pdb=" N GLN G 509 " --> pdb=" O ASP G 505 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ILE G 513 " --> pdb=" O GLN G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 556 Processing helix chain 'G' and resid 581 through 595 removed outlier: 3.891A pdb=" N LYS G 593 " --> pdb=" O LYS G 589 " (cutoff:3.500A) removed outlier: 4.261A pdb=" N THR G 594 " --> pdb=" O ASP G 590 " (cutoff:3.500A) Processing helix chain 'G' and resid 599 through 603 Processing helix chain 'G' and resid 757 through 765 removed outlier: 3.573A pdb=" N HIS G 765 " --> pdb=" O ILE G 761 " (cutoff:3.500A) Processing helix chain 'G' and resid 794 through 801 removed outlier: 3.723A pdb=" N ILE G 801 " --> pdb=" O ALA G 797 " (cutoff:3.500A) Processing helix chain 'G' and resid 829 through 831 No H-bonds generated for 'chain 'G' and resid 829 through 831' Processing helix chain 'G' and resid 841 through 845 Processing helix chain 'H' and resid 21 through 30 removed outlier: 3.844A pdb=" N GLN H 29 " --> pdb=" O GLU H 25 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N LYS H 30 " --> pdb=" O ARG H 26 " (cutoff:3.500A) Processing helix chain 'H' and resid 32 through 45 removed outlier: 3.692A pdb=" N LYS H 44 " --> pdb=" O GLU H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 45 through 55 removed outlier: 3.913A pdb=" N THR H 55 " --> pdb=" O LYS H 51 " (cutoff:3.500A) Processing helix chain 'H' and resid 62 through 67 removed outlier: 3.535A pdb=" N ASN H 67 " --> pdb=" O GLN H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 69 through 83 removed outlier: 4.225A pdb=" N ASN H 83 " --> pdb=" O ALA H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 101 removed outlier: 3.961A pdb=" N ALA H 101 " --> pdb=" O GLU H 98 " (cutoff:3.500A) Processing helix chain 'H' and resid 115 through 126 removed outlier: 3.723A pdb=" N ILE H 126 " --> pdb=" O PHE H 122 " (cutoff:3.500A) Processing helix chain 'H' and resid 216 through 229 Processing helix chain 'H' and resid 231 through 235 removed outlier: 3.521A pdb=" N LYS H 234 " --> pdb=" O TRP H 231 " (cutoff:3.500A) Processing helix chain 'H' and resid 236 through 250 Processing helix chain 'H' and resid 250 through 260 removed outlier: 3.975A pdb=" N ASN H 255 " --> pdb=" O TYR H 251 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ASN H 256 " --> pdb=" O THR H 252 " (cutoff:3.500A) Processing helix chain 'H' and resid 261 through 266 Processing helix chain 'H' and resid 268 through 285 removed outlier: 4.246A pdb=" N LYS H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) removed outlier: 4.327A pdb=" N GLU H 285 " --> pdb=" O ALA H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 308 through 312 Processing helix chain 'H' and resid 315 through 327 removed outlier: 3.857A pdb=" N ILE H 319 " --> pdb=" O LYS H 315 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'A' and resid 300 through 311 removed outlier: 6.886A pdb=" N ASN A 392 " --> pdb=" O GLU A 305 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N LEU A 307 " --> pdb=" O ASN A 390 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN A 390 " --> pdb=" O LEU A 307 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ILE A 309 " --> pdb=" O TYR A 388 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR A 388 " --> pdb=" O ILE A 309 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 438 through 439 removed outlier: 3.907A pdb=" N ALA A 387 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 360 through 382 removed outlier: 3.689A pdb=" N SER F 370 " --> pdb=" O SER F 324 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASN G 371 " --> pdb=" O ARG F 325 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ASN F 329 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N VAL G 367 " --> pdb=" O ASN F 329 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 361 through 382 current: chain 'E' and resid 313 through 335 removed outlier: 3.564A pdb=" N THR E 332 " --> pdb=" O ASP E 362 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL E 367 " --> pdb=" O ASN D 329 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP D 362 " --> pdb=" O THR D 332 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THR D 361 " --> pdb=" O ASN C 335 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N SER C 364 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP C 375 " --> pdb=" O LYS B 321 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N THR A 361 " --> pdb=" O ASN G 335 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.765A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 404 " --> pdb=" O ASN A 432 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN A 432 " --> pdb=" O TYR A 404 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 418 through 423 removed outlier: 6.765A pdb=" N LEU A 412 " --> pdb=" O LEU A 419 " (cutoff:3.500A) removed outlier: 4.395A pdb=" N THR A 421 " --> pdb=" O THR A 410 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N THR A 410 " --> pdb=" O THR A 421 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 423 " --> pdb=" O PRO A 408 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS A 405 " --> pdb=" O GLY A 485 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLY A 485 " --> pdb=" O LYS A 405 " (cutoff:3.500A) removed outlier: 6.314A pdb=" N THR A 407 " --> pdb=" O VAL A 483 " (cutoff:3.500A) removed outlier: 4.771A pdb=" N VAL A 483 " --> pdb=" O THR A 407 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N THR A 409 " --> pdb=" O THR A 481 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 489 through 490 Processing sheet with id=AA8, first strand: chain 'A' and resid 526 through 531 removed outlier: 9.288A pdb=" N ILE A 611 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 6.464A pdb=" N SER A 516 " --> pdb=" O ILE A 611 " (cutoff:3.500A) removed outlier: 7.850A pdb=" N ILE A 613 " --> pdb=" O SER A 516 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N ILE A 518 " --> pdb=" O ILE A 613 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 558 through 559 Processing sheet with id=AB1, first strand: chain 'A' and resid 618 through 620 removed outlier: 3.518A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 618 through 620 removed outlier: 3.518A pdb=" N TYR A 618 " --> pdb=" O ILE A 738 " (cutoff:3.500A) removed outlier: 5.317A pdb=" N LEU A 733 " --> pdb=" O LYS A 676 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LYS A 676 " --> pdb=" O LEU A 733 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ASN A 735 " --> pdb=" O TYR A 674 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N TYR A 674 " --> pdb=" O ASN A 735 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 655 through 658 removed outlier: 3.882A pdb=" N ILE A 656 " --> pdb=" O ILE A 723 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE A 723 " --> pdb=" O ILE A 656 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 768 through 773 removed outlier: 6.279A pdb=" N PHE A 769 " --> pdb=" O MET A 786 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N MET A 786 " --> pdb=" O PHE A 769 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N ASP A 771 " --> pdb=" O ASN A 784 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 815 through 821 removed outlier: 6.140A pdb=" N VAL A 806 " --> pdb=" O ILE A 818 " (cutoff:3.500A) removed outlier: 4.734A pdb=" N THR A 820 " --> pdb=" O TYR A 804 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N TYR A 804 " --> pdb=" O THR A 820 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N LYS A 803 " --> pdb=" O ILE A 863 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N ILE A 863 " --> pdb=" O LYS A 803 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU A 858 " --> pdb=" O SER A 874 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N SER A 874 " --> pdb=" O LEU A 858 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ILE A 860 " --> pdb=" O VAL A 872 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 826 through 827 Processing sheet with id=AB7, first strand: chain 'B' and resid 235 through 238 Processing sheet with id=AB8, first strand: chain 'B' and resid 300 through 311 removed outlier: 6.879A pdb=" N ASN B 392 " --> pdb=" O GLU B 305 " (cutoff:3.500A) removed outlier: 4.451A pdb=" N LEU B 307 " --> pdb=" O ASN B 390 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N ASN B 390 " --> pdb=" O LEU B 307 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ILE B 309 " --> pdb=" O TYR B 388 " (cutoff:3.500A) removed outlier: 6.310A pdb=" N TYR B 388 " --> pdb=" O ILE B 309 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 438 through 439 removed outlier: 3.806A pdb=" N ALA B 387 " --> pdb=" O ILE B 462 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.914A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N TYR B 404 " --> pdb=" O ASN B 432 " (cutoff:3.500A) removed outlier: 6.800A pdb=" N ASN B 432 " --> pdb=" O TYR B 404 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 418 through 423 removed outlier: 6.914A pdb=" N LEU B 412 " --> pdb=" O LEU B 419 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N THR B 421 " --> pdb=" O THR B 410 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N THR B 410 " --> pdb=" O THR B 421 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N LYS B 423 " --> pdb=" O PRO B 408 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N LYS B 405 " --> pdb=" O GLY B 485 " (cutoff:3.500A) removed outlier: 4.188A pdb=" N GLY B 485 " --> pdb=" O LYS B 405 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N THR B 407 " --> pdb=" O VAL B 483 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N VAL B 483 " --> pdb=" O THR B 407 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N THR B 409 " --> pdb=" O THR B 481 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 489 through 490 Processing sheet with id=AC4, first strand: chain 'B' and resid 526 through 531 removed outlier: 9.427A pdb=" N ILE B 611 " --> pdb=" O SER B 514 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N SER B 516 " --> pdb=" O ILE B 611 " (cutoff:3.500A) removed outlier: 8.054A pdb=" N ILE B 613 " --> pdb=" O SER B 516 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ILE B 518 " --> pdb=" O ILE B 613 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 558 through 559 Processing sheet with id=AC6, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.319A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N THR B 705 " --> pdb=" O SER B 675 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 618 through 620 removed outlier: 5.319A pdb=" N LEU B 733 " --> pdb=" O LYS B 676 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LYS B 676 " --> pdb=" O LEU B 733 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASN B 735 " --> pdb=" O TYR B 674 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N TYR B 674 " --> pdb=" O ASN B 735 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N THR B 713 " --> pdb=" O LYS B 667 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 655 through 658 removed outlier: 3.673A pdb=" N ILE B 656 " --> pdb=" O ILE B 723 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ILE B 723 " --> pdb=" O ILE B 656 