Starting phenix.real_space_refine on Mon Jul 6 19:54:56 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7vnn_32043/07_2026/7vnn_32043.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vnn_32043/07_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_32043/07_2026/7vnn_32043.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vnn_32043/07_2026/7vnn_32043.map" restraint_files = "/net/cci-nas-00/data/ceres_data/7vnn_32043/07_2026/7vnn_32043.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7vnn_32043/07_2026/7vnn_32043.cif" model { file = "/net/cci-nas-00/data/ceres_data/7vnn_32043/07_2026/7vnn_32043.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vnn_32043/07_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): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 11.50, per 1000 atoms: 0.30 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: 2.53 Conformation dependent library (CDL) restraints added in 2.3 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: 1.47 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: 9.02 Time building geometry restraints manager: 3.51 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: 5.600 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: 0.020 Extract box with map and model: 0.680 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 38.660 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.070 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:6.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 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/Z covalent geometry : bond 0.00269 / 0.13 (39520) covalent geometry : angle 0.53670 / 0.30 (53592) hydrogen bonds : bond 0.22834 / 15.27 ( 1322) hydrogen bonds : angle 8.63620 / 5.98 ( 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 : 1.422 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: 0.6347 time to fit residues: 293.2350 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 : 1.495 ------------------------------------------------------------------------------- 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... 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 = 0.155309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.120822 restraints weight = 179870.912| |-----------------------------------------------------------------------------| r_work (start): 0.3594 rms_B_bonded: 3.61 r_work: 0.3475 rms_B_bonded: 3.76 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 = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3471 r_free = 0.3471 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 9 (17 function evaluations) r_final: 0.3471 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1037 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= 0.120 Angle : 0.544 8.781 53592 Z= 0.295 Chirality : 0.045 0.175 6003 Planarity : 0.004 0.059 6990 Dihedral : 4.723 47.319 5327 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.44 % Favored : 94.56 % Rotamer: Outliers : 1.28 % Allowed : 5.89 % Favored : 92.83 % 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 0.019 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 H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (39520) covalent geometry : angle 0.54364 / 0.30 (53592) hydrogen bonds : bond 0.03520 / 2.35 ( 1322) hydrogen bonds : angle 5.59033 / 3.88 ( 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 346 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 296 time to evaluate : 1.207 Fit side-chains REVERT: A 689 LYS cc_start: 0.6197 (tmmt) cc_final: 0.5597 (ttpt) REVERT: A 722 GLU cc_start: 0.6847 (mt-10) cc_final: 0.6363 (mm-30) REVERT: B 627 ASN cc_start: 0.7903 (t0) cc_final: 0.7673 (t160) REVERT: B 786 MET cc_start: 0.8888 (tpp) cc_final: 0.8591 (tpp) REVERT: C 591 SER cc_start: 0.8491 (t) cc_final: 0.8207 (p) REVERT: C 664 LYS cc_start: 0.7736 (mmtp) cc_final: 0.7425 (mmmt) REVERT: C 736 LEU cc_start: 0.8712 (OUTLIER) cc_final: 0.8433 (mp) REVERT: C 853 MET cc_start: 0.7841 (mmm) cc_final: 0.7499 (mmm) REVERT: D 722 GLU cc_start: 0.6795 (OUTLIER) cc_final: 0.6461 (pm20) REVERT: F 290 ARG cc_start: 0.8190 (mtp180) cc_final: 0.7959 (mtm-85) REVERT: F 376 ASN cc_start: 0.7930 (m110) cc_final: 0.7624 (t0) REVERT: G 524 GLU cc_start: 0.7944 (tt0) cc_final: 0.7720 (tt0) REVERT: G 668 ARG cc_start: 0.7052 (tmm-80) cc_final: 0.6414 (pmt170) REVERT: G 689 LYS cc_start: 0.6487 (tmmt) cc_final: 0.6130 (ttpp) REVERT: H 20 GLU cc_start: 0.3564 (mm-30) cc_final: 0.1864 (pm20) REVERT: H 48 GLU cc_start: 0.4106 (OUTLIER) cc_final: 0.3893 (tt0) REVERT: H 120 ASN cc_start: 0.5144 (m-40) cc_final: 0.4579 (m-40) REVERT: H 284 ARG cc_start: 0.2260 (ttm-80) cc_final: 0.1377 (tmt-80) outliers start: 50 outliers final: 21 residues processed: 330 average time/residue: 0.5820 time to fit residues: 238.6277 Evaluate side-chains 269 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 245 time to evaluate : 1.097 ------------------------------------------------------------------------------- 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: 0.0370 chunk 78 optimal weight: 4.9990 chunk 330 optimal weight: 0.4980 chunk 102 optimal weight: 2.9990 chunk 235 optimal weight: 4.9990 chunk 103 optimal weight: 7.9990 chunk 431 optimal weight: 0.5980 chunk 458 optimal weight: 0.2980 chunk 73 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 265 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: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.155792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.121165 restraints weight = 201764.858| |-----------------------------------------------------------------------------| r_work (start): 0.3596 rms_B_bonded: 3.67 r_work: 0.3480 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3480 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3480 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3480 r_free = 0.3480 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 = 0.3480 r_free = 0.3480 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (9 function evaluations) r_final: 0.3480 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.1293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39520 Z= 0.097 Angle : 0.501 9.025 53592 Z= 0.271 Chirality : 0.043 0.177 6003 Planarity : 0.004 0.050 6990 Dihedral : 4.484 47.796 5327 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 