Starting phenix.real_space_refine on Tue Sep 15 18:01:19 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.map" model { file = "/net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uze_20958/09_2026/6uze_20958.cif" } resolution = 3.4 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= 0.007 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 14 9.91 5 S 54 5.16 5 C 26902 2.51 5 N 7305 2.21 5 O 8547 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 67 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 42822 Number of models: 1 Model: "" Number of chains: 16 Chain: "A" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "B" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "C" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "D" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "E" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "F" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "G" Number of atoms: 4438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4438 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Chain: "H" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5871 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "I" Number of atoms: 5871 Number of conformers: 1 Conformer: "" Number of residues, atoms: 720, 5871 Classifications: {'peptide': 720} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 20, 'TRANS': 699} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 8.77, per 1000 atoms: 0.20 Number of scatterers: 42822 At special positions: 0 Unit cell: (173.34, 174.41, 297.46, 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 14 19.99 S 54 16.00 O 8547 8.00 N 7305 7.00 C 26902 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.32 Conformation dependent library (CDL) restraints added in 1.7 seconds 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10200 Finding SS restraints... Secondary structure from input PDB file: 150 helices and 82 sheets defined 25.9% alpha, 31.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.67 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 207 through 212 removed outlier: 3.580A pdb=" N GLU A 212 " --> pdb=" O SER A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 234 through 241 removed outlier: 3.576A pdb=" N VAL A 239 " --> pdb=" O ASP A 235 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 252 removed outlier: 3.543A pdb=" N ARG A 252 " --> pdb=" O PRO A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.724A pdb=" N LEU A 401 " --> pdb=" O GLU A 398 " (cutoff:3.500A) Processing helix chain 'A' and resid 435 through 446 Processing helix chain 'A' and resid 480 through 485 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.693A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 530 Processing helix chain 'A' and resid 546 through 548 No H-bonds generated for 'chain 'A' and resid 546 through 548' Processing helix chain 'A' and resid 555 through 570 removed outlier: 3.512A pdb=" N ASN A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N GLU A 568 " --> pdb=" O ASN A 564 " (cutoff:3.500A) Processing helix chain 'A' and resid 609 through 615 removed outlier: 3.741A pdb=" N LYS A 613 " --> pdb=" O GLU A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 634 through 638 removed outlier: 3.545A pdb=" N LYS A 637 " --> pdb=" O ASP A 634 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 638 " --> pdb=" O ILE A 635 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 634 through 638' Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 207 through 212 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.625A pdb=" N ARG B 252 " --> pdb=" O PRO B 249 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 480 through 487 removed outlier: 3.654A pdb=" N GLU B 486 " --> pdb=" O PRO B 482 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N THR B 487 " --> pdb=" O GLN B 483 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 531 removed outlier: 3.579A pdb=" N PHE B 531 " --> pdb=" O LEU B 527 " (cutoff:3.500A) Processing helix chain 'B' and resid 546 through 548 No H-bonds generated for 'chain 'B' and resid 546 through 548' Processing helix chain 'B' and resid 555 through 570 removed outlier: 3.926A pdb=" N ASN B 561 " --> pdb=" O GLN B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 609 through 615 removed outlier: 4.054A pdb=" N LYS B 613 " --> pdb=" O GLU B 609 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N ALA B 615 " --> pdb=" O VAL B 611 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 609 through 615' Processing helix chain 'B' and resid 678 through 682 removed outlier: 3.902A pdb=" N TYR B 681 " --> pdb=" O PHE B 678 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 682 " --> pdb=" O LYS B 679 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 678 through 682' Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 207 through 212 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 252 Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.605A pdb=" N LEU C 401 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.611A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 530 Processing helix chain 'C' and resid 555 through 569 removed outlier: 3.609A pdb=" N GLU C 568 " --> pdb=" O ASN C 564 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU C 569 " --> pdb=" O GLN C 565 " (cutoff:3.500A) Processing helix chain 'C' and resid 731 through 735 removed outlier: 4.130A pdb=" N GLY C 735 " --> pdb=" O GLY C 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 731 through 735' Processing helix chain 'D' and resid 184 through 191 removed outlier: 3.668A pdb=" N GLU D 190 " --> pdb=" O SER D 186 " (cutoff:3.500A) Processing helix chain 'D' and resid 207 through 212 Processing helix chain 'D' and resid 234 through 241 removed outlier: 3.532A pdb=" N VAL D 239 " --> pdb=" O ASP D 235 " (cutoff:3.500A) Processing helix chain 'D' and resid 248 through 252 removed outlier: 3.632A pdb=" N ARG D 252 " --> pdb=" O PRO D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.841A pdb=" N LEU D 401 " --> pdb=" O GLU D 398 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 446 Processing helix chain 'D' and resid 480 through 486 Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.589A pdb=" N PHE D 531 " --> pdb=" O LEU D 527 " (cutoff:3.500A) Processing helix chain 'D' and resid 546 through 548 No H-bonds generated for 'chain 'D' and resid 546 through 548' Processing helix chain 'D' and resid 555 through 570 Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.666A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 