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 768 through 773 removed outlier: 6.452A pdb=" N PHE B 769 " --> pdb=" O MET B 786 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N MET B 786 " --> pdb=" O PHE B 769 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ASP B 771 " --> pdb=" O ASN B 784 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'B' and resid 815 through 821 removed outlier: 6.097A pdb=" N VAL B 806 " --> pdb=" O ILE B 818 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N THR B 820 " --> pdb=" O TYR B 804 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N TYR B 804 " --> pdb=" O THR B 820 " (cutoff:3.500A) removed outlier: 4.934A pdb=" N LYS B 803 " --> pdb=" O ILE B 863 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N ILE B 863 " --> pdb=" O LYS B 803 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU B 858 " --> pdb=" O SER B 874 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N SER B 874 " --> pdb=" O LEU B 858 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N ILE B 860 " --> pdb=" O VAL B 872 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'B' and resid 826 through 827 Processing sheet with id=AD3, first strand: chain 'C' and resid 235 through 238 Processing sheet with id=AD4, first strand: chain 'C' and resid 300 through 302 Processing sheet with id=AD5, first strand: chain 'C' and resid 306 through 311 removed outlier: 3.642A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 306 through 311 removed outlier: 3.642A pdb=" N LYS C 306 " --> pdb=" O ASN C 392 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ALA C 387 " --> pdb=" O ILE C 462 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N ILE C 460 " --> pdb=" O ILE C 389 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.845A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N TYR C 404 " --> pdb=" O ASN C 432 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N ASN C 432 " --> pdb=" O TYR C 404 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 418 through 423 removed outlier: 6.845A pdb=" N LEU C 412 " --> pdb=" O LEU C 419 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N THR C 421 " --> pdb=" O THR C 410 " (cutoff:3.500A) removed outlier: 6.334A pdb=" N THR C 410 " --> pdb=" O THR C 421 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS C 423 " --> pdb=" O PRO C 408 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N LYS C 405 " --> pdb=" O GLY C 485 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N GLY C 485 " --> pdb=" O LYS C 405 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N THR C 407 " --> pdb=" O VAL C 483 " (cutoff:3.500A) removed outlier: 4.871A pdb=" N VAL C 483 " --> pdb=" O THR C 407 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N THR C 409 " --> pdb=" O THR C 481 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 525 through 531 Processing sheet with id=AE1, first strand: chain 'C' and resid 558 through 559 Processing sheet with id=AE2, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.459A pdb=" N LEU C 736 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 672 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 738 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 670 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU C 740 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 668 " --> pdb=" O GLU C 740 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR C 705 " --> pdb=" O SER C 675 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 618 through 620 removed outlier: 4.459A pdb=" N LEU C 736 " --> pdb=" O SER C 672 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N SER C 672 " --> pdb=" O LEU C 736 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N ILE C 738 " --> pdb=" O VAL C 670 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N VAL C 670 " --> pdb=" O ILE C 738 " (cutoff:3.500A) removed outlier: 5.097A pdb=" N GLU C 740 " --> pdb=" O ARG C 668 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ARG C 668 " --> pdb=" O GLU C 740 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'C' and resid 655 through 658 removed outlier: 3.526A pdb=" N ILE C 656 " --> pdb=" O ILE C 723 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE C 723 " --> pdb=" O ILE C 656 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'C' and resid 770 through 773 removed outlier: 6.597A pdb=" N ASP C 771 " --> pdb=" O ASN C 784 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'C' and resid 815 through 821 removed outlier: 6.353A pdb=" N VAL C 806 " --> pdb=" O ILE C 818 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N THR C 820 " --> pdb=" O TYR C 804 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N TYR C 804 " --> pdb=" O THR C 820 " (cutoff:3.500A) removed outlier: 5.006A pdb=" N LYS C 803 " --> pdb=" O ILE C 863 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE C 863 " --> pdb=" O LYS C 803 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N LEU C 858 " --> pdb=" O SER C 874 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N SER C 874 " --> pdb=" O LEU C 858 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE C 860 " --> pdb=" O VAL C 872 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'C' and resid 826 through 827 Processing sheet with id=AE8, first strand: chain 'D' and resid 235 through 238 Processing sheet with id=AE9, first strand: chain 'D' and resid 300 through 311 removed outlier: 5.849A pdb=" N VAL D 302 " --> pdb=" O TYR D 396 " (cutoff:3.500A) removed outlier: 7.265A pdb=" N TYR D 396 " --> pdb=" O VAL D 302 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N MET D 304 " --> pdb=" O ARG D 394 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ARG D 394 " --> pdb=" O MET D 304 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LYS D 306 " --> pdb=" O ASN D 392 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 438 through 439 removed outlier: 4.110A pdb=" N ALA D 387 " --> pdb=" O ILE D 462 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ILE D 460 " --> pdb=" O ILE D 389 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.788A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N TYR D 404 " --> pdb=" O ASN D 432 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ASN D 432 " --> pdb=" O TYR D 404 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 418 through 423 removed outlier: 6.788A pdb=" N LEU D 412 " --> pdb=" O LEU D 419 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THR D 421 " --> pdb=" O THR D 410 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N THR D 410 " --> pdb=" O THR D 421 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N LYS D 423 " --> pdb=" O PRO D 408 " (cutoff:3.500A) removed outlier: 5.895A pdb=" N LYS D 405 " --> pdb=" O ASN D 486 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N ASN D 486 " --> pdb=" O LYS D 405 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLN D 482 " --> pdb=" O THR D 409 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ASN D 411 " --> pdb=" O THR D 480 " (cutoff:3.500A) removed outlier: 5.745A pdb=" N THR D 480 " --> pdb=" O ASN D 411 " (cutoff:3.500A) removed outlier: 7.249A pdb=" N VAL D 413 " --> pdb=" O LEU D 478 " (cutoff:3.500A) removed outlier: 5.652A pdb=" N LEU D 478 " --> pdb=" O VAL D 413 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'D' and resid 489 through 490 Processing sheet with id=AF5, first strand: chain 'D' and resid 525 through 531 Processing sheet with id=AF6, first strand: chain 'D' and resid 558 through 559 Processing sheet with id=AF7, first strand: chain 'D' and resid 618 through 620 removed outlier: 4.276A pdb=" N LEU D 736 " --> pdb=" O SER D 672 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N SER D 672 " --> pdb=" O LEU D 736 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N ILE D 738 " --> pdb=" O VAL D 670 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N VAL D 670 " --> pdb=" O ILE D 738 " (cutoff:3.500A) removed outlier: 4.731A pdb=" N GLU D 740 " --> pdb=" O ARG D 668 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N ARG D 668 " --> pdb=" O GLU D 740 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'D' and resid 655 through 658 removed outlier: 4.908A pdb=" N GLU D 722 " --> pdb=" O LYS D 689 " (cutoff:3.500A) removed outlier: 4.270A pdb=" N LYS D 689 " --> pdb=" O GLU D 722 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LEU D 698 " --> pdb=" O ILE D 684 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP D 696 " --> pdb=" O VAL D 686 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'D' and resid 768 through 773 removed outlier: 6.208A pdb=" N PHE D 769 " --> pdb=" O MET D 786 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N MET D 786 " --> pdb=" O PHE D 769 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N ASP D 771 " --> pdb=" O ASN D 784 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'D' and resid 815 through 821 removed outlier: 6.054A pdb=" N VAL D 806 " --> pdb=" O ILE D 818 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR D 820 " --> pdb=" O TYR D 804 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N TYR D 804 " --> pdb=" O THR D 820 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N LYS D 803 " --> pdb=" O ILE D 863 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ILE D 863 " --> pdb=" O LYS D 803 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N LEU D 858 " --> pdb=" O SER D 874 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N SER D 874 " --> pdb=" O LEU D 858 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N ILE D 860 " --> pdb=" O VAL D 872 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'D' and resid 826 through 827 Processing sheet with id=AG3, first strand: chain 'E' and resid 235 through 238 Processing sheet with id=AG4, first strand: chain 'E' and resid 300 through 311 removed outlier: 5.598A pdb=" N VAL E 302 " --> pdb=" O TYR E 396 " (cutoff:3.500A) removed outlier: 7.031A pdb=" N TYR E 396 " --> pdb=" O VAL E 302 " (cutoff:3.500A) removed outlier: 5.599A pdb=" N MET E 304 " --> pdb=" O ARG E 394 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ARG E 394 " --> pdb=" O MET E 304 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS E 306 " --> pdb=" O ASN E 392 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'E' and resid 438 through 439 removed outlier: 4.004A pdb=" N ALA E 387 " --> pdb=" O ILE E 462 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'E' and resid 418 through 423 removed outlier: 7.009A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N TYR E 404 " --> pdb=" O ASN E 432 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASN E 432 " --> pdb=" O TYR E 404 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'E' and resid 418 through 423 removed outlier: 7.009A pdb=" N LEU E 412 " --> pdb=" O LEU E 419 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N THR E 421 " --> pdb=" O THR E 410 " (cutoff:3.500A) removed outlier: 6.345A pdb=" N THR E 410 " --> pdb=" O THR E 421 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N LYS E 423 " --> pdb=" O PRO E 408 " (cutoff:3.500A) removed outlier: 5.801A pdb=" N LYS E 405 " --> pdb=" O ASN E 486 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N ASN E 