1.26 % Allowed : 8.24 % Favored : 90.50 % 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: 0.83 (0.20), residues: 687 sheet: 0.75 (0.14), residues: 1495 loop : -1.15 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 325 TYR 0.029 0.001 TYR H 397 PHE 0.033 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/Z covalent geometry : bond 0.00215 / 0.10 (39520) covalent geometry : angle 0.50062 / 0.27 (53592) hydrogen bonds : bond 0.02906 / 1.95 ( 1322) hydrogen bonds : angle 5.04099 / 3.50 ( 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 335 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 286 time to evaluate : 1.427 Fit side-chains revert: symmetry clash REVERT: A 689 LYS cc_start: 0.6257 (tmmt) cc_final: 0.5445 (ttpt) REVERT: A 696 ASP cc_start: 0.5956 (OUTLIER) cc_final: 0.5502 (t70) REVERT: A 722 GLU cc_start: 0.6788 (mt-10) cc_final: 0.6320 (mm-30) REVERT: B 627 ASN cc_start: 0.7845 (t0) cc_final: 0.7615 (t160) REVERT: B 668 ARG cc_start: 0.7150 (tmm-80) cc_final: 0.6913 (tmm-80) REVERT: B 701 GLU cc_start: 0.7126 (mt-10) cc_final: 0.6824 (mt-10) REVERT: B 786 MET cc_start: 0.8916 (tpp) cc_final: 0.8635 (tpp) REVERT: C 591 SER cc_start: 0.8469 (t) cc_final: 0.8177 (p) REVERT: C 664 LYS cc_start: 0.7723 (mmtp) cc_final: 0.7398 (mmmt) REVERT: C 712 GLU cc_start: 0.7480 (mm-30) cc_final: 0.7231 (pt0) REVERT: C 736 LEU cc_start: 0.8661 (OUTLIER) cc_final: 0.8401 (mp) REVERT: C 853 MET cc_start: 0.7824 (mmm) cc_final: 0.7488 (mmm) REVERT: D 722 GLU cc_start: 0.6476 (OUTLIER) cc_final: 0.6157 (pm20) REVERT: E 660 MET cc_start: 0.6861 (tpt) cc_final: 0.6472 (tpt) REVERT: F 290 ARG cc_start: 0.8192 (mtp180) cc_final: 0.7896 (mtm-85) REVERT: F 376 ASN cc_start: 0.7887 (m-40) cc_final: 0.7620 (t0) REVERT: F 786 MET cc_start: 0.8103 (OUTLIER) cc_final: 0.7726 (tpp) REVERT: F 826 ARG cc_start: 0.7501 (OUTLIER) cc_final: 0.7149 (mtt90) REVERT: G 524 GLU cc_start: 0.7935 (tt0) cc_final: 0.7722 (tt0) REVERT: G 595 LEU cc_start: 0.7284 (OUTLIER) cc_final: 0.6979 (mm) REVERT: G 668 ARG cc_start: 0.7006 (tmm-80) cc_final: 0.6471 (pmt170) REVERT: G 689 LYS cc_start: 0.6395 (tmmt) cc_final: 0.6137 (ttpp) REVERT: H 20 GLU cc_start: 0.3578 (mm-30) cc_final: 0.1936 (pm20) REVERT: H 48 GLU cc_start: 0.3809 (OUTLIER) cc_final: 0.3568 (tt0) REVERT: H 120 ASN cc_start: 0.5137 (m-40) cc_final: 0.4576 (m-40) REVERT: H 149 GLU cc_start: 0.3879 (pp20) cc_final: 0.2754 (tp30) REVERT: H 159 LYS cc_start: 0.4272 (tttt) cc_final: 0.2435 (mttt) REVERT: H 179 ILE cc_start: 0.2584 (pt) cc_final: 0.2321 (pp) REVERT: H 225 LYS cc_start: 0.3902 (OUTLIER) cc_final: 0.3667 (ptmt) REVERT: H 284 ARG cc_start: 0.2313 (ttm-80) cc_final: 0.1419 (tmt-80) REVERT: H 327 GLU cc_start: 0.3473 (tt0) cc_final: 0.1704 (tm-30) outliers start: 49 outliers final: 25 residues processed: 319 average time/residue: 0.5997 time to fit residues: 237.2939 Evaluate side-chains 283 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 250 time to evaluate : 1.462 ------------------------------------------------------------------------------- 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 668 ARG 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 480 THR 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 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 H residue 48 GLU Chi-restraints excluded: chain H residue 201 ILE 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 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: 9.9990 chunk 202 optimal weight: 5.9990 chunk 134 optimal weight: 2.9990 chunk 197 optimal weight: 0.6980 chunk 53 optimal weight: 3.9990 chunk 339 optimal weight: 0.0980 chunk 261 optimal weight: 0.4980 chunk 404 optimal weight: 0.7980 chunk 270 optimal weight: 2.9990 chunk 190 optimal weight: 0.0770 overall best weight: 0.4338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN A 811 GLN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** 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 = 0.4083 r_free = 0.4083 target = 0.156305 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121886 restraints weight = 185348.181| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 3.65 r_work: 0.3489 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3491 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3491 r_free = 0.3491 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3491 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.1493 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= 0.091 Angle : 0.486 9.356 53592 Z= 0.262 Chirality : 0.043 0.157 6003 Planarity : 0.003 0.048 6990 Dihedral : 4.341 48.654 5327 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 1.37 % Allowed : 9.41 % Favored : 89.22 % 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: -0.29 (0.12), residues: 4893 helix: 0.92 (0.20), residues: 691 sheet: 0.87 (0.14), residues: 1489 loop : -1.15 (0.12), residues: 2713 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 668 TYR 0.021 0.001 TYR H 397 PHE 0.021 0.001 PHE B 774 TRP 0.008 0.001 TRP D 375 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00202 / 0.09 (39520) covalent geometry : angle 0.48553 / 0.26 (53592) hydrogen bonds : bond 0.02550 / 1.71 ( 1322) hydrogen bonds : angle 4.74746 / 3.29 ( 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 330 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 277 time to evaluate : 1.452 Fit side-chains REVERT: A 477 LYS cc_start: 0.8181 (mtpt) cc_final: 0.7916 (mptt) REVERT: A 689 LYS cc_start: 0.6198 (tmmt) cc_final: 0.5085 (mtmt) REVERT: A 696 ASP cc_start: 0.6044 (OUTLIER) cc_final: 0.5583 (t70) REVERT: A 722 GLU cc_start: 0.6808 (mt-10) cc_final: 0.6364 (mm-30) REVERT: B 627 ASN cc_start: 0.7811 (t0) cc_final: 0.7606 (t160) REVERT: B 701 GLU cc_start: 0.7109 (mt-10) cc_final: 0.6812 (mt-10) REVERT: B 786 MET cc_start: 0.8895 (tpp) cc_final: 0.8604 (tpp) REVERT: C 305 GLU cc_start: 0.8053 (OUTLIER) cc_final: 0.6786 (mm-30) REVERT: C 319 GLN cc_start: 0.7954 (pt0) cc_final: 0.7642 (pt0) REVERT: C 591 SER cc_start: 0.8423 (t) cc_final: 0.8111 (p) REVERT: C 660 MET cc_start: 0.5741 (tmm) cc_final: 0.5480 (tpp) REVERT: C 716 LYS cc_start: 0.5622 (tptt) cc_final: 0.4828 (ptmm) REVERT: C 853 MET cc_start: 0.7805 (mmm) cc_final: 0.7500 (mmm) REVERT: D 722 GLU cc_start: 0.6333 (OUTLIER) cc_final: 0.6132 (pm20) REVERT: D 793 THR cc_start: 0.8848 (p) cc_final: 0.8301 (t) REVERT: E 606 GLU cc_start: 0.8054 (OUTLIER) cc_final: 0.6980 (mt-10) REVERT: E 660 MET cc_start: 0.6800 (tpt) cc_final: 0.6536 (tpt) REVERT: F 376 ASN cc_start: 0.7847 (m-40) cc_final: 0.7564 (t0) REVERT: F 721 ILE cc_start: 0.7757 (mt) cc_final: 0.7495 (mt) REVERT: F 786 MET cc_start: 0.8092 (OUTLIER) cc_final: 0.7724 (tpp) REVERT: G 524 GLU cc_start: 0.7857 (tt0) cc_final: 0.7627 (tt0) REVERT: G 668 ARG cc_start: 0.6972 (tmm-80) cc_final: 0.6475 (pmt170) REVERT: G 689 LYS cc_start: 0.6346 (tmmt) cc_final: 0.6091 (ttpp) REVERT: G 875 VAL cc_start: 0.7147 (t) cc_final: 0.6817 (p) REVERT: H 20 GLU cc_start: 0.3580 (mm-30) cc_final: 0.1959 (pm20) REVERT: H 120 ASN cc_start: 0.5184 (m-40) cc_final: 0.4593 (m-40) REVERT: H 179 ILE cc_start: 0.2831 (pt) cc_final: 0.2599 (pp) REVERT: H 225 LYS cc_start: 0.3915 (OUTLIER) cc_final: 0.3683 (ptmt) REVERT: H 284 ARG cc_start: 0.2350 (ttm-80) cc_final: 0.1419 (tmt-80) REVERT: H 327 GLU cc_start: 0.3482 (tt0) cc_final: 0.1554 (tm-30) REVERT: H 384 ASN cc_start: 0.3802 (OUTLIER) cc_final: 0.2977 (m-40) outliers start: 53 outliers final: 22 residues processed: 314 average time/residue: 0.5973 time to fit residues: 232.5990 Evaluate side-chains 269 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 240 time to evaluate : 1.326 ------------------------------------------------------------------------------- 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 668 ARG 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 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 699 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 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 773 ASN Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 755 ILE Chi-restraints excluded: chain H residue 225 LYS Chi-restraints excluded: chain H residue 337 ILE Chi-restraints excluded: chain H residue 379 TYR Chi-restraints excluded: chain H residue 384 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 24 optimal weight: 0.4980 chunk 77 optimal weight: 6.9990 chunk 350 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 450 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 401 optimal weight: 0.0070 chunk 42 optimal weight: 0.0270 chunk 64 optimal weight: 0.9990 chunk 259 optimal weight: 0.0870 chunk 214 optimal weight: 1.9990 overall best weight: 0.2434 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** H 157 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.157956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3678 r_free = 0.3678 target = 0.123446 restraints weight = 209676.956| |-----------------------------------------------------------------------------| r_work (start): 0.3622 rms_B_bonded: 3.85 r_work: 0.3506 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3507 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3507 r_free = 0.3507 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3507 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8324 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39520 Z= 0.083 Angle : 0.466 9.447 53592 Z= 0.250 Chirality : 0.042 0.174 6003 Planarity : 0.003 0.046 6990 Dihedral : 4.135 48.832 5327 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.95 % Favored : 95.05 % Rotamer: Outliers : 1.23 % Allowed : 10.09 % Favored : 88.68 % 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: -0.17 (0.12), residues: 4893 helix: 1.05 (0.21), residues: 691 sheet: 0.95 (0.14), residues: 1460 loop : -1.05 (0.12), residues: 2742 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 668 TYR 0.021 0.001 TYR H 397 PHE 0.028 0.001 PHE G 774 TRP 0.008 0.001 TRP D 375 HIS 0.006 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00181 / 0.08 (39520) covalent geometry : angle 0.46605 / 0.25 (53592) hydrogen bonds : bond 0.02237 / 1.50 ( 1322) hydrogen bonds : angle 4.49662 / 3.12 ( 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 348 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 301 time to evaluate : 1.604 Fit side-chains REVERT: A 370 SER cc_start: 0.7142 (p) cc_final: 0.6833 (t) REVERT: A 668 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7574 (tmm-80) REVERT: A 689 LYS cc_start: 0.6231 (tmmt) cc_final: 0.5079 (mtmt) REVERT: A 722 GLU cc_start: 0.6809 (mt-10) cc_final: 0.6386 (mm-30) REVERT: B 594 THR cc_start: 0.8614 (OUTLIER) cc_final: 0.8394 (m) REVERT: B 627 ASN cc_start: 0.7818 (t0) cc_final: 0.7598 (t160) REVERT: B 687 LYS cc_start: 0.6456 (tttt) cc_final: 0.5880 (ptmt) REVERT: B 701 GLU cc_start: 0.7110 (mt-10) cc_final: 0.6850 (mt-10) REVERT: B 786 MET cc_start: 0.8858 (tpp) cc_final: 0.8614 (tpp) REVERT: C 319 GLN cc_start: 0.7925 (pt0) cc_final: 0.7457 (tt0) REVERT: C 369 ASP cc_start: 0.6322 (t70) cc_final: 0.5925 (m-30) REVERT: C 591 SER cc_start: 0.8383 (t) cc_final: 0.8154 (p) REVERT: C 716 LYS cc_start: 0.5574 (tptt) cc_final: 0.4685 (ptmm) REVERT: C 721 ILE cc_start: 0.7338 (OUTLIER) cc_final: 0.6928 (tp) REVERT: C 736 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8276 (mp) REVERT: C 853 MET cc_start: 0.7781 (mmm) cc_final: 0.7439 (mmm) REVERT: D 297 TYR cc_start: 0.8331 (t80) cc_final: 0.7932 (t80) REVERT: D 712 GLU cc_start: 0.6992 (tt0) cc_final: 0.6703 (pt0) REVERT: D 793 THR cc_start: 0.8773 (p) cc_final: 0.8206 (t) REVERT: E 569 ILE cc_start: 0.7465 (mp) cc_final: 0.6964 (tp) REVERT: E 606 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7040 (mt-10) REVERT: E 660 MET cc_start: 0.6802 (tpt) cc_final: 0.6538 (tpt) REVERT: F 650 LEU cc_start: 0.2900 (OUTLIER) cc_final: 0.1852 (mt) REVERT: F 660 MET cc_start: 0.7230 (tpp) cc_final: 0.6409 (tmm) REVERT: F 714 THR cc_start: 0.7058 (OUTLIER) cc_final: 0.6545 (p) REVERT: F 721 ILE cc_start: 0.7735 (mt) cc_final: 0.7500 (mt) REVERT: F 786 MET cc_start: 0.8084 (OUTLIER) cc_final: 0.7816 (tpp) REVERT: F 825 MET cc_start: 0.7797 (mmm) cc_final: 0.7344 (mmm) REVERT: F 826 ARG cc_start: 0.7438 (OUTLIER) cc_final: 0.6109 (mmt90) REVERT: G 371 ASN cc_start: 0.6450 (p0) cc_final: 0.5826 (p0) REVERT: G 524 GLU cc_start: 0.7882 (tt0) cc_final: 0.7677 (tt0) REVERT: G 668 ARG cc_start: 0.6955 (tmm-80) cc_final: 0.6528 (pmt170) REVERT: G 689 LYS cc_start: 0.6529 (tmmt) cc_final: 0.6170 (ttpp) REVERT: G 875 VAL cc_start: 0.7227 (t) cc_final: 0.6938 (p) REVERT: H 20 GLU cc_start: 0.3721 (mm-30) cc_final: 