637 Processing helix chain 'E' and resid 184 through 191 removed outlier: 3.792A pdb=" N VAL E 189 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLU E 190 " --> pdb=" O SER E 186 " (cutoff:3.500A) Processing helix chain 'E' and resid 207 through 212 removed outlier: 3.781A pdb=" N GLU E 212 " --> pdb=" O SER E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 removed outlier: 3.629A pdb=" N VAL E 239 " --> pdb=" O ASP E 235 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.580A pdb=" N LEU E 401 " --> pdb=" O GLU E 398 " (cutoff:3.500A) Processing helix chain 'E' and resid 435 through 446 Processing helix chain 'E' and resid 480 through 485 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.646A pdb=" N THR E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 514 through 518' Processing helix chain 'E' and resid 522 through 531 removed outlier: 3.511A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) Processing helix chain 'E' and resid 546 through 548 No H-bonds generated for 'chain 'E' and resid 546 through 548' Processing helix chain 'E' and resid 555 through 569 removed outlier: 3.579A pdb=" N GLU E 568 " --> pdb=" O ASN E 564 " (cutoff:3.500A) Processing helix chain 'E' and resid 573 through 577 Processing helix chain 'E' and resid 610 through 615 removed outlier: 3.653A pdb=" N ALA E 615 " --> pdb=" O VAL E 611 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 637 Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 214 removed outlier: 3.723A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS F 214 " --> pdb=" O ILE F 210 " (cutoff:3.500A) Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 397 through 401 removed outlier: 3.642A pdb=" N LEU F 401 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 480 through 485 Processing helix chain 'F' and resid 522 through 531 removed outlier: 3.681A pdb=" N ALA F 530 " --> pdb=" O ALA F 526 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N PHE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 546 through 548 No H-bonds generated for 'chain 'F' and resid 546 through 548' Processing helix chain 'F' and resid 556 through 568 removed outlier: 3.560A pdb=" N ASN F 561 " --> pdb=" O GLN F 557 " (cutoff:3.500A) Processing helix chain 'F' and resid 573 through 581 removed outlier: 4.963A pdb=" N LEU F 578 " --> pdb=" O TYR F 575 " (cutoff:3.500A) removed outlier: 5.518A pdb=" N ASP F 579 " --> pdb=" O THR F 576 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 613 removed outlier: 4.148A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N LYS F 613 " --> pdb=" O GLU F 609 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 608 through 613' Processing helix chain 'F' and resid 634 through 638 Processing helix chain 'F' and resid 704 through 706 No H-bonds generated for 'chain 'F' and resid 704 through 706' Processing helix chain 'F' and resid 730 through 735 removed outlier: 3.750A pdb=" N ILE F 734 " --> pdb=" O LYS F 730 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N GLY F 735 " --> pdb=" O GLY F 731 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 730 through 735' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 207 through 212 removed outlier: 3.967A pdb=" N GLU G 212 " --> pdb=" O SER G 208 " (cutoff:3.500A) Processing helix chain 'G' and resid 234 through 241 removed outlier: 3.545A pdb=" N VAL G 239 " --> pdb=" O ASP G 235 " (cutoff:3.500A) Processing helix chain 'G' and resid 248 through 252 Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 476 through 479 Processing helix chain 'G' and resid 480 through 486 removed outlier: 3.623A pdb=" N GLU G 486 " --> pdb=" O PRO G 482 " (cutoff:3.500A) Processing helix chain 'G' and resid 513 through 518 removed outlier: 3.714A pdb=" N THR G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 531 removed outlier: 3.594A pdb=" N PHE G 531 " --> pdb=" O LEU G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 546 through 548 No H-bonds generated for 'chain 'G' and resid 546 through 548' Processing helix chain 'G' and resid 555 through 570 removed outlier: 3.572A pdb=" N ASN G 564 " --> pdb=" O GLN G 560 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N GLU G 568 " --> pdb=" O ASN G 564 " (cutoff:3.500A) Processing helix chain 'G' and resid 573 through 577 removed outlier: 3.579A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 632 through 637 removed outlier: 3.553A pdb=" N LYS G 637 " --> pdb=" O LYS G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 659 through 663 Processing helix chain 'G' and resid 717 through 721 removed outlier: 4.416A pdb=" N GLY G 720 " --> pdb=" O SER G 717 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N ILE G 721 " --> pdb=" O THR G 718 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 717 through 721' Processing helix chain 'H' and resid 21 through 29 Processing helix chain 'H' and resid 41 through 54 removed outlier: 4.144A pdb=" N LYS H 45 " --> pdb=" O GLU H 41 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE H 46 " --> pdb=" O THR H 42 " (cutoff:3.500A) Processing helix chain 'H' and resid 57 through 67 removed outlier: 4.238A pdb=" N LEU H 61 " --> pdb=" O PRO H 57 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N GLU H 62 " --> pdb=" O LYS H 58 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N LEU H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.920A pdb=" N GLU H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N VAL H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N TYR H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 145 through 150 Processing helix chain 'H' and resid 156 through 169 removed outlier: 3.573A pdb=" N ASP H 168 " --> pdb=" O LYS H 164 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 177 Processing helix chain 'H' and resid 178 through 189 removed outlier: 3.592A pdb=" N GLU H 186 " --> pdb=" O LYS H 182 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N LEU H 187 " --> pdb=" O GLU H 183 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ASN H 188 " --> pdb=" O LYS H 184 " (cutoff:3.500A) Processing helix chain 'H' and resid 193 through 200 removed outlier: 3.804A pdb=" N ILE H 197 " --> pdb=" O ASP H 193 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS H 198 " --> pdb=" O ILE H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 200 through 217 removed outlier: 3.693A pdb=" N PHE H 208 " --> pdb=" O PHE H 204 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 211 " --> pdb=" O ALA H 207 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 228 removed outlier: 3.506A