486 " --> pdb=" O LYS E 405 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N GLN E 482 " --> pdb=" O THR E 409 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ASN E 411 " --> pdb=" O THR E 480 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N THR E 480 " --> pdb=" O ASN E 411 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N VAL E 413 " --> pdb=" O LEU E 478 " (cutoff:3.500A) removed outlier: 5.625A pdb=" N LEU E 478 " --> pdb=" O VAL E 413 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'E' and resid 489 through 490 Processing sheet with id=AG9, first strand: chain 'E' and resid 524 through 531 removed outlier: 3.795A pdb=" N GLU E 524 " --> pdb=" O THR E 521 " (cutoff:3.500A) removed outlier: 9.472A pdb=" N ILE E 611 " --> pdb=" O SER E 514 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N SER E 516 " --> pdb=" O ILE E 611 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N ILE E 613 " --> pdb=" O SER E 516 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE E 518 " --> pdb=" O ILE E 613 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'E' and resid 558 through 559 Processing sheet with id=AH2, first strand: chain 'E' and resid 618 through 620 removed outlier: 3.648A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 736 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 672 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE E 738 " --> pdb=" O VAL E 670 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 670 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU E 740 " --> pdb=" O ARG E 668 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG E 668 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'E' and resid 618 through 620 removed outlier: 3.648A pdb=" N TYR E 618 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU E 736 " --> pdb=" O SER E 672 " (cutoff:3.500A) removed outlier: 6.775A pdb=" N SER E 672 " --> pdb=" O LEU E 736 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ILE E 738 " --> pdb=" O VAL E 670 " (cutoff:3.500A) removed outlier: 6.251A pdb=" N VAL E 670 " --> pdb=" O ILE E 738 " (cutoff:3.500A) removed outlier: 5.033A pdb=" N GLU E 740 " --> pdb=" O ARG E 668 " (cutoff:3.500A) removed outlier: 7.371A pdb=" N ARG E 668 " --> pdb=" O GLU E 740 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'E' and resid 655 through 658 removed outlier: 3.739A pdb=" N GLU E 722 " --> pdb=" O LYS E 689 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU E 698 " --> pdb=" O ILE E 684 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE E 688 " --> pdb=" O LYS E 694 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS E 694 " --> pdb=" O ILE E 688 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'E' and resid 768 through 773 removed outlier: 6.478A pdb=" N PHE E 769 " --> pdb=" O MET E 786 " (cutoff:3.500A) removed outlier: 4.717A pdb=" N MET E 786 " --> pdb=" O PHE E 769 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N ASP E 771 " --> pdb=" O ASN E 784 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'E' and resid 815 through 821 removed outlier: 6.007A pdb=" N VAL E 806 " --> pdb=" O ILE E 818 " (cutoff:3.500A) removed outlier: 4.833A pdb=" N THR E 820 " --> pdb=" O TYR E 804 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TYR E 804 " --> pdb=" O THR E 820 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N LYS E 803 " --> pdb=" O ILE E 863 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE E 863 " --> pdb=" O LYS E 803 " (cutoff:3.500A) removed outlier: 6.724A pdb=" N LEU E 858 " --> pdb=" O SER E 874 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N SER E 874 " --> pdb=" O LEU E 858 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE E 860 " --> pdb=" O VAL E 872 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'E' and resid 826 through 827 Processing sheet with id=AH8, first strand: chain 'F' and resid 235 through 238 Processing sheet with id=AH9, first strand: chain 'F' and resid 300 through 311 removed outlier: 6.876A pdb=" N ASN F 392 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N LEU F 307 " --> pdb=" O ASN F 390 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN F 390 " --> pdb=" O LEU F 307 " (cutoff:3.500A) removed outlier: 4.575A pdb=" N ILE F 309 " --> pdb=" O TYR F 388 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR F 388 " --> pdb=" O ILE F 309 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'F' and resid 438 through 439 removed outlier: 3.916A pdb=" N ALA F 387 " --> pdb=" O ILE F 462 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'F' and resid 418 through 423 removed outlier: 6.776A pdb=" N LEU F 412 " --> pdb=" O LEU F 419 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N THR F 421 " --> pdb=" O THR F 410 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N THR F 410 " --> pdb=" O THR F 421 " (cutoff:3.500A) removed outlier: 4.691A pdb=" N LYS F 423 " --> pdb=" O PRO F 408 " (cutoff:3.500A) removed outlier: 6.852A pdb=" N LYS F 405 " --> pdb=" O GLY F 485 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLY F 485 " --> pdb=" O LYS F 405 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N THR F 407 " --> pdb=" O VAL F 483 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N VAL F 483 " --> pdb=" O THR F 407 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N THR F 409 " --> pdb=" O THR F 481 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'F' and resid 489 through 490 removed outlier: 3.555A pdb=" N VAL F 497 " --> pdb=" O THR F 489 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'F' and resid 524 through 531 removed outlier: 3.787A pdb=" N GLU F 524 " --> pdb=" O THR F 521 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLU F 577 " --> pdb=" O LYS F 614 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'F' and resid 558 through 559 Processing sheet with id=AI6, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.722A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER F 675 " --> pdb=" O THR F 705 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N THR F 705 " --> pdb=" O SER F 675 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'F' and resid 618 through 620 removed outlier: 5.722A pdb=" N LEU F 733 " --> pdb=" O LYS F 676 " (cutoff:3.500A) removed outlier: 7.141A pdb=" N LYS F 676 " --> pdb=" O LEU F 733 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N ASN F 735 " --> pdb=" O TYR F 674 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N TYR F 674 " --> pdb=" O ASN F 735 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N PHE F 711 " --> pdb=" O TYR F 669 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'F' and resid 655 through 658 removed outlier: 3.607A pdb=" N GLU F 722 " --> pdb=" O LYS F 689 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS F 694 " --> pdb=" O ILE F 688 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'F' and resid 768 through 773 removed outlier: 6.376A pdb=" N PHE F 769 " --> pdb=" O MET F 786 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N MET F 786 " --> pdb=" O PHE F 769 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ASP F 771 " --> pdb=" O ASN F 784 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'F' and resid 815 through 821 removed outlier: 6.405A pdb=" N VAL F 806 " --> pdb=" O ILE F 818 " (cutoff:3.500A) removed outlier: 4.679A pdb=" N THR F 820 " --> pdb=" O TYR F 804 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR F 804 " --> pdb=" O THR F 820 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N LYS F 803 " --> pdb=" O ILE F 863 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ILE F 863 " --> pdb=" O LYS F 803 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N LEU F 858 " --> pdb=" O SER F 874 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N SER F 874 " --> pdb=" O LEU F 858 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N ILE F 860 " --> pdb=" O VAL F 872 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'F' and resid 826 through 827 Processing sheet with id=AJ3, first strand: chain 'G' and resid 235 through 238 Processing sheet with id=AJ4, first strand: chain 'G' and resid 300 through 311 removed outlier: 6.825A pdb=" N ASN G 392 " --> pdb=" O GLU G 305 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N LEU G 307 " --> pdb=" O ASN G 390 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N ASN G 390 " --> pdb=" O LEU G 307 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N ILE G 309 " --> pdb=" O TYR G 388 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N TYR G 388 " --> pdb=" O ILE G 309 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'G' and resid 438 through 439 removed outlier: 3.704A pdb=" N ALA G 387 " --> pdb=" O ILE G 462 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'G' and resid 418 through 423 removed outlier: 6.739A pdb=" N LEU G 412 " --> pdb=" O LEU G 419 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N THR G 421 " --> pdb=" O THR G 410 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N THR G 410 " --> pdb=" O THR G 421 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LYS G 423 " --> pdb=" O PRO G 408 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N LYS G 405 " --> pdb=" O ASN G 486 " (cutoff:3.500A) removed outlier: 4.861A pdb=" N ASN G 486 " --> pdb=" O LYS G 405 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N GLN G 482 " --> pdb=" O THR G 409 " (cutoff:3.500A) removed outlier: 6.529A pdb=" N ASN G 411 " --> pdb=" O THR G 480 " (cutoff:3.500A) removed outlier: 5.669A pdb=" N THR G 480 " --> pdb=" O ASN G 411 " (cutoff:3.500A) removed outlier: 7.087A pdb=" N VAL G 413 " --> pdb=" O LEU G 478 " (cutoff:3.500A) removed outlier: 5.564A pdb=" N LEU G 478 " --> pdb=" O VAL G 413 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'G' and resid 489 through 490 Processing sheet with id=AJ8, first strand: chain 'G' and resid 525 through 531 Processing sheet with id=AJ9, first strand: chain 'G' and resid 558 through 559 Processing sheet with id=AK1, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.737A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N THR G 705 " --> pdb=" O SER G 675 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'G' and resid 618 through 620 removed outlier: 5.737A pdb=" N LEU G 733 " --> pdb=" O LYS G 676 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N LYS G 676 " --> pdb=" O LEU G 733 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N ASN G 735 " --> pdb=" O TYR G 674 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N TYR G 674 " --> pdb=" O ASN G 735 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'G' and resid 655 through 658 removed outlier: 3.847A pdb=" N GLU G 722 " --> pdb=" O LYS G 689 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS G 689 " --> pdb=" O GLU G 722 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LYS G 687 " --> pdb=" O THR G 724 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N ASP G 696 " --> pdb=" O VAL G 686 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'G' and resid 768 through 773 removed outlier: 3.563A pdb=" N PHE G 769 " --> pdb=" O TYR G 787 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N ASN G 773 " --> pdb=" O ILE G 783 