0.2173 (pm20) REVERT: H 84 LYS cc_start: 0.5200 (mppt) cc_final: 0.4394 (mmmt) REVERT: H 120 ASN cc_start: 0.5179 (m-40) cc_final: 0.4602 (m-40) REVERT: H 149 GLU cc_start: 0.3828 (pp20) cc_final: 0.2761 (tp30) REVERT: H 166 MET cc_start: 0.1988 (tpt) cc_final: 0.0969 (tmm) REVERT: H 225 LYS cc_start: 0.3905 (OUTLIER) cc_final: 0.3693 (ptmt) REVERT: H 284 ARG cc_start: 0.2357 (ttm-80) cc_final: 0.1442 (tmt-80) REVERT: H 327 GLU cc_start: 0.3478 (tt0) cc_final: 0.1484 (tm-30) REVERT: H 397 TYR cc_start: 0.4032 (p90) cc_final: 0.3329 (p90) outliers start: 47 outliers final: 17 residues processed: 334 average time/residue: 0.6328 time to fit residues: 265.2247 Evaluate side-chains 280 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 253 time to evaluate : 1.605 ------------------------------------------------------------------------------- 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 668 ARG Chi-restraints excluded: chain A residue 695 THR 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 328 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 699 VAL Chi-restraints excluded: chain C residue 721 ILE Chi-restraints excluded: chain C residue 736 LEU Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 318 ASP Chi-restraints excluded: chain E residue 281 PHE 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 F residue 281 PHE Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 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 H residue 225 LYS 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: 2.9990 chunk 30 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 336 optimal weight: 0.6980 chunk 169 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 103 optimal weight: 0.0030 chunk 354 optimal weight: 1.9990 chunk 459 optimal weight: 0.2980 chunk 415 optimal weight: 4.9990 overall best weight: 0.7994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN ** B 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 390 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 811 GLN ** G 491 ASN A ** both conformations clash, **PLEASE CHECK MANUALLY** G 780 ASN ** 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 = 0.4074 r_free = 0.4074 target = 0.155529 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3639 r_free = 0.3639 target = 0.121004 restraints weight = 183842.986| |-----------------------------------------------------------------------------| r_work (start): 0.3591 rms_B_bonded: 3.51 r_work: 0.3477 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3479 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3479 r_free = 0.3479 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3479 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1674 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 : 0.503 9.454 53592 Z= 0.271 Chirality : 0.044 0.173 6003 Planarity : 0.003 0.047 6990 Dihedral : 4.351 50.573 5327 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 1.48 % Allowed : 10.96 % Favored : 87.56 % 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: -0.24 (0.12), residues: 4893 helix: 1.01 (0.20), residues: 691 sheet: 0.90 (0.14), residues: 1477 loop : -1.12 (0.12), residues: 2725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 668 TYR 0.016 0.001 TYR H 397 PHE 0.015 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/Z covalent geometry : bond 0.00248 / 0.11 (39520) covalent geometry : angle 0.50311 / 0.27 (53592) hydrogen bonds : bond 0.02640 / 1.77 ( 1322) hydrogen bonds : angle 4.55365 / 3.16 ( 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 319 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 262 time to evaluate : 1.703 Fit side-chains REVERT: A 689 LYS cc_start: 0.6274 (tmmt) cc_final: 0.5967 (mmmt) REVERT: A 722 GLU cc_start: 0.6798 (mt-10) cc_final: 0.6322 (mm-30) REVERT: B 627 ASN cc_start: 0.7903 (t0) cc_final: 0.7666 (t160) REVERT: B 687 LYS cc_start: 0.6372 (tttt) cc_final: 0.5853 (ptmt) REVERT: B 701 GLU cc_start: 0.7154 (mt-10) cc_final: 0.6878 (mt-10) REVERT: B 786 MET cc_start: 0.8879 (tpp) cc_final: 0.8570 (tpp) REVERT: C 319 GLN cc_start: 0.7808 (pt0) cc_final: 0.7464 (tt0) REVERT: C 369 ASP cc_start: 0.6292 (t70) cc_final: 0.5903 (m-30) REVERT: C 590 ASP cc_start: 0.6830 (t0) cc_final: 0.6480 (m-30) REVERT: C 591 SER cc_start: 0.8469 (t) cc_final: 0.8144 (p) REVERT: C 660 MET cc_start: 0.5692 (tpp) cc_final: 0.5208 (tpp) REVERT: C 736 LEU cc_start: 0.8529 (OUTLIER) cc_final: 0.8241 (mp) REVERT: C 853 MET cc_start: 0.7804 (mmm) cc_final: 0.7473 (mmm) REVERT: D 793 THR cc_start: 0.8867 (p) cc_final: 0.8320 (t) REVERT: E 569 ILE cc_start: 0.7472 (mp) cc_final: 0.6959 (tp) REVERT: E 606 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7029 (mt-10) REVERT: E 660 MET cc_start: 0.6817 (tpt) cc_final: 0.6474 (tpt) REVERT: F 714 THR cc_start: 0.7067 (OUTLIER) cc_final: 0.6540 (p) REVERT: F 786 MET cc_start: 0.8144 (OUTLIER) cc_final: 0.7778 (tpp) REVERT: F 825 MET cc_start: 0.7941 (mmm) cc_final: 0.7433 (mmm) REVERT: F 826 ARG cc_start: 0.7414 (OUTLIER) cc_final: 0.6216 (mmt90) REVERT: G 524 GLU cc_start: 0.7879 (tt0) cc_final: 0.7650 (tt0) REVERT: G 595 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.7003 (mm) REVERT: G 668 ARG cc_start: 0.6993 (tmm-80) cc_final: 0.6459 (pmt170) REVERT: G 875 VAL cc_start: 0.7180 (t) cc_final: 0.6864 (p) REVERT: H 20 GLU cc_start: 0.3632 (mm-30) cc_final: 0.2038 (pm20) REVERT: H 120 ASN cc_start: 0.5276 (m-40) cc_final: 0.4892 (m-40) REVERT: H 149 GLU cc_start: 0.4077 (pp20) cc_final: 0.2883 (tp30) REVERT: H 166 MET cc_start: 0.2193 (OUTLIER) cc_final: 0.1000 (tmm) REVERT: H 284 ARG cc_start: 0.2340 (ttm-80) cc_final: 0.1400 (tmt-80) REVERT: H 327 GLU cc_start: 0.3497 (tt0) cc_final: 0.1590 (tm-30) REVERT: H 346 MET cc_start: 0.2288 (OUTLIER) cc_final: 0.1497 (mmt) REVERT: H 397 TYR cc_start: 0.3930 (p90) cc_final: 0.3283 (p90) outliers start: 57 outliers final: 30 residues processed: 297 average time/residue: 0.6446 time to fit residues: 239.7015 Evaluate side-chains 280 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 242 time to evaluate : 1.784 ------------------------------------------------------------------------------- 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 668 ARG Chi-restraints excluded: chain A residue 695 THR 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 