pdb=" N LEU H 224 " --> pdb=" O HIS H 220 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU H 226 " --> pdb=" O THR H 222 " (cutoff:3.500A) Processing helix chain 'H' and resid 228 through 240 removed outlier: 3.503A pdb=" N LYS H 240 " --> pdb=" O ASN H 236 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 253 removed outlier: 3.999A pdb=" N GLU H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 270 Processing helix chain 'H' and resid 275 through 290 removed outlier: 3.791A pdb=" N ALA H 279 " --> pdb=" O VAL H 275 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE H 285 " --> pdb=" O ALA H 281 " (cutoff:3.500A) Processing helix chain 'H' and resid 299 through 308 removed outlier: 4.014A pdb=" N THR H 303 " --> pdb=" O ASN H 299 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 removed outlier: 3.879A pdb=" N LEU H 337 " --> pdb=" O ASP H 334 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER H 338 " --> pdb=" O GLN H 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 334 through 338' Processing helix chain 'H' and resid 345 through 361 removed outlier: 3.972A pdb=" N THR H 359 " --> pdb=" O LYS H 355 " (cutoff:3.500A) Processing helix chain 'H' and resid 374 through 380 removed outlier: 4.605A pdb=" N GLU H 378 " --> pdb=" O HIS H 374 " (cutoff:3.500A) Processing helix chain 'H' and resid 479 through 484 Processing helix chain 'H' and resid 488 through 504 removed outlier: 3.778A pdb=" N LEU H 499 " --> pdb=" O GLY H 495 " (cutoff:3.500A) Processing helix chain 'H' and resid 517 through 530 removed outlier: 4.067A pdb=" N ARG H 526 " --> pdb=" O GLN H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 574 through 585 Processing helix chain 'H' and resid 626 through 637 removed outlier: 3.717A pdb=" N ILE H 637 " --> pdb=" O ASN H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 652 through 672 Processing helix chain 'H' and resid 680 through 704 removed outlier: 3.623A pdb=" N GLU H 698 " --> pdb=" O GLN H 694 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU H 703 " --> pdb=" O ILE H 699 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 733 removed outlier: 4.068A pdb=" N ARG H 722 " --> pdb=" O TYR H 718 " (cutoff:3.500A) Processing helix chain 'H' and resid 739 through 747 removed outlier: 3.579A pdb=" N LEU H 747 " --> pdb=" O LEU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 765 removed outlier: 3.537A pdb=" N VAL H 759 " --> pdb=" O ASP H 755 " (cutoff:3.500A) Processing helix chain 'I' and resid 21 through 30 Processing helix chain 'I' and resid 43 through 54 Processing helix chain 'I' and resid 57 through 66 removed outlier: 3.834A pdb=" N LEU I 61 " --> pdb=" O PRO I 57 " (cutoff:3.500A) Processing helix chain 'I' and resid 88 through 93 removed outlier: 3.682A pdb=" N ASN I 93 " --> pdb=" O GLU I 89 " (cutoff:3.500A) Processing helix chain 'I' and resid 131 through 144 removed outlier: 3.727A pdb=" N GLU I 135 " --> pdb=" O GLU I 131 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N VAL I 136 " --> pdb=" O GLN I 132 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N TYR I 137 " --> pdb=" O SER I 133 " (cutoff:3.500A) Processing helix chain 'I' and resid 144 through 149 removed outlier: 3.870A pdb=" N ILE I 148 " --> pdb=" O ILE I 144 " (cutoff:3.500A) Processing helix chain 'I' and resid 156 through 169 removed outlier: 3.749A pdb=" N ASP I 169 " --> pdb=" O SER I 165 " (cutoff:3.500A) Processing helix chain 'I' and resid 170 through 177 Processing helix chain 'I' and resid 179 through 185 Processing helix chain 'I' and resid 193 through 200 Processing helix chain 'I' and resid 200 through 217 removed outlier: 3.521A pdb=" N PHE I 204 " --> pdb=" O ASN I 200 " (cutoff:3.500A) Processing helix chain 'I' and resid 221 through 228 Processing helix chain 'I' and resid 230 through 240 Processing helix chain 'I' and resid 241 through 255 removed outlier: 4.145A pdb=" N GLU I 253 " --> pdb=" O SER I 249 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL I 255 " --> pdb=" O LYS I 251 " (cutoff:3.500A) Processing helix chain 'I' and resid 266 through 273 Processing helix chain 'I' and resid 275 through 290 Processing helix chain 'I' and resid 299 through 307 removed outlier: 3.605A pdb=" N LEU I 305 " --> pdb=" O LEU I 301 " (cutoff:3.500A) Processing helix chain 'I' and resid 334 through 338 removed outlier: 3.532A pdb=" N LEU I 337 " --> pdb=" O ASP I 334 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N SER I 338 " --> pdb=" O GLN I 335 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 334 through 338' Processing helix chain 'I' and resid 346 through 361 Processing helix chain 'I' and resid 376 through 381 Processing helix chain 'I' and resid 467 through 473 Processing helix chain 'I' and resid 478 through 483 Processing helix chain 'I' and resid 489 through 504 Processing helix chain 'I' and resid 517 through 530 Processing helix chain 'I' and resid 531 through 535 removed outlier: 3.689A pdb=" N GLY I 535 " --> pdb=" O LYS I 532 " (cutoff:3.500A) Processing helix chain 'I' and resid 574 through 586 Processing helix chain 'I' and resid 626 through 636 Processing helix chain 'I' and resid 651 through 672 removed outlier: 3.607A pdb=" N SER I 669 " --> pdb=" O ALA I 665 " (cutoff:3.500A) Processing helix chain 'I' and resid 680 through 702 removed outlier: 3.505A pdb=" N LYS I 684 " --> pdb=" O SER I 680 " (cutoff:3.500A) Processing helix chain 'I' and resid 709 through 734 Processing helix chain 'I' and resid 739 through 747 removed outlier: 3.517A pdb=" N LEU I 743 " --> pdb=" O GLU I 739 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU I 747 " --> pdb=" O LEU I 743 " (cutoff:3.500A) Processing helix chain 'I' and resid 755 through 765 Processing sheet with id=AA1, first strand: chain 'A' and resid 192 through 196 Processing sheet with id=AA2, first strand: chain 'A' and resid 262 through 269 removed outlier: 6.459A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 262 through 269 removed outlier: 6.459A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 272 through 273 removed outlier: 3.632A pdb=" N ALA A 358 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 4.773A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 276 through 288 removed outlier: 3.996A pdb=" N ASP A 276 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N GLY A 351 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N THR A 282 " --> pdb=" O THR A 345 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N SER A 284 " --> pdb=" O GLU A 343 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU B 308 " --> pdb=" O SER B 319 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 276 through 288 removed outlier: 3.717A pdb=" N THR A 279 " --> pdb=" O MET G 350 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR G 279 " --> pdb=" O MET F 350 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N MET F 350 " --> pdb=" O THR G 279 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N TRP F 346 " --> pdb=" O ASP G 283 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N GLY F 342 " --> pdb=" O ARG G 287 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER F 284 " --> pdb=" O GLU F 343 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N GLN F 280 " --> pdb=" O ALA F 347 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N THR F 279 " --> pdb=" O MET E 350 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N SER E 296 " --> pdb=" O THR E 331 " (cutoff:3.500A) removed outlier: 4.537A pdb=" N ASN E 292 " --> pdb=" O ASP E 335 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR E 288 " --> pdb=" O SER E 339 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N THR E 282 " --> pdb=" O THR E 345 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG E 287 " --> pdb=" O GLY D 342 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N LEU D 340 " --> pdb=" O ILE E 289 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ILE D 334 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL D 332 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D 337 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER D 337 " --> pdb=" O SER D 290 " (cutoff:3.500A) removed outlier: 4.055A pdb=" N SER D 284 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N THR C 345 " --> pdb=" O THR C 282 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N GLN C 280 " --> pdb=" O ALA C 347 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N THR C 279 " --> pdb=" O MET B 350 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N MET B 350 " --> pdb=" O THR C 279 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 285 through 297 removed outlier: 3.519A pdb=" N SER C 290 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP C 335 " --> pdb=" O ASN C 292 " (cutoff:3.500A) removed outlier: 5.463A pdb=" N VAL C 332 " --> pdb=" O ARG D 297 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG D 297 " --> pdb=" O VAL C 332 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY E 305 " --> pdb=" O PHE D 324 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ASN D 326 " --> pdb=" O VAL E 303 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR E 300 " --> pdb=" O SER E 327 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ASN F 292 " --> pdb=" O ASP F 335 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ASN G 292 " --> pdb=" O ASP G 335 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 308 through 310 removed outlier: 3.565A pdb=" N VAL E 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N HIS E 304 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU E 308 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N SER E 319 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLY E 317 " --> pdb=" O HIS E 310 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N VAL E 320 " --> pdb=" O VAL F 309 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N VAL F 309 " --> pdb=" O VAL E 320 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER G 319 " --> pdb=" O GLU G 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 323 through 351 removed outlier: 3.816A pdb=" N ILE A 334 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N SER B 329 " --> pdb=" O THR B 298 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N VAL B 332 " --> pdb=" O ARG C 297 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLY B 342 " --> pdb=" O ARG C 287 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ASP B 276 " --> pdb=" O GLY B 351 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N TRP A 346 " --> pdb=" O ASP B 283 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ALA A 333 " --> pdb=" O SER A 294 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 307 through 309 Processing sheet with id=AB2, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.749A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N TYR A 375 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE A 404 " --> pdb=" O TYR A 375 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N SER A 402 " --> pdb=" O VAL A 377 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.749A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.787A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.699A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N VAL A 377 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N TYR A 456 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLN A 454 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N THR A 381 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N THR A 452 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LEU A 383 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N LEU A 450 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N LEU A 385 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N LEU A 448 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 10.643A pdb=" N VAL A 455 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 8.396A pdb=" N ASN A 476 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 10.187A pdb=" N GLY A 457 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 8.482A pdb=" N GLY A 474 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N THR A 461 " --> pdb=" O ARG A 470 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 503 through 506 removed outlier: 7.527A pdb=" N THR A 488 " --> pdb=" O MET A 587 " (cutoff:3.500A) removed outlier: 9.045A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.242A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 596 through 598 removed outlier: 3.673A pdb=" N GLY A 606 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 619 through 622 removed outlier: 3.981A pdb=" N ASN A 621 " --> pdb=" O LEU A 628 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.691A pdb=" N GLU A 654 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 4.416A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ASN A 697 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB9, first strand: chain 'B' and resid 262 through 269 removed outlier: 6.779A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 262 through 269 removed outlier: 6.779A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 