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ILE G 783 " --> pdb=" O ASN G 773 " (cutoff:3.500A) Processing sheet with id=AK5, first strand: chain 'G' and resid 815 through 821 removed outlier: 6.061A pdb=" N VAL G 806 " --> pdb=" O ILE G 818 " (cutoff:3.500A) removed outlier: 4.915A pdb=" N THR G 820 " --> pdb=" O TYR G 804 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N TYR G 804 " --> pdb=" O THR G 820 " (cutoff:3.500A) removed outlier: 5.106A pdb=" N LYS G 803 " --> pdb=" O ILE G 863 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE G 863 " --> pdb=" O LYS G 803 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N ALA G 862 " --> pdb=" O LEU G 871 " (cutoff:3.500A) removed outlier: 5.944A pdb=" N LEU G 871 " --> pdb=" O ALA G 862 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'G' and resid 826 through 827 Processing sheet with id=AK7, first strand: chain 'H' and resid 89 through 94 removed outlier: 3.630A pdb=" N TYR H 93 " --> pdb=" O MET H 156 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET H 156 " --> pdb=" O TYR H 93 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL H 207 " --> pdb=" O LYS H 159 " (cutoff:3.500A) removed outlier: 4.350A pdb=" N LYS H 189 " --> pdb=" O GLU H 204 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N SER H 206 " --> pdb=" O ILE H 187 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N ILE H 187 " --> pdb=" O SER H 206 " (cutoff:3.500A) removed outlier: 7.169A pdb=" N VAL H 208 " --> pdb=" O ILE H 185 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N ILE H 185 " --> pdb=" O VAL H 208 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N TYR H 183 " --> pdb=" O GLN H 133 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'H' and resid 136 through 139 removed outlier: 3.857A pdb=" N LEU H 178 " --> pdb=" O LEU H 167 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N LEU H 167 " --> pdb=" O LEU H 178 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'H' and resid 291 through 297 removed outlier: 4.147A pdb=" N ILE H 354 " --> pdb=" O SER H 297 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N TYR H 397 " --> pdb=" O LYS H 404 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N LYS H 393 " --> pdb=" O ASP H 408 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N THR H 410 " --> pdb=" O ILE H 391 " (cutoff:3.500A) removed outlier: 5.629A pdb=" N ILE H 391 " --> pdb=" O THR H 410 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N SER H 387 " --> pdb=" O TYR H 333 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'H' and resid 337 through 340 removed outlier: 3.804A pdb=" N ILE H 337 " --> pdb=" O LEU H 383 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N LEU H 382 " --> pdb=" O ALA H 367 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ALA H 367 " --> pdb=" O LEU H 382 " (cutoff:3.500A) 1382 hydrogen bonds defined for protein. 3615 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: 10.92 Time building geometry restraints manager: 4.44 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: 12742 1.34 - 1.46: 7837 1.46 - 1.58: 18798 1.58 - 1.70: 0 1.70 - 1.81: 143 Bond restraints: 39520 Sorted by residual: bond pdb=" N ASP B 282 " pdb=" CA ASP B 282 " ideal model delta sigma weight residual 1.456 1.490 -0.034 1.28e-02 6.10e+03 6.86e+00 bond pdb=" N PHE A 281 " pdb=" CA PHE A 281 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.17e-02 7.31e+03 6.74e+00 bond pdb=" N PHE F 281 " pdb=" CA PHE F 281 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.17e-02 7.31e+03 6.56e+00 bond pdb=" N PHE E 281 " pdb=" CA PHE E 281 " ideal model delta sigma weight residual 1.458 1.487 -0.030 1.17e-02 7.31e+03 6.40e+00 bond pdb=" N PHE C 281 " pdb=" CA PHE C 281 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.41e-02 5.03e+03 6.40e+00 ... (remaining 39515 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.94: 52896 1.94 - 3.88: 642 3.88 - 5.81: 47 5.81 - 7.75: 6 7.75 - 9.69: 1 Bond angle restraints: 53592 Sorted by residual: angle pdb=" CA PHE A 281 " pdb=" CB PHE A 281 " pdb=" CG PHE A 281 " ideal model delta sigma weight residual 113.80 119.34 -5.54 1.00e+00 1.00e+00 3.07e+01 angle pdb=" CA PHE B 281 " pdb=" CB PHE B 281 " pdb=" CG PHE B 281 " ideal model delta sigma weight residual 113.80 119.24 -5.44 1.00e+00 1.00e+00 2.95e+01 angle pdb=" CA PHE D 281 " pdb=" CB PHE D 281 " pdb=" CG PHE D 281 " ideal model delta sigma weight residual 113.80 119.21 -5.41 1.00e+00 1.00e+00 2.93e+01 angle pdb=" CA PHE E 281 " pdb=" CB PHE E 281 " pdb=" CG PHE E 281 " ideal model delta sigma weight residual 113.80 119.19 -5.39 1.00e+00 1.00e+00 2.90e+01 angle pdb=" CA PHE G 281 " pdb=" CB PHE G 281 " pdb=" CG PHE G 281 " ideal model delta sigma weight residual 113.80 118.69 -4.89 1.00e+00 1.00e+00 2.39e+01 ... (remaining 53587 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 21959 17.83 - 35.66: 1700 35.66 - 53.49: 291 53.49 - 71.32: 91 71.32 - 89.15: 39 Dihedral angle restraints: 24080 sinusoidal: 9648 harmonic: 14432 Sorted by residual: dihedral pdb=" CA TYR C 709 " pdb=" C TYR C 709 " pdb=" N GLU C 710 " pdb=" CA GLU C 710 " ideal model delta harmonic sigma weight residual 180.00 -156.44 -23.56 0 5.00e+00 4.00e-02 2.22e+01 dihedral pdb=" CA THR E 714 " pdb=" C THR E 714 " pdb=" N GLU E 715 " pdb=" CA GLU E 715 " ideal model delta harmonic sigma weight residual -180.00 -158.36 -21.64 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA ASN G 775 " pdb=" C ASN G 775 " pdb=" N PRO G 776 " pdb=" CA PRO G 776 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 24077 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 4061 0.035 - 0.071: 1239 0.071 - 0.106: 470 0.106 - 0.141: 226 0.141 - 0.177: 7 Chirality restraints: 6003 Sorted by residual: chirality pdb=" CA PHE B 281 " pdb=" N PHE B 281 " pdb=" C PHE B 281 " pdb=" CB PHE B 281 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.79e-01 chirality pdb=" CA PHE D 281 " pdb=" N PHE D 281 " pdb=" C PHE D 281 " pdb=" CB PHE D 281 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA PHE G 281 " pdb=" N PHE G 281 " pdb=" C PHE G 281 " pdb=" CB PHE G 281 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 6000 not shown) Planarity restraints: 6990 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS G 664 " -0.050 5.00e-02 4.00e+02 7.58e-02 9.20e+00 pdb=" N PRO G 665 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO G 665 " -0.040 5.00e-02 4.00e+02 pdb=" CD PRO G 665 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR F 864 " 0.029 5.00e-02 4.00e+02 4.35e-02 3.02e+00 pdb=" N PRO F 865 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO F 865 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO F 865 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU H 117 " -0.008 2.00e-02 2.50e+03 1.56e-02 2.44e+00 pdb=" C GLU H 117 " 0.027 2.00e-02 2.50e+03 pdb=" O GLU H 117 " -0.010 2.00e-02 2.50e+03 pdb=" N LYS H 118 " -0.009 2.00e-02 2.50e+03 ... (remaining 6987 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1613 2.72 - 3.26: 37092 3.26 - 3.81: 59979 3.81 - 4.35: 79635 4.35 - 4.90: 133864 Nonbonded interactions: 312183 Sorted by model distance: nonbonded pdb=" OG1 THR G 864 " pdb=" OD1 ASP G 866 " model vdw 2.169 3.040 nonbonded pdb=" O PHE E 788 " pdb=" OG1 THR E 837 " model vdw 2.172 3.040 nonbonded pdb=" O ASN E 775 " pdb=" ND2 ASN E 780 " model vdw 2.184 3.120 nonbonded pdb=" OD2 ASP H 212 " pdb=" OG1 THR H 292 " model vdw 2.191 3.040 nonbonded pdb=" NH2 ARG E 394 " pdb=" O LEU E 444 " model vdw 2.212 3.120 ... (remaining 312178 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 217 through 487 or resid 498 through 903)) selection = (chain 'B' and (resid 217 through 487 or resid 498 through 903)) selection = (chain 'C' and (resid 217 through 487 or resid 498 through 903)) selection = (chain 'D' and (resid 217 through 487 or resid 498 through 903)) selection = (chain 'E' and (resid 217 through 487 or resid 498 through 903)) selection = (chain 'F' and (resid 217 through 487 or resid 498 through 903)) selection = (chain 'G' and (resid 217 through 487 or resid 498 through 903)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 max=1.00 mean=0.99 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: 5.290 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: 0.700 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 46.150 Find NCS groups from input model: 0.950 Set up NCS constraints: 0.120 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:6.930 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 39520 Z= 0.134 Angle : 0.537 9.691 53592 Z= 0.305 Chirality : 0.044 0.177 6003 Planarity : 0.004 0.076 6990 Dihedral : 13.907 89.147 14848 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.73 % Favored : 94.27 % Rotamer: Outliers : 0.37 % Allowed : 0.55 % Favored : 99.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.92 (0.12), residues: 4893 helix: -0.03 (0.19), residues: 745 sheet: 0.21 (0.14), residues: 1466 loop : -1.27 (0.12), residues: 2682 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG F 325 TYR 0.016 0.001 TYR A 230 PHE 0.015 0.001 PHE H 322 TRP 0.012 0.001 TRP D 375 HIS 0.003 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00269 (39520) covalent geometry : angle 0.53670 (53592) hydrogen bonds : bond 0.22834 ( 1322) hydrogen bonds : angle 8.63620 ( 3615) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 365 time to evaluate : 1.561 Fit side-chains REVERT: B 627 ASN cc_start: 0.7700 (t0) cc_final: 0.7495 (t160) REVERT: B 786 MET cc_start: 0.8670 (tpp) cc_final: 0.8438 (tpp) REVERT: C 660 MET cc_start: 0.5143 (tpt) cc_final: 0.4758 (tpt) REVERT: C 853 MET cc_start: 0.7768 (mmm) cc_final: 0.7476 (mmm) REVERT: D 773 ASN cc_start: 0.7380 (t160) cc_final: 0.6899 (p0) REVERT: E 698 LEU cc_start: 0.5846 (pt) cc_final: 0.5609 (pt) REVERT: F 376 ASN cc_start: 0.7884 (m110) cc_final: 0.7659 (t0) REVERT: H 49 ILE cc_start: 0.4760 (mt) cc_final: 0.4537 (mt) REVERT: H 120 ASN cc_start: 0.4950 (m-40) cc_final: 0.4537 (m-40) REVERT: H 149 GLU cc_start: 0.4089 (pp20) cc_final: 0.3084 (tp30) REVERT: H 284 ARG cc_start: 0.2217 (ttm-80) cc_final: 0.1260 (tmt-80) outliers start: 12 outliers final: 7 residues processed: 376 average time/residue: 0.7319 time to fit residues: 335.9043 Evaluate side-chains 235 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 228 time to evaluate : 1.