328 THR Chi-restraints excluded: chain C residue 480 THR Chi-restraints excluded: chain C residue 568 ASP 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 241 ILE Chi-restraints excluded: chain D residue 269 ASP 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 480 THR Chi-restraints excluded: chain E residue 281 PHE 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 773 ASN Chi-restraints excluded: chain E residue 870 LEU Chi-restraints excluded: chain F residue 281 PHE Chi-restraints excluded: chain F residue 684 ILE Chi-restraints excluded: chain F residue 714 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 595 LEU Chi-restraints excluded: chain H residue 166 MET Chi-restraints excluded: chain H residue 292 THR 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: 4.9990 chunk 170 optimal weight: 0.7980 chunk 259 optimal weight: 0.6980 chunk 479 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 408 optimal weight: 0.6980 chunk 351 optimal weight: 2.9990 chunk 396 optimal weight: 0.6980 chunk 447 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 247 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN B 390 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 773 ASN ** 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 = 0.4074 r_free = 0.4074 target = 0.155564 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.120759 restraints weight = 195417.825| |-----------------------------------------------------------------------------| r_work (start): 0.3584 rms_B_bonded: 3.70 r_work: 0.3472 rms_B_bonded: 3.72 restraints_weight: 0.5000 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3473 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3473 r_free = 0.3473 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 = 0.3473 r_free = 0.3473 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3473 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 39520 Z= 0.105 Angle : 0.505 8.928 53592 Z= 0.271 Chirality : 0.044 0.175 6003 Planarity : 0.003 0.046 6990 Dihedral : 4.375 49.976 5327 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 4.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.62 % Allowed : 11.30 % Favored : 87.08 % 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: -0.15 (0.12), residues: 4893 helix: 1.30 (0.21), residues: 655 sheet: 0.90 (0.14), residues: 1476 loop : -1.05 (0.12), residues: 2762 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 325 TYR 0.015 0.001 TYR H 397 PHE 0.011 0.001 PHE E 707 TRP 0.005 0.001 TRP F 503 HIS 0.008 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00239 / 0.10 (39520) covalent geometry : angle 0.50475 / 0.27 (53592) hydrogen bonds : bond 0.02560 / 1.71 ( 1322) hydrogen bonds : angle 4.53094 / 3.14 ( 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 316 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 254 time to evaluate : 1.443 Fit side-chains REVERT: A 370 SER cc_start: 0.7184 (p) cc_final: 0.6819 (t) REVERT: A 689 LYS cc_start: 0.6314 (tmmt) cc_final: 0.5910 (mmmt) REVERT: A 696 ASP cc_start: 0.5966 (OUTLIER) cc_final: 0.5467 (t70) REVERT: A 722 GLU cc_start: 0.6855 (mt-10) cc_final: 0.6408 (mm-30) REVERT: B 627 ASN cc_start: 0.7902 (t0) cc_final: 0.7651 (t160) REVERT: B 687 LYS cc_start: 0.6367 (tttt) cc_final: 0.5859 (ptmt) REVERT: B 701 GLU cc_start: 0.7139 (mt-10) cc_final: 0.6862 (mt-10) REVERT: B 786 MET cc_start: 0.8866 (tpp) cc_final: 0.8550 (tpp) REVERT: C 305 GLU cc_start: 0.8041 (OUTLIER) cc_final: 0.6938 (mm-30) REVERT: C 319 GLN cc_start: 0.7774 (pt0) cc_final: 0.7435 (tt0) REVERT: C 591 SER cc_start: 0.8471 (t) cc_final: 0.8165 (p) REVERT: C 660 MET cc_start: 0.5644 (tpp) cc_final: 0.5301 (tpp) REVERT: C 736 LEU cc_start: 0.8534 (OUTLIER) cc_final: 0.8260 (mp) REVERT: C 853 MET cc_start: 0.7815 (mmm) cc_final: 0.7441 (mmm) REVERT: D 325 ARG cc_start: 0.6788 (ttp80) cc_final: 0.6209 (ttp-110) REVERT: D 762 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7349 (mpp) REVERT: D 793 THR cc_start: 0.8870 (p) cc_final: 0.8316 (t) REVERT: E 569 ILE cc_start: 0.7475 (mp) cc_final: 0.7005 (tp) REVERT: E 606 GLU cc_start: 0.8105 (OUTLIER) cc_final: 0.7043 (mt-10) REVERT: E 660 MET cc_start: 0.6816 (tpt) cc_final: 0.6480 (tpt) REVERT: E 772 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7830 (mp) REVERT: F 480 THR cc_start: 0.8633 (OUTLIER) cc_final: 0.8407 (t) REVERT: F 660 MET cc_start: 0.7275 (tpp) cc_final: 0.6614 (tmm) REVERT: F 714 THR cc_start: 0.7072 (OUTLIER) cc_final: 0.6554 (p) REVERT: F 786 MET cc_start: 0.8171 (OUTLIER) cc_final: 0.7806 (tpp) REVERT: F 825 MET cc_start: 0.7880 (mmm) cc_final: 0.7377 (mmm) REVERT: F 826 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.6484 (mmt90) REVERT: G 524 GLU cc_start: 0.7870 (tt0) cc_final: 0.7637 (tt0) REVERT: G 668 ARG cc_start: 0.7007 (tmm-80) cc_final: 0.6354 (pmt170) REVERT: G 710 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7678 (tt0) REVERT: G 875 VAL cc_start: 0.7164 (t) cc_final: 0.6843 (p) REVERT: H 20 GLU cc_start: 0.3598 (mm-30) cc_final: 0.2012 (pm20) REVERT: H 120 ASN cc_start: 0.5287 (m-40) cc_final: 0.4899 (m-40) REVERT: H 166 MET cc_start: 0.2106 (OUTLIER) cc_final: 0.0955 (tmm) REVERT: H 284 ARG cc_start: 0.2293 (ttm-80) cc_final: 0.1354 (tmt-80) REVERT: H 327 GLU cc_start: 0.3463 (tt0) cc_final: 0.1562 (tm-30) REVERT: H 346 MET cc_start: 0.2270 (OUTLIER) cc_final: 0.1493 (mmt) REVERT: H 397 TYR cc_start: 0.3989 (p90) cc_final: 0.3299 (p90) outliers start: 62 outliers final: 37 residues processed: 294 average time/residue: 0.5631 time to fit residues: 207.0977 Evaluate side-chains 291 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 242 time to evaluate : 1.380 ------------------------------------------------------------------------------- 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 668 ARG 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 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 241 ILE 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 480 THR Chi-restraints excluded: chain D residue 698 LEU 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 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 480 THR Chi-restraints excluded: chain F residue 650 LEU Chi-restraints excluded: chain F residue 714 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 523 ASN Chi-restraints