272 through 273 Processing sheet with id=AC3, first strand: chain 'B' and resid 389 through 390 removed outlier: 6.904A pdb=" N TYR B 375 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.423A pdb=" N ILE B 404 " --> pdb=" O TYR B 375 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER B 402 " --> pdb=" O VAL B 377 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 394 through 395 removed outlier: 8.668A pdb=" N ILE B 374 " --> pdb=" O ALA B 460 " (cutoff:3.500A) removed outlier: 8.087A pdb=" N ALA B 460 " --> pdb=" O ILE B 374 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ASN B 376 " --> pdb=" O ASN B 458 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N ASN B 458 " --> pdb=" O ASN B 376 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N GLN B 454 " --> pdb=" O THR B 380 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N SER B 382 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 5.889A pdb=" N THR B 452 " --> pdb=" O SER B 382 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N VAL B 384 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 5.466A pdb=" N LEU B 450 " --> pdb=" O VAL B 384 " (cutoff:3.500A) removed outlier: 10.746A pdb=" N VAL B 455 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N ASN B 476 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 9.421A pdb=" N GLY B 457 " --> pdb=" O GLY B 474 " (cutoff:3.500A) removed outlier: 8.386A pdb=" N GLY B 474 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 501 through 506 Processing sheet with id=AC6, first strand: chain 'B' and resid 597 through 598 removed outlier: 3.919A pdb=" N GLY B 606 " --> pdb=" O HIS B 597 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 639 through 643 removed outlier: 6.224A pdb=" N VAL B 701 " --> pdb=" O SER B 640 " (cutoff:3.500A) removed outlier: 5.264A pdb=" N TYR B 642 " --> pdb=" O TYR B 699 " (cutoff:3.500A) removed outlier: 6.823A pdb=" N TYR B 699 " --> pdb=" O TYR B 642 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 700 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N LEU B 725 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 645 through 646 Processing sheet with id=AC9, first strand: chain 'B' and resid 666 through 668 removed outlier: 3.655A pdb=" N SER B 667 " --> pdb=" O PHE B 675 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AD2, first strand: chain 'C' and resid 262 through 269 removed outlier: 6.613A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 262 through 269 removed outlier: 6.613A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 272 through 273 removed outlier: 4.736A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.914A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR C 375 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ILE C 404 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.914A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.634A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 4.278A pdb=" N VAL C 377 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N TYR C 456 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.910A pdb=" N GLN C 454 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N THR C 381 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N THR C 452 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.080A pdb=" N LEU C 383 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N LEU C 450 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 7.241A pdb=" N LEU C 385 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 7.339A pdb=" N LEU C 448 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 10.856A pdb=" N VAL C 455 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 8.706A pdb=" N ASN C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 10.381A pdb=" N GLY C 457 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 8.607A pdb=" N GLY C 474 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 501 through 506 removed outlier: 7.480A pdb=" N THR C 488 " --> pdb=" O MET C 587 " (cutoff:3.500A) removed outlier: 8.875A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.794A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.393A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.039A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AD9, first strand: chain 'C' and resid 618 through 622 removed outlier: 5.802A pdb=" N VAL C 619 " --> pdb=" O ASN C 630 " (cutoff:3.500A) removed outlier: 7.522A pdb=" N ASN C 630 " --> pdb=" O VAL C 619 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N ASN C 621 " --> pdb=" O LEU C 628 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'C' and resid 654 through 655 removed outlier: 4.041A pdb=" N GLU C 654 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ILE C 646 " --> pdb=" O GLU C 654 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N GLY C 641 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N VAL C 701 " --> pdb=" O GLY C 641 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ILE C 643 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N TYR C 699 " --> pdb=" O ILE C 643 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N LYS C 729 " --> pdb=" O VAL C 696 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AE3, first strand: chain 'D' and resid 262 through 269 removed outlier: 6.614A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 262 through 269 removed outlier: 6.614A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 272 through 273 Processing sheet with id=AE6, first strand: chain 'D' and resid 389 through 394 removed outlier: 6.850A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N TYR D 375 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N ILE D 404 " --> pdb=" O TYR D 375 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 389 through 394 removed outlier: 6.850A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N TYR D 375 " --> pdb=" O ASN D 458 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N VAL D 377 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N TYR D 456 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N GLN D 454 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N THR D 381 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N THR D 452 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N LEU D 383 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 7.105A pdb=" N LEU D 450 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N LEU D 385 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU D 448 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 10.953A