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 432 optimal weight: 3.9990 chunk 197 optimal weight: 0.1980 chunk 388 optimal weight: 0.9990 chunk 455 optimal weight: 2.9990 chunk 215 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 0.8980 chunk 207 optimal weight: 2.9990 chunk 470 optimal weight: 0.0570 overall best weight: 0.8302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 390 ASN C 392 ASN C 586 ASN D 602 ASN ** D 773 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 376 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.155261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120725 restraints weight = 180950.535| |-----------------------------------------------------------------------------| r_work (start): 0.3592 rms_B_bonded: 3.64 r_work: 0.3474 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3475 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3475 r_free = 0.3475 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 39520 Z= 0.121 Angle : 0.545 8.720 53592 Z= 0.297 Chirality : 0.045 0.183 6003 Planarity : 0.004 0.059 6990 Dihedral : 4.717 47.217 5327 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.26 % Allowed : 5.89 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.60 (0.12), residues: 4893 helix: 0.57 (0.20), residues: 688 sheet: 0.43 (0.14), residues: 1485 loop : -1.16 (0.12), residues: 2720 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.018 0.001 TYR H 397 PHE 0.016 0.001 PHE C 711 TRP 0.011 0.001 TRP D 375 HIS 0.003 0.001 HIS B 314 Details of bonding type rmsd covalent geometry : bond 0.00273 (39520) covalent geometry : angle 0.54503 (53592) hydrogen bonds : bond 0.03505 ( 1322) hydrogen bonds : angle 5.62604 ( 3615) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 344 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 295 time to evaluate : 1.529 Fit side-chains REVERT: A 689 LYS cc_start: 0.6217 (tmmt) cc_final: 0.5606 (ttpt) REVERT: A 722 GLU cc_start: 0.6852 (mt-10) cc_final: 0.6360 (mm-30) REVERT: B 627 ASN cc_start: 0.7903 (t0) cc_final: 0.7668 (t160) REVERT: B 786 MET cc_start: 0.8890 (tpp) cc_final: 0.8592 (tpp) REVERT: C 591 SER cc_start: 0.8489 (t) cc_final: 0.8197 (p) REVERT: C 664 LYS cc_start: 0.7736 (mmtp) cc_final: 0.7419 (mmmt) REVERT: C 736 LEU cc_start: 0.8709 (OUTLIER) cc_final: 0.8419 (mp) REVERT: C 853 MET cc_start: 0.7838 (mmm) cc_final: 0.7494 (mmm) REVERT: D 722 GLU cc_start: 0.6802 (OUTLIER) cc_final: 0.6470 (pm20) REVERT: F 290 ARG cc_start: 0.8187 (mtp180) cc_final: 0.7954 (mtm-85) REVERT: F 376 ASN cc_start: 0.7949 (m110) cc_final: 0.7625 (t0) REVERT: G 524 GLU cc_start: 0.7946 (tt0) cc_final: 0.7718 (tt0) REVERT: G 668 ARG cc_start: 0.7063 (tmm-80) cc_final: 0.6409 (pmt170) REVERT: G 689 LYS cc_start: 0.6482 (tmmt) cc_final: 0.6120 (ttpp) REVERT: H 20 GLU cc_start: 0.3603 (mm-30) cc_final: 0.1912 (pm20) REVERT: H 48 GLU cc_start: 0.4136 (OUTLIER) cc_final: 0.3833 (tt0) REVERT: H 120 ASN cc_start: 0.5136 (m-40) cc_final: 0.4571 (m-40) REVERT: H 284 ARG cc_start: 0.2231 (ttm-80) cc_final: 0.1367 (tmt-80) outliers start: 49 outliers final: 21 residues processed: 329 average time/residue: 0.6824 time to fit residues: 277.2012 Evaluate side-chains 268 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 244 time to evaluate : 1.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 773 ASN Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 49 optimal weight: 5.9990 chunk 78 optimal weight: 4.9990 chunk 330 optimal weight: 0.0470 chunk 102 optimal weight: 3.9990 chunk 235 optimal weight: 0.9980 chunk 103 optimal weight: 7.9990 chunk 431 optimal weight: 0.0980 chunk 458 optimal weight: 0.7980 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 0.9990 overall best weight: 0.5880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 811 GLN A 851 ASN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 811 GLN C 390 ASN D 363 ASN D 368 GLN F 376 ASN F 392 ASN F 583 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN H 157 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.155469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.120766 restraints weight = 200321.717| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 3.82 r_work: 0.3470 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3470 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3469 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3469 r_free = 0.3469 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3469 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39520 Z= 0.101 Angle : 0.503 8.807 53592 Z= 0.272 Chirality : 0.043 0.175 6003 Planarity : 0.004 0.050 6990 Dihedral : 4.511 48.023 5327 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 4.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.39 % Allowed : 8.17 % Favored : 90.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.39 (0.12), residues: 4893 helix: 0.81 (0.20), residues: 687 sheet: 0.74 (0.14), residues: 1497 loop : -1.16 (0.12), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.027 0.001 TYR H 397 PHE 0.032 0.001 PHE G 774 TRP 0.009 0.001 TRP D 375 HIS 0.004 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00225 (39520) covalent geometry : angle 0.50330 (53592) hydrogen bonds : bond 0.02933 ( 1322) hydrogen bonds : angle 5.02791 ( 3615) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 285 time to evaluate : 1.516 Fit side-chains revert: symmetry clash REVERT: A 689 LYS cc_start: 0.6263 (tmmt) cc_final: 0.5437 (ttpt) REVERT: A 696 ASP cc_start: 0.5949 (OUTLIER) cc_final: 0.5497 (t70) REVERT: A 722 GLU cc_start: 0.6787 (mt-10) cc_final: 0.6290 (mm-30) REVERT: B 627 ASN cc_start: 0.7837 (t0) cc_final: 0.7618 (t160) REVERT: B 701 GLU cc_start: 0.7133 (mt-10) cc_final: 0.6830 (mt-10) REVERT: B 786 MET cc_start: 0.8919 (tpp) cc_final: 0.8638 (tpp) REVERT: C 591 SER cc_start: 0.8446 (t) cc_final: 0.8134 (p) REVERT: C 664 LYS cc_start: 0.7730 (mmtp) cc_final: 0.7387 (mmmt) REVERT: C 712 GLU cc_start: 0.7490 (mm-30) cc_final: 0.7244 (pt0) REVERT: C 736 LEU cc_start: 0.8668 (OUTLIER) cc_final: 0.8402 (mp) REVERT: C 853 MET cc_start: 0.7835 (mmm) cc_final: 0.7502 (mmm) REVERT: D 325 ARG cc_start: 0.6860 (ttm-80) cc_final: 0.6657 (ttp80) REVERT: D 722 GLU cc_start: 0.6479 (OUTLIER) cc_final: 0.6156 (pm20) REVERT: E 606 GLU cc_start: 0.8052 (OUTLIER) cc_final: 0.7012 (mt-10) REVERT: E 660 MET cc_start: 0.6892 (tpt) cc_final: 0.6477 (tpt) REVERT: F 290 ARG cc_start: 0.8194 (mtp180) cc_final: 0.7896 (mtm-85) REVERT: F 376 ASN cc_start: 0.7894 (m-40) cc_final: 0.7632 (t0) REVERT: F 786 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7807 (tpp) REVERT: F 826 ARG cc_start: 0.7511 (OUTLIER) cc_final: 0.7144 (mtt90) REVERT: G 524 GLU cc_start: 0.7930 (tt0) cc_final: 0.7681 (tt0) REVERT: G 595 LEU cc_start: 0.7254 (OUTLIER) cc_final: 0.6945 (mm) REVERT: G 668 ARG cc_start: 0.7019 (tmm-80) cc_final: 0.6475 (pmt170) REVERT: H 20 GLU cc_start: 0.3621 (mm-30) cc_final: 0.2015 (pm20) REVERT: H 48 GLU cc_start: 0.3820 (OUTLIER) cc_final: 0.3583 (tt0) REVERT: H 93 TYR cc_start: 0.4843 (p90) cc_final: 0.4623 (p90) REVERT: H 120 ASN cc_start: 0.5162 (m-40) cc_final: 0.4598 (m-40) REVERT: H 149 GLU cc_start: 0.3851 (pp20) cc_final: 0.2778 (tp30) REVERT: H 159 LYS cc_start: 0.4246 (tttt) cc_final: 0.2430 (mttt) REVERT: H 225 LYS cc_start: 0.3921 (OUTLIER) cc_final: 0.3690 (ptmt) REVERT: H 284 ARG cc_start: 0.2286 (ttm-80) cc_final: 0.1399 (tmt-80) REVERT: H 327 GLU cc_start: 0.3489 (tt0) cc_final: 0.1714 (tm-30) outliers start: 55 outliers final: 27 residues processed: 324 average time/residue: 0.6893 time to fit residues: 276.3264 Evaluate side-chains 282 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 246 time to evaluate : 1.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 695 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 722 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 694 LYS Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain H residue 48 GLU Chi-restraints excluded: chain H residue 225 LYS Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 266 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 202 optimal weight: 3.9990 chunk 134 optimal weight: 3.9990 chunk 197 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 339 optimal weight: 0.4980 chunk 261 optimal weight: 2.9990 chunk 404 optimal weight: 1.9990 chunk 270 optimal weight: 0.5980 chunk 190 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 265 ASN A 411 ASN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 ASN ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 720 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 811 GLN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4051 r_free = 0.4051 target = 0.153764 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.119064 restraints weight = 188921.011| |-----------------------------------------------------------------------------| r_work (start): 0.3565 rms_B_bonded: 3.58 r_work: 0.3456 rms_B_bonded: 3.59 restraints_weight: 0.5000 r_work (final): 0.3456 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3455 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3455 r_free = 0.3455 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3455 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39520 Z= 0.133 Angle : 0.538 9.679 53592 Z= 0.290 Chirality : 0.045 0.173 6003 Planarity : 0.004 0.049 6990 Dihedral : 4.707 48.375 5327 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 1.78 % Allowed : 9.68 % Favored : 88.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.49 (0.12), residues: 4893 helix: 0.70 (0.20), residues: 692 sheet: 0.69 (0.14), residues: 1469 loop : -1.22 (0.12), residues: 2732 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 325 TYR 0.019 0.001 TYR H 397 PHE 0.016 0.001 PHE B 774 TRP 0.006 0.001 TRP F 503 HIS 0.003 0.001 HIS H 385 Details of bonding type rmsd covalent geometry : bond 0.00312 (39520) covalent geometry : angle 0.53771 (53592) hydrogen bonds : bond 0.03103 ( 1322) hydrogen bonds : angle 4.95588 ( 3615) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 260 time to evaluate : 1.556 Fit side-chains REVERT: A 689 LYS cc_start: 0.6327 (tmmt) cc_final: 0.5295 (mtmt) REVERT: A 696 ASP cc_start: 0.6033 (OUTLIER) cc_final: 0.5563 (t70) REVERT: A 722 GLU cc_start: 0.6864 (mt-10) cc_final: 0.6403 (mm-30) REVERT: B 627 ASN cc_start: 0.7898 (t0) cc_final: 0.7641 (t160) REVERT: B 701 GLU cc_start: 0.7137 (mt-10) cc_final: 0.6822 (mt-10) REVERT: B 786 MET cc_start: 0.8908 (tpp) cc_final: 0.8617 (tpp) REVERT: C 305 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.6945 (mm-30) REVERT: C 591 SER cc_start: 0.8441 (t) cc_final: 0.8128 (p) REVERT: C 655 LYS cc_start: 0.6700 (OUTLIER) cc_final: 0.6363 (mttt) REVERT: C 660 MET cc_start: 0.5891 (tmm) cc_final: 0.5525 (tpp) REVERT: C 664 LYS cc_start: 0.7861 (mmtp) cc_final: 0.7460 (mmmt) REVERT: C 712 GLU cc_start: 0.7431 (mm-30) cc_final: 0.7199 (pt0) REVERT: C 736 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8411 (mp) REVERT: C 740 GLU cc_start: 0.7861 (mt-10) cc_final: 0.7659 (tt0) REVERT: C 853 MET cc_start: 0.7856 (mmm) cc_final: 0.7518 (mmm) REVERT: D 417 ASP cc_start: 0.8053 (OUTLIER) cc_final: 0.7767 (m-30) REVERT: D 522 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7373 (tp30) REVERT: E 606 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: E 660 MET cc_start: 0.6886 (tpt) cc_final: 0.6535 (tpt) REVERT: E 853 MET cc_start: 0.7543 (mmm) cc_final: 0.7318 (mmp) REVERT: F 290 ARG cc_start: 0.8115 (mtp180) cc_final: 0.7873 (mtm-85) REVERT: F 305 GLU cc_start: 0.7990 (OUTLIER) cc_final: 0.7438 (mt-10) REVERT: F 376 ASN cc_start: 0.7850 (m-40) cc_final: 0.7561 (t0) REVERT: F 786 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7792 (tpp) REVERT: F 826 ARG cc_start: 0.7461 (OUTLIER) cc_final: 0.6186 (mmt90) REVERT: G 595 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6815 (mm) REVERT: G 668 ARG cc_start: 0.7066 (tmm-80) cc_final: 0.6468 (pmt170) REVERT: H 20 GLU cc_start: 0.3545 (mm-30) cc_final: 0.1853 (pm20) REVERT: H 120 ASN cc_start: 0.5320 (m-40) cc_final: 0.4938 (m-40) REVERT: H 284 ARG cc_start: 0.2258 (ttm-80) cc_final: 0.1394 (ttp-110) REVERT: H 327 GLU cc_start: 0.3595 (tt0) cc_final: 0.1822 (tm-30) REVERT: H 346 MET cc_start: 0.2190 (OUTLIER) cc_final: 0.1388 (mmt) REVERT: H 384 ASN cc_start: 0.3482 (OUTLIER) cc_final: 0.2655 (m-40) REVERT: H 397 TYR cc_start: 0.3866 (p90) cc_final: 0.3334 (p90) outliers start: 71 outliers final: 33 residues processed: 308 average time/residue: 0.7160 time to fit residues: 270.6219 Evaluate side-chains 283 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 237 time to evaluate : 1.