excluded: chain G residue 670 VAL Chi-restraints excluded: chain H residue 166 MET 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 Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 481 random chunks: chunk 343 optimal weight: 3.9990 chunk 334 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 360 optimal weight: 8.9990 chunk 314 optimal weight: 3.9990 chunk 231 optimal weight: 7.9990 chunk 133 optimal weight: 3.9990 chunk 50 optimal weight: 0.0370 chunk 287 optimal weight: 3.9990 chunk 147 optimal weight: 2.9990 chunk 319 optimal weight: 0.7980 overall best weight: 1.3664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN C 390 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 392 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 312 ASN E 610 ASN ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4045 r_free = 0.4045 target = 0.153370 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3601 r_free = 0.3601 target = 0.118649 restraints weight = 219129.636| |-----------------------------------------------------------------------------| r_work (start): 0.3554 rms_B_bonded: 3.78 r_work: 0.3437 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.3437 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3442 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3442 r_free = 0.3442 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 = 0.3442 r_free = 0.3442 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3442 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.1667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 39520 Z= 0.148 Angle : 0.560 11.058 53592 Z= 0.302 Chirality : 0.045 0.196 6003 Planarity : 0.004 0.045 6990 Dihedral : 4.756 47.528 5327 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % Rotamer: Outliers : 1.69 % Allowed : 11.58 % Favored : 86.74 % 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: 0.78 (0.20), residues: 692 sheet: 0.81 (0.14), residues: 1472 loop : -1.20 (0.12), residues: 2729 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 325 TYR 0.016 0.001 TYR G 704 PHE 0.013 0.002 PHE C 711 TRP 0.006 0.001 TRP F 503 HIS 0.009 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 (39520) covalent geometry : angle 0.55980 / 0.30 (53592) hydrogen bonds : bond 0.03078 / 2.05 ( 1322) hydrogen bonds : angle 4.74286 / 3.30 ( 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 310 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 245 time to evaluate : 1.274 Fit side-chains REVERT: A 660 MET cc_start: 0.7286 (OUTLIER) cc_final: 0.7032 (tpt) REVERT: A 696 ASP cc_start: 0.6123 (OUTLIER) cc_final: 0.5601 (t70) REVERT: A 722 GLU cc_start: 0.6899 (mt-10) cc_final: 0.6489 (mm-30) REVERT: B 325 ARG cc_start: 0.7354 (OUTLIER) cc_final: 0.6509 (ttp80) REVERT: B 701 GLU cc_start: 0.7153 (mt-10) cc_final: 0.6873 (mt-10) REVERT: B 786 MET cc_start: 0.8893 (tpp) cc_final: 0.8582 (tpp) REVERT: C 305 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.6981 (mm-30) REVERT: C 319 GLN cc_start: 0.7833 (pt0) cc_final: 0.7442 (tt0) REVERT: C 591 SER cc_start: 0.8418 (t) cc_final: 0.8175 (p) REVERT: C 660 MET cc_start: 0.5660 (tpp) cc_final: 0.5214 (tpp) REVERT: C 736 LEU cc_start: 0.8655 (OUTLIER) cc_final: 0.8365 (mp) REVERT: C 853 MET cc_start: 0.7833 (mmm) cc_final: 0.7502 (mmm) REVERT: D 325 ARG cc_start: 0.6772 (ttp80) cc_final: 0.6201 (ttp-110) REVERT: D 762 MET cc_start: 0.8750 (OUTLIER) cc_final: 0.7339 (mpp) REVERT: E 660 MET cc_start: 0.6923 (tpt) cc_final: 0.6592 (tpt) REVERT: F 480 THR cc_start: 0.8768 (OUTLIER) cc_final: 0.8506 (t) REVERT: F 622 PHE cc_start: 0.7019 (m-80) cc_final: 0.6817 (m-80) REVERT: F 660 MET cc_start: 0.7236 (tpp) cc_final: 0.6447 (tmm) REVERT: F 714 THR cc_start: 0.7162 (OUTLIER) cc_final: 0.6582 (p) REVERT: F 786 MET cc_start: 0.8211 (OUTLIER) cc_final: 0.7780 (tpp) REVERT: F 825 MET cc_start: 0.8057 (mmm) cc_final: 0.7504 (mmm) REVERT: F 826 ARG cc_start: 0.7453 (OUTLIER) cc_final: 0.6586 (mmt90) REVERT: G 668 ARG cc_start: 0.7110 (tmm-80) cc_final: 0.6394 (pmt170) REVERT: G 691 LYS cc_start: 0.5778 (OUTLIER) cc_final: 0.4693 (ttmt) REVERT: G 710 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7651 (tt0) REVERT: H 20 GLU cc_start: 0.3588 (mm-30) cc_final: 0.1997 (pm20) REVERT: H 120 ASN cc_start: 0.5238 (m-40) cc_final: 0.4764 (m-40) REVERT: H 149 GLU cc_start: 0.3678 (pp20) cc_final: 0.2631 (tp30) REVERT: H 166 MET cc_start: 0.2745 (OUTLIER) cc_final: 0.1900 (tpt) REVERT: H 284 ARG cc_start: 0.2181 (ttm-80) cc_final: 0.1320 (ttp-110) REVERT: H 327 GLU cc_start: 0.3629 (tt0) cc_final: 0.1748 (tm-30) REVERT: H 346 MET cc_start: 0.2349 (OUTLIER) cc_final: 0.1612 (mmt) REVERT: H 397 TYR cc_start: 0.4070 (p90) cc_final: 0.3421 (p90) outliers start: 65 outliers final: 38 residues processed: 290 average time/residue: 0.5806 time to fit residues: 211.5023 Evaluate side-chains 290 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 239 time to evaluate : 1.535 ------------------------------------------------------------------------------- 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 660 MET Chi-restraints excluded: chain A residue 668 ARG 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 325 ARG 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 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 241 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 480 THR Chi-restraints excluded: chain D residue 698 LEU 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 480 THR Chi-restraints excluded: chain F residue 714 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 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 166 MET 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: 1.9990 chunk 176 optimal weight: 4.9990 chunk 11 optimal weight: 5.9990 chunk 258 optimal weight: 1.9990 chunk 427 optimal weight: 2.9990 chunk 202 optimal weight: 4.9990 chunk 149 optimal weight: 1.9990 chunk 329 optimal weight: 10.0000 chunk 201 optimal weight: 6.9990 chunk 41 optimal weight: 1.9990 chunk 125 optimal weight: 0.9980 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 773 ASN A 851 ASN B 627 ASN ** D 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 319 GLN ** E 648 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 720 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: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4031 