pdb=" N VAL D 455 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 8.762A pdb=" N ASN D 476 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 10.681A pdb=" N GLY D 457 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N GLY D 474 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 501 through 506 removed outlier: 3.516A pdb=" N PHE D 493 " --> pdb=" O VAL D 501 " (cutoff:3.500A) removed outlier: 9.145A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.785A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.221A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 596 through 598 removed outlier: 6.775A pdb=" N HIS D 597 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 619 through 622 removed outlier: 3.565A pdb=" N ASN D 621 " --> pdb=" O LEU D 628 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N THR D 674 " --> pdb=" O LEU D 629 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 639 through 647 removed outlier: 3.918A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 7.219A pdb=" N ALA D 700 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU D 725 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AF4, first strand: chain 'E' and resid 262 through 269 removed outlier: 6.683A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 269 removed outlier: 6.683A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 272 through 273 Processing sheet with id=AF7, first strand: chain 'E' and resid 389 through 394 removed outlier: 6.898A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 402 through 405 removed outlier: 6.422A pdb=" N ILE E 404 " --> pdb=" O TYR E 375 " (cutoff:3.500A) removed outlier: 6.876A pdb=" N TYR E 375 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL E 377 " --> pdb=" O TYR E 456 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N TYR E 456 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.952A pdb=" N GLN E 454 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 10.710A pdb=" N VAL E 455 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 8.700A pdb=" N ASN E 476 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 10.040A pdb=" N GLY E 457 " --> pdb=" O GLY E 474 " (cutoff:3.500A) removed outlier: 8.726A pdb=" N GLY E 474 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.949A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.979A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 596 through 598 Processing sheet with id=AG2, first strand: chain 'E' and resid 626 through 629 removed outlier: 3.918A pdb=" N THR E 674 " --> pdb=" O LEU E 629 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N PHE E 675 " --> pdb=" O SER E 667 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'E' and resid 639 through 647 removed outlier: 3.633A pdb=" N LYS E 695 " --> pdb=" O GLU E 647 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS E 729 " --> pdb=" O VAL E 696 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AG5, first strand: chain 'F' and resid 262 through 273 removed outlier: 6.680A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.668A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.781A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 389 through 395 removed outlier: 3.542A pdb=" N GLN F 389 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 389 through 395 removed outlier: 3.542A pdb=" N GLN F 389 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.658A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 4.311A pdb=" N VAL F 377 " --> pdb=" O TYR F 456 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N TYR F 456 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLN F 454 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 11.000A pdb=" N VAL F 455 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 8.989A pdb=" N ASN F 476 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 10.102A pdb=" N GLY F 457 " --> pdb=" O GLY F 474 " (cutoff:3.500A) removed outlier: 8.725A pdb=" N GLY F 474 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.824A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 619 through 622 removed outlier: 3.885A pdb=" N ASN F 621 " --> pdb=" O LEU F 628 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 639 through 647 removed outlier: 3.603A pdb=" N GLU F 645 " --> pdb=" O ASN F 697 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AH4, first strand: chain 'G' and resid 262 through 269 removed outlier: 6.669A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 262 through 269 removed outlier: 6.669A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 272 through 273 Processing sheet with id=AH7, first strand: chain 'G' and resid 389 through 395 removed outlier: 4.927A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ILE G 374 " --> pdb=" O LEU G 405 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 389 through 395 removed outlier: 4.927A pdb=" N THR G 390 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU G 385 " --> pdb=" O THR G 390 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N ALA G 392 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL G 377 " --> pdb=" O TYR G 456 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N TYR G 456 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.633A pdb=" N GLN G 454 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N THR G 381 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N THR G 452 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N LEU G 383 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N LEU G 450 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N LEU G 385 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N LEU G 448 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 4.460A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 503 through 505 removed outlier: 3.592A pdb=" N ASP G 551 " --> pdb=" O ARG G 592 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 596 through 598 removed outlier: 3.841A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 626 through 627 Processing sheet with id=AI3, first strand: chain 'G' and resid 643 through 646 removed outlier: 4.100A pdb=" N ILE G 643 " --> pdb=" O TYR G 699 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N TYR G 699 " --> pdb=" O ILE G 643 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N ASN G 697 " --> pdb=" O GLU G 645 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N LYS G 729 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL G 698 " --> pdb=" O PHE G 727 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE G 727 " --> pdb=" O VAL G 