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 219 LEU Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 318 ASP Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 522 GLU Chi-restraints excluded: chain D residue 698 LEU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 595 LEU Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 384 ASN Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 24 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 350 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 450 optimal weight: 0.0030 chunk 25 optimal weight: 0.5980 chunk 401 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 259 optimal weight: 1.9990 chunk 214 optimal weight: 0.0040 overall best weight: 0.6604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 639 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.154997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.120298 restraints weight = 209240.495| |-----------------------------------------------------------------------------| r_work (start): 0.3581 rms_B_bonded: 3.83 r_work: 0.3463 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3462 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3462 r_free = 0.3462 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3462 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 39520 Z= 0.101 Angle : 0.503 9.248 53592 Z= 0.271 Chirality : 0.043 0.181 6003 Planarity : 0.004 0.046 6990 Dihedral : 4.523 48.378 5327 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.38 % Favored : 94.62 % Rotamer: Outliers : 1.64 % Allowed : 10.25 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.37 (0.12), residues: 4893 helix: 0.81 (0.20), residues: 692 sheet: 0.88 (0.14), residues: 1479 loop : -1.22 (0.12), residues: 2722 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 325 TYR 0.017 0.001 TYR H 397 PHE 0.029 0.001 PHE G 774 TRP 0.007 0.001 TRP D 375 HIS 0.005 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00228 (39520) covalent geometry : angle 0.50294 (53592) hydrogen bonds : bond 0.02668 ( 1322) hydrogen bonds : angle 4.74824 ( 3615) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 330 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 265 time to evaluate : 1.483 Fit side-chains REVERT: A 477 LYS cc_start: 0.8254 (mtpt) cc_final: 0.7950 (mptt) REVERT: A 689 LYS cc_start: 0.6259 (tmmt) cc_final: 0.5160 (mtmt) REVERT: A 722 GLU cc_start: 0.6894 (mt-10) cc_final: 0.6405 (mm-30) REVERT: B 627 ASN cc_start: 0.7895 (t0) cc_final: 0.7670 (t160) REVERT: B 701 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6836 (mt-10) REVERT: B 786 MET cc_start: 0.8953 (tpp) cc_final: 0.8640 (tpp) REVERT: C 305 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.6911 (mm-30) REVERT: C 319 GLN cc_start: 0.7963 (pt0) cc_final: 0.7527 (tt0) REVERT: C 591 SER cc_start: 0.8410 (t) cc_final: 0.8085 (p) REVERT: C 655 LYS cc_start: 0.6686 (OUTLIER) cc_final: 0.6336 (mttt) REVERT: C 664 LYS cc_start: 0.7845 (mmtp) cc_final: 0.7449 (mmmt) REVERT: C 736 LEU cc_start: 0.8652 (OUTLIER) cc_final: 0.8393 (mp) REVERT: C 853 MET cc_start: 0.7836 (mmm) cc_final: 0.7523 (mmm) REVERT: D 325 ARG cc_start: 0.6862 (ttm-80) cc_final: 0.6590 (ttp80) REVERT: D 417 ASP cc_start: 0.8074 (OUTLIER) cc_final: 0.7871 (m-30) REVERT: D 793 THR cc_start: 0.8898 (p) cc_final: 0.8417 (t) REVERT: E 660 MET cc_start: 0.6853 (tpt) cc_final: 0.6505 (tpt) REVERT: E 853 MET cc_start: 0.7545 (mmm) cc_final: 0.7323 (mmp) REVERT: F 290 ARG cc_start: 0.8142 (mtp180) cc_final: 0.7848 (mtm-85) REVERT: F 376 ASN cc_start: 0.7854 (m-40) cc_final: 0.7571 (t0) REVERT: F 714 THR cc_start: 0.7235 (OUTLIER) cc_final: 0.6704 (p) REVERT: F 786 MET cc_start: 0.8157 (OUTLIER) cc_final: 0.7790 (tpp) REVERT: F 826 ARG cc_start: 0.7435 (OUTLIER) cc_final: 0.6543 (mmt90) REVERT: G 668 ARG cc_start: 0.7067 (tmm-80) cc_final: 0.6478 (pmt170) REVERT: H 20 GLU cc_start: 0.3544 (mm-30) cc_final: 0.1949 (pm20) REVERT: H 120 ASN cc_start: 0.5325 (m-40) cc_final: 0.4930 (m-40) REVERT: H 149 GLU cc_start: 0.3822 (pp20) cc_final: 0.2628 (tp30) REVERT: H 166 MET cc_start: 0.2237 (OUTLIER) cc_final: 0.1512 (tpt) REVERT: H 284 ARG cc_start: 0.2259 (ttm-80) cc_final: 0.1403 (ttp-110) REVERT: H 327 GLU cc_start: 0.3606 (tt0) cc_final: 0.1673 (tm-30) REVERT: H 346 MET cc_start: 0.2236 (OUTLIER) cc_final: 0.1466 (mmt) REVERT: H 397 TYR cc_start: 0.4001 (p90) cc_final: 0.3373 (p90) outliers start: 65 outliers final: 29 residues processed: 308 average time/residue: 0.6820 time to fit residues: 257.6661 Evaluate side-chains 279 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 241 time to evaluate : 1.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain D residue 869 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 278 optimal weight: 3.9990 chunk 402 optimal weight: 0.0470 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 336 optimal weight: 0.0870 chunk 169 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 103 optimal weight: 6.9990 chunk 354 optimal weight: 0.0010 chunk 459 optimal weight: 4.9990 chunk 415 optimal weight: 1.9990 overall best weight: 0.8266 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN B 390 ASN C 390 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4060 r_free = 0.4060 target = 0.154525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.120186 restraints weight = 178664.800| |-----------------------------------------------------------------------------| r_work (start): 0.3576 rms_B_bonded: 3.64 r_work: 0.3466 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3465 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3465 r_free = 0.3465 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3466 r_free = 0.3466 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3466 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 39520 Z= 0.110 Angle : 0.512 9.274 53592 Z= 0.276 Chirality : 0.044 0.165 6003 Planarity : 0.004 0.048 6990 Dihedral : 4.543 48.763 5327 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.67 % Allowed : 11.00 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.41 (0.12), residues: 4893 helix: 0.80 (0.20), residues: 692 sheet: 0.81 (0.14), residues: 1462 loop : -1.22 (0.12), residues: 2739 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 325 TYR 0.015 0.001 TYR D 861 PHE 0.020 0.001 PHE B 774 TRP 0.006 0.001 TRP F 503 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00254 (39520) covalent geometry : angle 0.51236 (53592) hydrogen bonds : bond 0.02725 ( 1322) hydrogen bonds : angle 4.70086 ( 3615) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 256 time to evaluate : 1.559 Fit side-chains REVERT: A 477 LYS cc_start: 0.8246 (mtpt) cc_final: 0.7959 (mptt) REVERT: A 689 LYS cc_start: 0.6246 (tmmt) cc_final: 0.5892 (mmmt) REVERT: A 696 ASP cc_start: 0.5975 (OUTLIER) cc_final: 0.5502 (t70) REVERT: A 722 GLU cc_start: 0.6893 (mt-10) cc_final: 0.6383 (mm-30) REVERT: B 627 ASN cc_start: 0.7961 (t0) cc_final: 0.7690 (t160) REVERT: B 701 GLU cc_start: 0.7147 (mt-10) cc_final: 0.6847 (mt-10) REVERT: B 786 MET cc_start: 0.8951 (tpp) cc_final: 0.8629 (tpp) REVERT: C 305 GLU cc_start: 0.8157 (OUTLIER) cc_final: 0.6910 (mm-30) REVERT: C 319 GLN cc_start: 0.7979 (pt0) cc_final: 0.7587 (tt0) REVERT: C 591 SER cc_start: 0.8388 (t) cc_final: 0.8124 (p) REVERT: C 655 LYS cc_start: 0.6726 (OUTLIER) cc_final: 0.6367 (mttt) REVERT: C 705 THR cc_start: 0.5395 (OUTLIER) cc_final: 0.5165 (t) REVERT: C 736 LEU cc_start: 0.8640 (OUTLIER) cc_final: 0.8391 (mp) REVERT: C 853 MET cc_start: 0.7814 (mmm) cc_final: 0.7492 (mmm) REVERT: D 793 THR cc_start: 0.8852 (p) cc_final: 0.8385 (t) REVERT: E 606 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7018 (mt-10) REVERT: E 660 MET cc_start: 0.6862 (tpt) cc_final: 0.6510 (tpt) REVERT: E 772 LEU cc_start: 0.8099 (OUTLIER) cc_final: 0.7850 (mp) REVERT: E 853 MET cc_start: 0.7493 (mmm) cc_final: 0.7273 (mmp) REVERT: F 290 ARG cc_start: 0.8133 (mtp180) cc_final: 0.7852 (mtm-85) REVERT: F 305 GLU cc_start: 0.7895 (OUTLIER) cc_final: 0.7360 (mt-10) REVERT: F 376 ASN cc_start: 0.7749 (m-40) cc_final: 0.7548 (t0) REVERT: F 480 THR cc_start: 0.8575 (OUTLIER) cc_final: 0.8344 (t) REVERT: F 660 MET cc_start: 0.7230 (tpp) cc_final: 0.6500 (tmm) REVERT: F 714 THR cc_start: 0.7217 (OUTLIER) cc_final: 0.6634 (p) REVERT: F 786 MET cc_start: 0.8162 (OUTLIER) cc_final: 0.7894 (tpp) REVERT: F 826 ARG cc_start: 0.7456 (OUTLIER) cc_final: 0.5992 (mmt90) REVERT: G 668 ARG cc_start: 0.7079 (tmm-80) cc_final: 0.6334 (pmt170) REVERT: G 710 GLU cc_start: 0.8279 (mt-10) cc_final: 0.7606 (tt0) REVERT: H 20 GLU cc_start: 0.3624 (mm-30) cc_final: 0.2040 (pm20) REVERT: H 120 ASN cc_start: 0.5296 (m-40) cc_final: 0.4902 (m-40) REVERT: H 284 ARG cc_start: 0.2152 (ttm-80) cc_final: 0.1305 (ttp-110) REVERT: H 327 GLU cc_start: 0.3570 (tt0) cc_final: 0.1693 (tm-30) REVERT: H 346 MET cc_start: 0.2231 (OUTLIER) cc_final: 0.1456 (mmt) REVERT: H 397 TYR cc_start: 0.4017 (p90) cc_final: 0.3380 (p90) outliers start: 65 outliers final: 38 residues processed: 300 average time/residue: 0.6789 time to fit residues: 251.1133 Evaluate side-chains 289 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 238 time to evaluate : 1.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 LYS Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 869 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 762 MET Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 139 optimal weight: 3.9990 chunk 170 optimal weight: 0.0770 chunk 259 optimal weight: 0.9990 chunk 479 optimal weight: 0.5980 chunk 42 optimal weight: 0.2980 chunk 408 optimal weight: 1.9990 chunk 351 optimal weight: 2.9990 chunk 396 optimal weight: 1.9990 chunk 447 optimal weight: 6.9990 chunk 115 optimal weight: 3.9990 chunk 247 optimal weight: 4.9990 overall best weight: 0.7942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 583 ASN H 54 GLN H 157 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4062 r_free = 0.4062 target = 0.154733 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.119974 restraints weight = 192822.071| |-----------------------------------------------------------------------------| r_work (start): 0.3574 rms_B_bonded: 3.68 r_work: 0.3462 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.3462 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3464 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3464 r_free = 0.3464 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3464 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1584 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 39520 Z= 0.108 Angle : 0.509 9.419 53592 Z= 0.275 Chirality : 0.044 0.194 6003 Planarity : 0.004 0.046 6990 Dihedral : 4.525 48.824 5327 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.76 % Allowed : 11.26 % Favored : 86.