r_free = 0.4031 target = 0.152128 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.117527 restraints weight = 203453.073| |-----------------------------------------------------------------------------| r_work (start): 0.3538 rms_B_bonded: 3.73 r_work: 0.3420 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3425 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3425 r_free = 0.3425 target_work(ls_wunit_k1) = 0.107 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3425 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8441 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 : 0.004 0.039 39520 Z= 0.182 Angle : 0.605 12.447 53592 Z= 0.326 Chirality : 0.047 0.200 6003 Planarity : 0.004 0.050 6990 Dihedral : 5.094 46.305 5327 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 1.78 % Allowed : 11.74 % 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: -0.56 (0.12), residues: 4893 helix: 0.65 (0.20), residues: 680 sheet: 0.68 (0.14), residues: 1470 loop : -1.28 (0.11), residues: 2743 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 325 TYR 0.020 0.002 TYR D 666 PHE 0.016 0.002 PHE C 707 TRP 0.007 0.001 TRP F 503 HIS 0.011 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00435 / 0.18 (39520) covalent geometry : angle 0.60483 / 0.33 (53592) hydrogen bonds : bond 0.03426 / 2.29 ( 1322) hydrogen bonds : angle 4.94595 / 3.45 ( 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 315 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 247 time to evaluate : 1.371 Fit side-chains REVERT: A 560 LYS cc_start: 0.5797 (mttm) cc_final: 0.5408 (mmpt) REVERT: A 696 ASP cc_start: 0.6140 (OUTLIER) cc_final: 0.5572 (t70) REVERT: A 722 GLU cc_start: 0.6929 (mt-10) cc_final: 0.6491 (mm-30) REVERT: B 325 ARG cc_start: 0.7413 (OUTLIER) cc_final: 0.6551 (ttp80) REVERT: B 471 ASP cc_start: 0.7811 (p0) cc_final: 0.7529 (p0) REVERT: B 701 GLU cc_start: 0.7175 (mt-10) cc_final: 0.6877 (mt-10) REVERT: B 786 MET cc_start: 0.8915 (tpp) cc_final: 0.8660 (tpp) REVERT: C 305 GLU cc_start: 0.8264 (OUTLIER) cc_final: 0.7104 (mm-30) REVERT: C 319 GLN cc_start: 0.7862 (pt0) cc_final: 0.7399 (tt0) REVERT: C 591 SER cc_start: 0.8451 (t) cc_final: 0.8200 (p) REVERT: C 660 MET cc_start: 0.5808 (tpp) cc_final: 0.5395 (tpp) REVERT: C 853 MET cc_start: 0.7875 (mmm) cc_final: 0.7510 (mmm) REVERT: D 325 ARG cc_start: 0.6762 (ttp80) cc_final: 0.6223 (ttp-110) REVERT: D 762 MET cc_start: 0.8830 (OUTLIER) cc_final: 0.7355 (mpp) REVERT: E 660 MET cc_start: 0.7005 (tpt) cc_final: 0.6772 (tpt) REVERT: F 480 THR cc_start: 0.8725 (OUTLIER) cc_final: 0.8452 (t) REVERT: F 660 MET cc_start: 0.7243 (tpp) cc_final: 0.6473 (tmm) REVERT: F 714 THR cc_start: 0.7209 (OUTLIER) cc_final: 0.6653 (p) REVERT: F 758 ASP cc_start: 0.7550 (m-30) cc_final: 0.7342 (m-30) REVERT: F 786 MET cc_start: 0.8232 (OUTLIER) cc_final: 0.7839 (tpp) REVERT: F 825 MET cc_start: 0.8057 (mmm) cc_final: 0.7552 (mmm) REVERT: F 826 ARG cc_start: 0.7468 (OUTLIER) cc_final: 0.6571 (mmt90) REVERT: G 668 ARG cc_start: 0.7170 (tmm-80) cc_final: 0.6333 (pmt170) REVERT: G 691 LYS cc_start: 0.5827 (OUTLIER) cc_final: 0.4699 (ttmt) REVERT: G 710 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7599 (tt0) REVERT: H 20 GLU cc_start: 0.3586 (mm-30) cc_final: 0.1954 (pm20) REVERT: H 57 ASN cc_start: 0.3701 (p0) cc_final: 0.3441 (p0) REVERT: H 120 ASN cc_start: 0.5350 (m-40) cc_final: 0.4711 (m110) REVERT: H 149 GLU cc_start: 0.3706 (pp20) cc_final: 0.2583 (tp30) REVERT: H 284 ARG cc_start: 0.2102 (ttm-80) cc_final: 0.1178 (ttp-110) REVERT: H 346 MET cc_start: 0.2390 (OUTLIER) cc_final: 0.1551 (mmt) REVERT: H 397 TYR cc_start: 0.4064 (p90) cc_final: 0.3483 (p90) outliers start: 68 outliers final: 47 residues processed: 293 average time/residue: 0.6307 time to fit residues: 231.2940 Evaluate side-chains 285 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 228 time to evaluate : 1.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 246 GLU Chi-restraints excluded: chain A residue 281 PHE Chi-restraints excluded: chain A residue 318 ASP Chi-restraints excluded: chain A residue 403 MET Chi-restraints excluded: chain A residue 596 SER Chi-restraints excluded: chain A residue 668 ARG Chi-restraints excluded: chain A residue 695 THR Chi-restraints excluded: chain A residue 696 ASP 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 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 679 LEU 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 241 ILE Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 377 THR Chi-restraints excluded: chain D residue 380 SER 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 480 THR Chi-restraints excluded: chain F residue 542 THR Chi-restraints excluded: chain F residue 635 VAL Chi-restraints excluded: chain F residue 714 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 670 VAL Chi-restraints excluded: chain G residue 691 LYS Chi-restraints excluded: chain H residue 166 MET 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: 0.9990 chunk 274 optimal weight: 0.0040 chunk 406 optimal weight: 4.9990 chunk 12 optimal weight: 2.9990 chunk 168 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 396 optimal weight: 0.3980 chunk 315 optimal weight: 0.0970 chunk 219 optimal weight: 0.0170 chunk 217 optimal weight: 1.9990 chunk 20 optimal weight: 0.0870 overall best weight: 0.1206 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 ASN C 627 ASN D 223 ASN D 648 ASN ** D 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 223 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 610 ASN F 720 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: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.156662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.122246 restraints weight = 208165.056| |-----------------------------------------------------------------------------| r_work (start): 0.3603 rms_B_bonded: 3.86 r_work: 0.3489 rms_B_bonded: 3.83 restraints_weight: 0.5000 r_work (final): 0.3489 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3496 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3496 r_free = 0.3496 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3496 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 39520 Z= 0.091 Angle : 0.500 9.892 53592 Z= 0.269 Chirality : 0.043 0.193 6003 