698 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'H' and resid 70 through 74 removed outlier: 5.958A pdb=" N GLU H 70 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N ILE H 121 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N TYR H 72 " --> pdb=" O ILE H 121 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 293 through 295 removed outlier: 3.621A pdb=" N ILE H 563 " --> pdb=" O ILE H 293 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N PHE H 561 " --> pdb=" O PHE H 295 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 311 through 312 removed outlier: 6.818A pdb=" N ALA H 311 " --> pdb=" O THR H 456 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'H' and resid 401 through 402 removed outlier: 3.965A pdb=" N LEU H 402 " --> pdb=" O PHE H 411 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N PHE H 411 " --> pdb=" O LEU H 402 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'H' and resid 508 through 509 removed outlier: 4.244A pdb=" N LEU H 516 " --> pdb=" O LYS H 508 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'I' and resid 70 through 74 removed outlier: 6.161A pdb=" N GLU I 70 " --> pdb=" O LEU I 119 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N ILE I 121 " --> pdb=" O GLU I 70 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N TYR I 72 " --> pdb=" O ILE I 121 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'I' and resid 365 through 367 removed outlier: 4.198A pdb=" N LYS I 453 " --> pdb=" O LYS I 446 " (cutoff:3.500A) 1430 hydrogen bonds defined for protein. 3942 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 10.84 Time building geometry restraints manager: 4.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 9129 1.32 - 1.45: 9467 1.45 - 1.57: 24853 1.57 - 1.69: 0 1.69 - 1.81: 108 Bond restraints: 43557 Sorted by residual: bond pdb=" N ASP F 497 " pdb=" CA ASP F 497 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.15e-02 7.56e+03 1.09e+01 bond pdb=" N GLU H 766 " pdb=" CA GLU H 766 " ideal model delta sigma weight residual 1.457 1.500 -0.042 1.29e-02 6.01e+03 1.07e+01 bond pdb=" N ILE H 764 " pdb=" CA ILE H 764 " ideal model delta sigma weight residual 1.462 1.499 -0.037 1.17e-02 7.31e+03 9.78e+00 bond pdb=" N ASP H 193 " pdb=" CA ASP H 193 " ideal model delta sigma weight residual 1.454 1.490 -0.035 1.17e-02 7.31e+03 9.07e+00 bond pdb=" N ILE I 194 " pdb=" CA ILE I 194 " ideal model delta sigma weight residual 1.461 1.497 -0.035 1.17e-02 7.31e+03 9.01e+00 ... (remaining 43552 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.02: 56131 2.02 - 4.04: 2467 4.04 - 6.06: 266 6.06 - 8.08: 62 8.08 - 10.10: 11 Bond angle restraints: 58937 Sorted by residual: angle pdb=" C ILE C 708 " pdb=" N ASN C 709 " pdb=" CA ASN C 709 " ideal model delta sigma weight residual 120.68 130.05 -9.37 1.52e+00 4.33e-01 3.80e+01 angle pdb=" C PHE I 38 " pdb=" N THR I 39 " pdb=" CA THR I 39 " ideal model delta sigma weight residual 121.54 131.55 -10.01 1.91e+00 2.74e-01 2.75e+01 angle pdb=" C ASN F 682 " pdb=" N ASP F 683 " pdb=" CA ASP F 683 " ideal model delta sigma weight residual 122.82 129.84 -7.02 1.42e+00 4.96e-01 2.45e+01 angle pdb=" C LEU H 289 " pdb=" N ASN H 290 " pdb=" CA ASN H 290 " ideal model delta sigma weight residual 122.82 129.70 -6.88 1.42e+00 4.96e-01 2.35e+01 angle pdb=" C ASN C 682 " pdb=" N ASP C 683 " pdb=" CA ASP C 683 " ideal model delta sigma weight residual 121.54 130.22 -8.68 1.91e+00 2.74e-01 2.07e+01 ... (remaining 58932 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 23279 17.77 - 35.55: 2807 35.55 - 53.32: 451 53.32 - 71.10: 90 71.10 - 88.87: 37 Dihedral angle restraints: 26664 sinusoidal: 10894 harmonic: 15770 Sorted by residual: dihedral pdb=" C GLU H 766 " pdb=" N GLU H 766 " pdb=" CA GLU H 766 " pdb=" CB GLU H 766 " ideal model delta harmonic sigma weight residual -122.60 -137.15 14.55 0 2.50e+00 1.60e-01 3.39e+01 dihedral pdb=" CA LYS I 55 " pdb=" C LYS I 55 " pdb=" N ILE I 56 " pdb=" CA ILE I 56 " ideal model delta harmonic sigma weight residual 180.00 151.40 28.60 0 5.00e+00 4.00e-02 3.27e+01 dihedral pdb=" CA TYR H 594 " pdb=" C TYR H 594 " pdb=" N PHE H 595 " pdb=" CA PHE H 595 " ideal model delta harmonic sigma weight residual -180.00 -152.23 -27.77 0 5.00e+00 4.00e-02 3.09e+01 ... (remaining 26661 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.106: 6025 0.106 - 0.211: 585 0.211 - 0.317: 29 0.317 - 0.423: 4 0.423 - 0.528: 2 Chirality restraints: 6645 Sorted by residual: chirality pdb=" CA GLU H 766 " pdb=" N GLU H 766 " pdb=" C GLU H 766 " pdb=" CB GLU H 766 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 6.98e+00 chirality pdb=" CA ASP F 497 " pdb=" N ASP F 497 " pdb=" C ASP F 497 " pdb=" CB ASP F 497 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.80e+00 chirality pdb=" CA ASP B 497 " pdb=" N ASP B 497 " pdb=" C ASP B 497 " pdb=" CB ASP B 497 " both_signs ideal model delta sigma weight residual False 2.51 2.12 0.39 2.00e-01 2.50e+01 3.79e+00 ... (remaining 6642 not shown) Planarity restraints: 7701 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU G 250 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C GLU G 250 " 0.060 2.00e-02 2.50e+03 pdb=" O GLU G 250 " -0.023 2.00e-02 2.50e+03 pdb=" N ALA G 251 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE I 624 " -0.055 5.00e-02 4.00e+02 8.29e-02 1.10e+01 pdb=" N PRO I 625 " 0.143 5.00e-02 4.00e+02 pdb=" CA PRO I 625 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO I 625 " -0.045 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN H 564 " -0.050 5.00e-02 4.00e+02 7.55e-02 9.12e+00 pdb=" N PRO H 565 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO H 565 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 565 " -0.042 5.00e-02 4.00e+02 ... (remaining 7698 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 9095 2.77 - 3.31: 37119 3.31 - 3.84: 69779 3.84 - 4.37: 81299 4.37 - 4.90: 143148 Nonbonded interactions: 340440 Sorted by model distance: nonbonded pdb=" N ASP I 193 " pdb=" OD1 ASP I 193 " model vdw 2.243 3.120 nonbonded pdb=" O ILE H 624 " pdb=" OH TYR H 672 " model vdw 2.245 3.040 nonbonded pdb=" O ASN I 304 " pdb=" OG SER I 308 " model vdw 2.246 3.040 nonbonded pdb=" O LYS I 720 " pdb=" OG1 THR I 724 " model vdw 2.248 3.040 nonbonded pdb=" O PHE D 236 " pdb=" OG1 THR D 240 " model vdw 2.250 3.040 ... (remaining 340435 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: 0.02 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } ncs_group { reference = chain 'H' selection = chain 'I' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.740 