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.28 (0.12), residues: 4893 helix: 1.17 (0.21), residues: 656 sheet: 0.84 (0.14), residues: 1466 loop : -1.15 (0.12), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.015 0.001 TYR D 666 PHE 0.028 0.001 PHE G 774 TRP 0.006 0.001 TRP F 503 HIS 0.007 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00249 (39520) covalent geometry : angle 0.50941 (53592) hydrogen bonds : bond 0.02676 ( 1322) hydrogen bonds : angle 4.64968 ( 3615) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 251 time to evaluate : 1.450 Fit side-chains REVERT: A 657 LYS cc_start: 0.7976 (mttm) cc_final: 0.6965 (pttt) REVERT: A 689 LYS cc_start: 0.6276 (tmmt) cc_final: 0.5542 (ttpt) REVERT: A 696 ASP cc_start: 0.5914 (OUTLIER) cc_final: 0.5402 (t70) REVERT: A 722 GLU cc_start: 0.6832 (mt-10) cc_final: 0.6380 (mm-30) REVERT: B 627 ASN cc_start: 0.7956 (t0) cc_final: 0.7699 (t160) REVERT: B 701 GLU cc_start: 0.7146 (mt-10) cc_final: 0.6848 (mt-10) REVERT: B 786 MET cc_start: 0.8943 (tpp) cc_final: 0.8622 (tpp) REVERT: C 305 GLU cc_start: 0.8185 (OUTLIER) cc_final: 0.6961 (mm-30) REVERT: C 319 GLN cc_start: 0.7969 (pt0) cc_final: 0.7610 (tt0) REVERT: C 590 ASP cc_start: 0.6827 (t0) cc_final: 0.6538 (m-30) REVERT: C 591 SER cc_start: 0.8468 (t) cc_final: 0.8140 (p) REVERT: C 655 LYS cc_start: 0.6777 (OUTLIER) cc_final: 0.6419 (mttt) REVERT: C 705 THR cc_start: 0.5413 (OUTLIER) cc_final: 0.5115 (t) REVERT: C 736 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8388 (mp) REVERT: C 853 MET cc_start: 0.7830 (mmm) cc_final: 0.7524 (mmm) REVERT: D 793 THR cc_start: 0.8841 (p) cc_final: 0.8369 (t) REVERT: E 319 GLN cc_start: 0.7592 (pt0) cc_final: 0.7142 (pt0) REVERT: E 606 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.7031 (mt-10) REVERT: E 660 MET cc_start: 0.6916 (tpt) cc_final: 0.6572 (tpt) REVERT: E 772 LEU cc_start: 0.8062 (OUTLIER) cc_final: 0.7826 (mp) REVERT: E 853 MET cc_start: 0.7481 (mmm) cc_final: 0.7261 (mmp) REVERT: F 290 ARG cc_start: 0.8160 (mtp180) cc_final: 0.7885 (mtm-85) REVERT: F 305 GLU cc_start: 0.7891 (OUTLIER) cc_final: 0.7359 (mt-10) REVERT: F 480 THR cc_start: 0.8571 (OUTLIER) cc_final: 0.8339 (t) REVERT: F 491 ASN cc_start: 0.5408 (t0) cc_final: 0.5141 (p0) REVERT: F 660 MET cc_start: 0.7300 (tpp) cc_final: 0.6638 (tmm) REVERT: F 714 THR cc_start: 0.7084 (OUTLIER) cc_final: 0.6555 (p) REVERT: F 786 MET cc_start: 0.8179 (OUTLIER) cc_final: 0.7840 (tpp) REVERT: F 826 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6546 (mmt90) REVERT: G 297 TYR cc_start: 0.8339 (t80) cc_final: 0.8107 (t80) REVERT: G 668 ARG cc_start: 0.7089 (tmm-80) cc_final: 0.6358 (pmt170) REVERT: G 710 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7654 (tt0) REVERT: H 20 GLU cc_start: 0.3720 (mm-30) cc_final: 0.2145 (pm20) REVERT: H 120 ASN cc_start: 0.5318 (m-40) cc_final: 0.4913 (m-40) REVERT: H 149 GLU cc_start: 0.3669 (pp20) cc_final: 0.2639 (tp30) REVERT: H 284 ARG cc_start: 0.2181 (ttm-80) cc_final: 0.1314 (ttp-110) REVERT: H 327 GLU cc_start: 0.3569 (tt0) cc_final: 0.1680 (tm-30) REVERT: H 346 MET cc_start: 0.2408 (OUTLIER) cc_final: 0.1592 (mmt) REVERT: H 397 TYR cc_start: 0.4058 (p90) cc_final: 0.3417 (p90) outliers start: 68 outliers final: 41 residues processed: 299 average time/residue: 0.6943 time to fit residues: 256.9693 Evaluate side-chains 297 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 243 time to evaluate : 2.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 869 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 606 GLU Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 343 optimal weight: 5.9990 chunk 334 optimal weight: 0.9980 chunk 33 optimal weight: 0.0370 chunk 360 optimal weight: 0.0060 chunk 314 optimal weight: 5.9990 chunk 231 optimal weight: 0.7980 chunk 133 optimal weight: 4.9990 chunk 50 optimal weight: 6.9990 chunk 287 optimal weight: 2.9990 chunk 147 optimal weight: 1.9990 chunk 319 optimal weight: 3.9990 overall best weight: 0.7676 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN D 648 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** H 54 GLN ** H 157 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 = 0.4064 r_free = 0.4064 target = 0.154830 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.120311 restraints weight = 212928.890| |-----------------------------------------------------------------------------| r_work (start): 0.3572 rms_B_bonded: 4.08 r_work: 0.3449 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3453 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3453 r_free = 0.3453 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3453 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 39520 Z= 0.107 Angle : 0.508 8.906 53592 Z= 0.274 Chirality : 0.044 0.183 6003 Planarity : 0.004 0.045 6990 Dihedral : 4.500 48.747 5327 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 1.71 % Allowed : 11.51 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.25 (0.12), residues: 4893 helix: 1.21 (0.21), residues: 656 sheet: 0.86 (0.14), residues: 1468 loop : -1.14 (0.12), residues: 2769 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.014 0.001 TYR E 704 PHE 0.020 0.001 PHE B 774 TRP 0.006 0.001 TRP F 503 HIS 0.008 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00245 (39520) covalent geometry : angle 0.50791 (53592) hydrogen bonds : bond 0.02637 ( 1322) hydrogen bonds : angle 4.61016 ( 3615) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 255 time to evaluate : 1.329 Fit side-chains revert: symmetry clash REVERT: A 370 SER cc_start: 0.7174 (p) cc_final: 0.6781 (t) REVERT: A 657 LYS cc_start: 0.7989 (mttm) cc_final: 0.6978 (pttt) REVERT: A 689 LYS cc_start: 0.6279 (tmmt) cc_final: 0.5832 (mmmt) REVERT: A 696 ASP cc_start: 0.5999 (OUTLIER) cc_final: 0.5482 (t70) REVERT: A 722 GLU cc_start: 0.6851 (mt-10) cc_final: 0.6364 (mm-30) REVERT: B 627 ASN cc_start: 0.7945 (t0) cc_final: 0.7671 (t160) REVERT: B 701 GLU cc_start: 0.7149 (mt-10) cc_final: 0.6853 (mt-10) REVERT: B 786 MET cc_start: 0.8958 (tpp) cc_final: 0.8646 (tpp) REVERT: C 305 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.6992 (mm-30) REVERT: C 319 GLN cc_start: 0.7949 (pt0) cc_final: 0.7585 (tt0) REVERT: C 590 ASP cc_start: 0.6882 (t0) cc_final: 0.6655 (m-30) REVERT: C 591 SER cc_start: 0.8486 (t) cc_final: 0.8146 (p) REVERT: C 655 LYS cc_start: 0.6703 (OUTLIER) cc_final: 0.6361 (mttt) REVERT: C 705 THR cc_start: 0.5652 (OUTLIER) cc_final: 0.5328 (t) REVERT: C 736 LEU cc_start: 0.8629 (OUTLIER) cc_final: 0.8368 (mp) REVERT: C 853 MET cc_start: 0.7806 (mmm) cc_final: 0.7496 (mmm) REVERT: D 793 THR cc_start: 0.8887 (p) cc_final: 0.8374 (t) REVERT: D 853 MET cc_start: 0.8103 (mmm) cc_final: 0.7435 (mpp) REVERT: E 660 MET cc_start: 0.6950 (tpt) cc_final: 0.6594 (tpt) REVERT: E 772 LEU cc_start: 0.8074 (OUTLIER) cc_final: 0.7866 (mp) REVERT: F 290 ARG cc_start: 0.8178 (mtp180) cc_final: 0.7885 (mtm-85) REVERT: F 305 GLU cc_start: 0.7910 (OUTLIER) cc_final: 0.7384 (mt-10) REVERT: F 480 THR cc_start: 0.8586 (OUTLIER) cc_final: 0.8357 (t) REVERT: F 660 MET cc_start: 0.7319 (tpp) cc_final: 0.6505 (tmm) REVERT: F 714 THR cc_start: 0.7070 (OUTLIER) cc_final: 0.6540 (p) REVERT: F 786 MET cc_start: 0.8182 (OUTLIER) cc_final: 0.7862 (tpp) REVERT: F 826 ARG cc_start: 0.7469 (OUTLIER) cc_final: 0.7083 (mtt90) REVERT: G 297 TYR cc_start: 0.8372 (t80) cc_final: 0.8130 (t80) REVERT: G 668 ARG cc_start: 0.7117 (tmm-80) cc_final: 0.6323 (pmt170) REVERT: G 710 GLU cc_start: 0.8289 (mt-10) cc_final: 0.7540 (tm-30) REVERT: H 20 GLU cc_start: 0.3681 (mm-30) cc_final: 0.2145 (pm20) REVERT: H 28 GLU cc_start: 0.4391 (OUTLIER) cc_final: 0.4140 (pt0) REVERT: H 120 ASN cc_start: 0.5228 (m-40) cc_final: 0.4831 (m-40) REVERT: H 149 GLU cc_start: 0.3784 (pp20) cc_final: 0.2710 (tp30) REVERT: H 284 ARG cc_start: 0.2186 (ttm-80) cc_final: 0.1303 (ttp-110) REVERT: H 327 GLU cc_start: 0.3527 (tt0) cc_final: 0.1644 (tm-30) REVERT: H 346 MET cc_start: 0.2325 (OUTLIER) cc_final: 0.1526 (mmt) REVERT: H 397 TYR cc_start: 0.4073 (p90) cc_final: 0.3476 (p90) outliers start: 66 outliers final: 45 residues processed: 302 average time/residue: 0.6670 time to fit residues: 250.1086 Evaluate side-chains 298 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 240 time to evaluate : 1.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 606 GLU Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 692 GLU Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain D residue 869 GLU Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 34 optimal weight: 2.9990 chunk 176 optimal weight: 0.9980 chunk 11 optimal weight: 7.9990 chunk 258 optimal weight: 1.9990 chunk 427 optimal weight: 10.0000 chunk 202 optimal weight: 2.9990 chunk 149 optimal weight: 2.9990 chunk 329 optimal weight: 1.9990 chunk 201 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 125 optimal weight: 0.5980 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 567 ASN C 390 ASN D 648 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 773 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 780 ASN H 54 GLN ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4054 r_free = 0.4054 target = 0.153995 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.119419 restraints weight = 202516.321| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.93 r_work: 0.3442 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3443 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3443 r_free = 0.3443 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3443 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 39520 Z= 0.125 Angle : 0.533 9.639 53592 Z= 0.287 Chirality : 0.044 0.183 6003 Planarity : 0.004 0.045 6990 Dihedral : 4.646 48.775 5327 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.76 % Allowed : 11.76 % Favored : 86.