Planarity : 0.004 0.046 6990 Dihedral : 4.406 44.834 5327 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.21 % Favored : 94.79 % Rotamer: Outliers : 1.12 % Allowed : 12.42 % 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: -0.18 (0.12), residues: 4893 helix: 1.25 (0.21), residues: 655 sheet: 0.94 (0.14), residues: 1483 loop : -1.11 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 843 TYR 0.015 0.001 TYR H 142 PHE 0.024 0.001 PHE B 774 TRP 0.010 0.001 TRP G 375 HIS 0.009 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00200 / 0.09 (39520) covalent geometry : angle 0.49998 / 0.27 (53592) hydrogen bonds : bond 0.02243 / 1.51 ( 1322) hydrogen bonds : angle 4.52892 / 3.14 ( 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 303 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 264 time to evaluate : 1.417 Fit side-chains REVERT: A 370 SER cc_start: 0.7128 (p) cc_final: 0.6816 (t) REVERT: A 657 LYS cc_start: 0.7933 (mttm) cc_final: 0.6944 (pttt) REVERT: A 689 LYS cc_start: 0.6291 (tmmt) cc_final: 0.5872 (mmmt) REVERT: A 722 GLU cc_start: 0.6825 (mt-10) cc_final: 0.6396 (mm-30) REVERT: B 325 ARG cc_start: 0.7357 (OUTLIER) cc_final: 0.6510 (ttp80) REVERT: B 471 ASP cc_start: 0.7581 (p0) cc_final: 0.7182 (p0) REVERT: B 687 LYS cc_start: 0.6389 (tttt) cc_final: 0.5766 (ptmt) REVERT: B 701 GLU cc_start: 0.7077 (mt-10) cc_final: 0.6835 (mt-10) REVERT: B 786 MET cc_start: 0.8921 (tpp) cc_final: 0.8640 (tpp) REVERT: C 305 GLU cc_start: 0.8082 (OUTLIER) cc_final: 0.6886 (mm-30) REVERT: C 319 GLN cc_start: 0.7772 (pt0) cc_final: 0.7444 (tt0) REVERT: C 591 SER cc_start: 0.8395 (t) cc_final: 0.8161 (p) REVERT: C 853 MET cc_start: 0.7817 (mmm) cc_final: 0.7503 (mmm) REVERT: D 325 ARG cc_start: 0.6574 (ttp80) cc_final: 0.6029 (ttp-110) REVERT: D 648 ASN cc_start: 0.5856 (t0) cc_final: 0.5308 (t0) REVERT: D 793 THR cc_start: 0.8880 (p) cc_final: 0.8410 (t) REVERT: E 660 MET cc_start: 0.6814 (tpt) cc_final: 0.6475 (tpt) REVERT: E 772 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7806 (mp) REVERT: F 480 THR cc_start: 0.8489 (OUTLIER) cc_final: 0.8270 (t) REVERT: F 660 MET cc_start: 0.7249 (tpp) cc_final: 0.6456 (tmm) REVERT: F 714 THR cc_start: 0.7167 (OUTLIER) cc_final: 0.6623 (p) REVERT: F 786 MET cc_start: 0.8137 (OUTLIER) cc_final: 0.7700 (tpp) REVERT: F 825 MET cc_start: 0.7707 (mmm) cc_final: 0.7249 (mmm) REVERT: G 569 ILE cc_start: 0.7823 (OUTLIER) cc_final: 0.7555 (tt) REVERT: G 668 ARG cc_start: 0.7102 (tmm-80) cc_final: 0.6310 (pmt170) REVERT: G 710 GLU cc_start: 0.8253 (mt-10) cc_final: 0.7551 (tm-30) REVERT: H 20 GLU cc_start: 0.3747 (mm-30) cc_final: 0.2088 (pm20) REVERT: H 57 ASN cc_start: 0.3881 (p0) cc_final: 0.3462 (p0) REVERT: H 120 ASN cc_start: 0.5214 (m-40) cc_final: 0.4769 (m-40) REVERT: H 149 GLU cc_start: 0.3745 (pp20) cc_final: 0.2802 (tp30) REVERT: H 166 MET cc_start: 0.1989 (OUTLIER) cc_final: 0.0981 (tmm) REVERT: H 284 ARG cc_start: 0.2196 (ttm-80) cc_final: 0.1298 (ttp-110) REVERT: H 327 GLU cc_start: 0.3389 (tt0) cc_final: 0.1504 (tm-30) REVERT: H 332 SER cc_start: 0.2917 (m) cc_final: 0.2557 (t) REVERT: H 397 TYR cc_start: 0.4037 (p90) cc_final: 0.3406 (p90) outliers start: 39 outliers final: 25 residues processed: 291 average time/residue: 0.6103 time to fit residues: 221.1223 Evaluate side-chains 272 residues out of total 4300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 239 time to evaluate : 1.527 ------------------------------------------------------------------------------- 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 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 699 VAL Chi-restraints excluded: chain C residue 753 VAL Chi-restraints excluded: chain D residue 281 PHE Chi-restraints excluded: chain D residue 380 SER Chi-restraints excluded: chain D residue 417 ASP Chi-restraints excluded: chain E residue 281 PHE 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 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 714 THR Chi-restraints excluded: chain F residue 786 MET Chi-restraints excluded: chain G residue 281 PHE Chi-restraints excluded: chain G residue 523 ASN Chi-restraints excluded: chain G residue 569 ILE Chi-restraints excluded: chain H residue 54 GLN Chi-restraints excluded: chain H residue 166 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: 0.8980 chunk 271 optimal weight: 2.9990 chunk 362 optimal weight: 1.9990 chunk 307 optimal weight: 4.9990 chunk 365 optimal weight: 2.9990 chunk 312 optimal weight: 0.7980 chunk 220 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 chunk 438 optimal weight: 0.9990 chunk 427 optimal weight: 4.9990 chunk 225 optimal weight: 0.4980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 411 ASN ** A 784 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 627 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** G 583 ASN ** 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 = 0.4084 r_free = 0.4084 target = 0.156480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.121980 restraints weight = 216311.174| |-----------------------------------------------------------------------------| r_work (start): 0.3600 rms_B_bonded: 3.93 r_work: 0.3486 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3490 r_free = 0.3490 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.44 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.159 39520 Z= 0.126 Angle : 0.616 59.172 53592 Z= 0.344 Chirality : 0.044 0.396 6003 Planarity : 0.004 0.046 6990 Dihedral : 4.405 44.879 5327 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 1.03 % Allowed : 13.01 % Favored : 85.96 % Cbeta Deviations : 0.02 % 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: -0.17 (0.12), residues: 4893 helix: 1.23 (0.21), residues: 655 sheet: 0.95 (0.14), residues: 1483 loop : -1.10 (0.12), residues: 2755 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG E 529 TYR 0.014 0.001 TYR H 142 PHE 0.018 0.001 PHE B 774 TRP 0.009 0.001 TRP G 375 HIS 0.008 0.001 HIS H 157 Details of bonding type rmsd/Z covalent geometry : bond 0.00274 / 0.13 (39520) covalent geometry : angle 0.61629 / 0.34 (53592) hydrogen bonds : bond 0.02318 / 1.57 ( 1322) hydrogen bonds : angle 4.53338 / 3.14 ( 3615) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14006.97 seconds wall clock time: 239 minutes 31.75 seconds (14371.75 seconds total)