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.40 (0.12), residues: 4893 helix: 0.87 (0.20), residues: 686 sheet: 0.79 (0.14), residues: 1474 loop : -1.22 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.017 0.001 TYR D 666 PHE 0.012 0.001 PHE C 711 TRP 0.006 0.001 TRP F 503 HIS 0.010 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00291 (39520) covalent geometry : angle 0.53320 (53592) hydrogen bonds : bond 0.02849 ( 1322) hydrogen bonds : angle 4.68084 ( 3615) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 252 time to evaluate : 1.568 Fit side-chains revert: symmetry clash REVERT: A 477 LYS cc_start: 0.8220 (mtpt) cc_final: 0.7881 (mttt) REVERT: A 657 LYS cc_start: 0.7977 (mttm) cc_final: 0.6961 (pttt) REVERT: A 689 LYS cc_start: 0.6191 (tmmt) cc_final: 0.5790 (mmmt) REVERT: A 696 ASP cc_start: 0.6074 (OUTLIER) cc_final: 0.5530 (t70) REVERT: A 722 GLU cc_start: 0.6848 (mt-10) cc_final: 0.6346 (mm-30) REVERT: B 627 ASN cc_start: 0.7977 (t0) cc_final: 0.7723 (t160) REVERT: B 701 GLU cc_start: 0.7174 (mt-10) cc_final: 0.6871 (mt-10) REVERT: B 786 MET cc_start: 0.8959 (tpp) cc_final: 0.8634 (tpp) REVERT: C 305 GLU cc_start: 0.8243 (OUTLIER) cc_final: 0.6990 (mm-30) REVERT: C 319 GLN cc_start: 0.7944 (pt0) cc_final: 0.7570 (tt0) REVERT: C 590 ASP cc_start: 0.6849 (t0) cc_final: 0.6560 (m-30) REVERT: C 591 SER cc_start: 0.8468 (t) cc_final: 0.8143 (p) REVERT: C 655 LYS cc_start: 0.6714 (OUTLIER) cc_final: 0.6376 (mttt) REVERT: C 705 THR cc_start: 0.5435 (OUTLIER) cc_final: 0.5179 (t) REVERT: C 736 LEU cc_start: 0.8646 (OUTLIER) cc_final: 0.8370 (mp) REVERT: C 853 MET cc_start: 0.7818 (mmm) cc_final: 0.7490 (mmm) REVERT: D 793 THR cc_start: 0.8874 (p) cc_final: 0.8414 (t) REVERT: E 660 MET cc_start: 0.6898 (tpt) cc_final: 0.6549 (tpt) REVERT: F 290 ARG cc_start: 0.8207 (mtp180) cc_final: 0.7917 (mtm-85) REVERT: F 305 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7396 (mt-10) REVERT: F 480 THR cc_start: 0.8626 (OUTLIER) cc_final: 0.8379 (t) REVERT: F 660 MET cc_start: 0.7276 (tpp) cc_final: 0.6492 (tmm) REVERT: F 714 THR cc_start: 0.7135 (OUTLIER) cc_final: 0.6543 (p) REVERT: F 786 MET cc_start: 0.8216 (OUTLIER) cc_final: 0.7886 (tpp) REVERT: F 826 ARG cc_start: 0.7451 (OUTLIER) cc_final: 0.6586 (mmt90) REVERT: G 297 TYR cc_start: 0.8382 (t80) cc_final: 0.8150 (t80) REVERT: G 668 ARG cc_start: 0.7139 (tmm-80) cc_final: 0.6309 (pmt170) REVERT: G 691 LYS cc_start: 0.5774 (OUTLIER) cc_final: 0.4647 (ttmt) REVERT: G 710 GLU cc_start: 0.8287 (mt-10) cc_final: 0.7557 (tm-30) REVERT: H 20 GLU cc_start: 0.3691 (mm-30) cc_final: 0.2145 (pm20) REVERT: H 28 GLU cc_start: 0.4409 (OUTLIER) cc_final: 0.4125 (pt0) REVERT: H 57 ASN cc_start: 0.3953 (p0) cc_final: 0.3563 (p0) REVERT: H 120 ASN cc_start: 0.5261 (m-40) cc_final: 0.4801 (m-40) REVERT: H 149 GLU cc_start: 0.3851 (pp20) cc_final: 0.2749 (tp30) REVERT: H 166 MET cc_start: 0.2099 (OUTLIER) cc_final: 0.1379 (tpt) REVERT: H 284 ARG cc_start: 0.2126 (ttm-80) cc_final: 0.1233 (ttp-110) REVERT: H 327 GLU cc_start: 0.3530 (tt0) cc_final: 0.1669 (tm-30) REVERT: H 346 MET cc_start: 0.2373 (OUTLIER) cc_final: 0.1571 (mmt) outliers start: 67 outliers final: 44 residues processed: 299 average time/residue: 0.6953 time to fit residues: 256.0193 Evaluate side-chains 301 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 243 time to evaluate : 1.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 328 THR Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 328 THR Chi-restraints excluded: chain C residue 463 ASN Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 322 THR Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 762 MET Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 305 GLU Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 54 GLN Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 292 THR Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 410 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 97 optimal weight: 1.9990 chunk 274 optimal weight: 1.9990 chunk 406 optimal weight: 5.9990 chunk 12 optimal weight: 9.9990 chunk 168 optimal weight: 5.9990 chunk 92 optimal weight: 2.9990 chunk 396 optimal weight: 0.0370 chunk 315 optimal weight: 0.0770 chunk 219 optimal weight: 0.0010 chunk 217 optimal weight: 2.9990 chunk 20 optimal weight: 0.0470 overall best weight: 0.4322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 648 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.155765 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.120951 restraints weight = 209553.857| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.76 r_work: 0.3475 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.3475 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3477 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3477 r_free = 0.3477 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3477 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 39520 Z= 0.092 Angle : 0.497 10.250 53592 Z= 0.267 Chirality : 0.043 0.179 6003 Planarity : 0.004 0.044 6990 Dihedral : 4.401 48.065 5327 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 1.32 % Allowed : 12.21 % Favored : 86.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.14 (0.12), residues: 4893 helix: 1.34 (0.21), residues: 649 sheet: 0.97 (0.14), residues: 1487 loop : -1.10 (0.12), residues: 2757 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 325 TYR 0.028 0.001 TYR H 397 PHE 0.024 0.001 PHE B 774 TRP 0.008 0.001 TRP D 375 HIS 0.010 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00204 (39520) covalent geometry : angle 0.49720 (53592) hydrogen bonds : bond 0.02368 ( 1322) hydrogen bonds : angle 4.54703 ( 3615) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9786 Ramachandran restraints generated. 4893 Oldfield, 0 Emsley, 4893 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 313 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 265 time to evaluate : 1.510 Fit side-chains revert: symmetry clash REVERT: A 370 SER cc_start: 0.7195 (p) cc_final: 0.6864 (t) REVERT: A 477 LYS cc_start: 0.8141 (mtpt) cc_final: 0.7857 (mttt) REVERT: A 657 LYS cc_start: 0.7973 (mttm) cc_final: 0.6986 (pttt) REVERT: A 689 LYS cc_start: 0.6227 (tmmt) cc_final: 0.5818 (mmmt) REVERT: A 722 GLU cc_start: 0.6861 (mt-10) cc_final: 0.6385 (mm-30) REVERT: B 325 ARG cc_start: 0.7323 (OUTLIER) cc_final: 0.6475 (ttp80) REVERT: B 471 ASP cc_start: 0.7615 (p0) cc_final: 0.7382 (p0) REVERT: B 627 ASN cc_start: 0.7868 (t0) cc_final: 0.7659 (t160) REVERT: B 687 LYS cc_start: 0.6345 (tttt) cc_final: 0.5765 (ptmt) REVERT: B 701 GLU cc_start: 0.7148 (mt-10) cc_final: 0.6866 (mt-10) REVERT: B 786 MET cc_start: 0.8928 (tpp) cc_final: 0.8619 (tpp) REVERT: C 305 GLU cc_start: 0.8121 (OUTLIER) cc_final: 0.6843 (mm-30) REVERT: C 319 GLN cc_start: 0.7888 (pt0) cc_final: 0.7592 (tt0) REVERT: C 591 SER cc_start: 0.8471 (t) cc_final: 0.8178 (p) REVERT: C 655 LYS cc_start: 0.6701 (OUTLIER) cc_final: 0.6335 (mttt) REVERT: C 705 THR cc_start: 0.5617 (OUTLIER) cc_final: 0.5366 (t) REVERT: C 736 LEU cc_start: 0.8571 (OUTLIER) cc_final: 0.8312 (mp) REVERT: C 853 MET cc_start: 0.7809 (mmm) cc_final: 0.7443 (mmm) REVERT: D 793 THR cc_start: 0.8854 (p) cc_final: 0.8334 (t) REVERT: E 660 MET cc_start: 0.6889 (tpt) cc_final: 0.6538 (tpt) REVERT: E 772 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7844 (mp) REVERT: F 290 ARG cc_start: 0.8206 (mtp180) cc_final: 0.7904 (mtm-85) REVERT: F 480 THR cc_start: 0.8521 (OUTLIER) cc_final: 0.8303 (t) REVERT: F 660 MET cc_start: 0.7283 (tpp) cc_final: 0.6557 (tmm) REVERT: F 714 THR cc_start: 0.7076 (OUTLIER) cc_final: 0.6537 (p) REVERT: F 786 MET cc_start: 0.8145 (OUTLIER) cc_final: 0.7743 (tpp) REVERT: F 826 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.7064 (mtt90) REVERT: G 668 ARG cc_start: 0.7109 (tmm-80) cc_final: 0.6358 (pmt170) REVERT: G 710 GLU cc_start: 0.8273 (mt-10) cc_final: 0.7548 (tm-30) REVERT: H 20 GLU cc_start: 0.3728 (mm-30) cc_final: 0.2057 (pm20) REVERT: H 28 GLU cc_start: 0.4466 (OUTLIER) cc_final: 0.4194 (pt0) REVERT: H 57 ASN cc_start: 0.4013 (p0) cc_final: 0.3569 (p0) REVERT: H 120 ASN cc_start: 0.5285 (m-40) cc_final: 0.4878 (m-40) REVERT: H 149 GLU cc_start: 0.3887 (pp20) cc_final: 0.2852 (tp30) REVERT: H 166 MET cc_start: 0.2064 (OUTLIER) cc_final: 0.1041 (tmm) REVERT: H 284 ARG cc_start: 0.2265 (ttm-80) cc_final: 0.1355 (ttp-110) REVERT: H 327 GLU cc_start: 0.3528 (tt0) cc_final: 0.1547 (tm-30) REVERT: H 346 MET cc_start: 0.2383 (OUTLIER) cc_final: 0.1597 (mmt) REVERT: H 397 TYR cc_start: 0.3892 (p90) cc_final: 0.3367 (p90) outliers start: 48 outliers final: 30 residues processed: 301 average time/residue: 0.6546 time to fit residues: 244.4126 Evaluate side-chains 290 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 247 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 713 THR Chi-restraints excluded: chain B residue 281 PHE Chi-restraints excluded: chain B residue 325 ARG Chi-restraints excluded: chain B residue 594 THR Chi-restraints excluded: chain B residue 699 VAL Chi-restraints excluded: chain C residue 281 PHE Chi-restraints excluded: chain C residue 305 GLU Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP Chi-restraints excluded: chain C residue 655 LYS Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 705 THR Chi-restraints excluded: chain C residue 712 GLU Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain C residue 757 THR Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 762 MET Chi-restraints excluded: chain E residue 281 PHE Chi-restraints excluded: chain E residue 588 ILE Chi-restraints excluded: chain E residue 594 THR Chi-restraints excluded: chain E residue 724 THR Chi-restraints excluded: chain E residue 772 LEU Chi-restraints excluded: chain E residue 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 480 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 THR Chi-restraints excluded: chain F residue 739 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain F residue 826 ARG Chi-restraints excluded: chain F residue 854 THR Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain H residue 28 GLU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 175 VAL Chi-restraints excluded: chain H residue 346 MET Chi-restraints excluded: chain H residue 379 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 455 optimal weight: 4.9990 chunk 271 optimal weight: 0.9980 chunk 362 optimal weight: 0.2980 chunk 307 optimal weight: 5.9990 chunk 365 optimal weight: 0.9980 chunk 312 optimal weight: 0.5980 chunk 220 optimal weight: 3.9990 chunk 89 optimal weight: 1.9990 chunk 438 optimal weight: 1.9990 chunk 427 optimal weight: 9.9990 chunk 225 optimal weight: 3.9990 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 411 ASN D 648 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 157 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4058 r_free = 0.4058 target = 0.154365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.119728 restraints weight = 217052.131| |-----------------------------------------------------------------------------| r_work (start): 0.3569 rms_B_bonded: 3.91 r_work: 0.3443 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.3443 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3446 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3446 r_free = 0.3446 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3446 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.1734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 39520 Z= 0.120 Angle : 0.527 10.199 53592 Z= 0.283 Chirality : 0.044 0.180 6003 Planarity : 0.004 0.045 6990 Dihedral : 4.558 48.969 5327 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.69 % Favored : 94.31 % Rotamer: Outliers : 1.37 % Allowed : 12.51 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.35 % 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: -0.34 (0.12), residues: 4893 helix: 0.93 (0.20), residues: 686 sheet: 0.85 (0.14), residues: 1474 loop : -1.19 (0.12), residues: 2733 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 668 TYR 0.025 0.001 TYR H 397 PHE 0.012 0.001 PHE E 774 TRP 0.006 0.001 TRP F 503 HIS 0.011 0.001 HIS H 157 Details of bonding type rmsd covalent geometry : bond 0.00279 (39520) covalent geometry : angle 0.52670 (53592) hydrogen bonds : bond 0.02734 ( 1322) hydrogen bonds : angle 4.60192 ( 3615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15286.01 seconds wall clock time: 261 minutes 10.12 seconds (15670.12 seconds total)