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: 0.760 Check model and map are aligned: 0.080 Set scattering table: 0.070 Process input model: 38.930 Find NCS groups from input model: 0.820 Set up NCS constraints: 0.090 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.098 43557 Z= 0.439 Angle : 0.959 10.102 58937 Z= 0.539 Chirality : 0.064 0.528 6645 Planarity : 0.007 0.083 7701 Dihedral : 15.554 88.873 16464 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.06 % Allowed : 7.93 % Favored : 92.02 % Rotamer: Outliers : 0.77 % Allowed : 9.44 % Favored : 89.79 % Cbeta Deviations : 0.06 % Peptide Plane: Cis-proline : 3.61 % 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: -4.13 (0.09), residues: 5348 helix: -3.04 (0.10), residues: 1150 sheet: -2.39 (0.13), residues: 1286 loop : -2.81 (0.09), residues: 2912 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 200 TYR 0.027 0.003 TYR G 732 PHE 0.030 0.003 PHE C 493 TRP 0.019 0.003 TRP E 226 HIS 0.012 0.002 HIS C 304 Details of bonding type rmsd/Z covalent geometry : bond 0.01033 / 0.44 (43557) covalent geometry : angle 0.95852 / 0.54 (58937) hydrogen bonds : bond 0.24305 / 16.58 ( 1369) hydrogen bonds : angle 9.72605 / 6.72 ( 3942) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 205 time to evaluate : 1.650 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.8415 (OUTLIER) cc_final: 0.7875 (p0) REVERT: A 356 ASP cc_start: 0.7673 (t70) cc_final: 0.7270 (t0) REVERT: C 356 ASP cc_start: 0.7954 (t0) cc_final: 0.7398 (t0) REVERT: D 356 ASP cc_start: 0.8305 (t0) cc_final: 0.8068 (t70) REVERT: D 521 MET cc_start: 0.8823 (tpp) cc_final: 0.8254 (tpt) REVERT: E 287 ARG cc_start: 0.7465 (ttp-170) cc_final: 0.7228 (ttm110) REVERT: E 465 GLU cc_start: 0.7592 (mp0) cc_final: 0.6905 (mp0) REVERT: F 434 MET cc_start: 0.8535 (ttp) cc_final: 0.8135 (ptm) REVERT: F 662 MET cc_start: 0.2085 (mtp) cc_final: 0.0858 (ppp) REVERT: H 165 SER cc_start: 0.7084 (OUTLIER) cc_final: 0.6877 (t) REVERT: H 235 MET cc_start: 0.8900 (tpp) cc_final: 0.8562 (mmm) REVERT: H 245 LYS cc_start: 0.7930 (mtmt) cc_final: 0.7693 (ttpt) REVERT: H 248 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8214 (mt-10) REVERT: H 574 ASN cc_start: 0.5488 (p0) cc_final: 0.5258 (t0) REVERT: H 718 TYR cc_start: 0.3632 (t80) cc_final: 0.3387 (t80) REVERT: H 753 GLU cc_start: 0.4964 (pt0) cc_final: 0.4313 (tt0) REVERT: I 671 TYR cc_start: 0.5821 (t80) cc_final: 0.5508 (t80) outliers start: 37 outliers final: 16 residues processed: 241 average time/residue: 0.2830 time to fit residues: 110.9423 Evaluate side-chains 162 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 144 time to evaluate : 1.574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 497 ASP Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 165 SER Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 310 VAL Chi-restraints excluded: chain H residue 330 TYR Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 322 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 394 optimal weight: 2.9990 chunk 430 optimal weight: 20.0000 chunk 41 optimal weight: 1.9990 chunk 265 optimal weight: 3.9990 chunk 523 optimal weight: 20.0000 chunk 497 optimal weight: 10.0000 chunk 414 optimal weight: 2.9990 chunk 310 optimal weight: 0.4980 chunk 488 optimal weight: 7.9990 chunk 366 optimal weight: 2.9990 chunk 223 optimal weight: 3.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 277 GLN A 292 ASN A 299 HIS A 363 ASN A 389 GLN A 539 ASN A 553 ASN A 691 ASN B 304 HIS B 389 GLN B 601 ASN C 281 ASN C 306 ASN C 363 ASN C 389 GLN C 403 GLN C 424 GLN C 601 ASN C 682 ASN C 719 ASN D 209 ASN D 281 ASN D 389 GLN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 561 ASN D 616 HIS ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 691 ASN D 705 ASN E 277 GLN E 292 ASN E 306 ASN E 389 GLN ** E 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN E 553 ASN ** E 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN F 292 ASN F 363 ASN F 389 GLN F 561 ASN F 584 ASN F 697 ASN F 719 ASN G 268 ASN G 304 HIS G 363 ASN G 437 ASN G 458 ASN G 553 ASN G 657 ASN H 47 GLN H 200 ASN H 220 HIS H 278 HIS H 383 ASN H 405 ASN H 447 ASN H 756 ASN I 200 ASN I 205 GLN I 383 ASN I 407 GLN I 493 GLN I 522 GLN I 528 ASN I 585 ASN I 676 ASN I 677 HIS I 717 GLN I 725 ASN I 756 ASN Total number of N/Q/H flips: 69 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.3279 r_free = 0.3279 target = 0.100478 restraints weight = 90441.915| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.40 r_work: 0.3044 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.1395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 43557 Z= 0.155 Angle : 0.568 8.224 58937 Z= 0.310 Chirality : 0.046 0.172 6645 Planarity : 0.005 0.062 7701 Dihedral : 5.875 44.801 5795 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.33 % Favored : 94.67 % Rotamer: Outliers : 1.06 % Allowed : 11.94 % Favored : 87.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.92 (0.10), residues: 5348 helix: -1.30 (0.14), residues: 1145 sheet: -1.74 (0.13), residues: 1316 loop : -2.32 (0.10), residues: 2887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 659 TYR 0.030 0.001 TYR H 593 PHE 0.018 0.001 PHE H 655 TRP 0.015 0.001 TRP B 346 HIS 0.006 0.001 HIS A 299 Details of bonding type rmsd/Z covalent geometry : bond 0.00355 / 0.15 (43557) covalent geometry : angle 0.56760 / 0.31 (58937) hydrogen bonds : bond 0.04121 / 2.80 ( 1369) hydrogen bonds : angle 6.45584 / 4.45 ( 3942) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 169 time to evaluate : 1.579 Fit side-chains revert: symmetry clash REVERT: A 340 LEU cc_start: 0.8454 (mp) cc_final: 0.8087 (mt) REVERT: A 356 ASP cc_start: 0.8454 (t70) cc_final: 0.7921 (t0) REVERT: B 203 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9011 (tt) REVERT: C 496 LYS cc_start: 0.9140 (tttt) cc_final: 0.8882 (tptp) REVERT: D 356 ASP cc_start: 0.8803 (t0) cc_final: 0.8459 (t70) REVERT: E 287 ARG cc_start: 0.7949 (ttp-170) cc_final: 0.7247 (mtp85) REVERT: F 662 MET cc_start: 0.2801 (mtp) cc_final: 0.1295 (ppp) REVERT: G 335 ASP cc_start: 0.6679 (m-30) cc_final: 0.6159 (t70) REVERT: G 338 LEU cc_start: 0.8120 (mp) cc_final: 0.7768 (tt) REVERT: H 248 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8244 (mt-10) REVERT: H 574 ASN cc_start: 0.5845 (p0) cc_final: 0.5250 (t0) REVERT: H 630 PHE cc_start: 0.5799 (t80) cc_final: 0.4890 (m-10) REVERT: H 753 GLU cc_start: 0.5095 (pt0) cc_final: 0.4383 (tt0) REVERT: I 383 ASN cc_start: 0.1617 (OUTLIER) cc_final: 0.1272 (t0) REVERT: I 671 TYR cc_start: 0.5805 (t80) cc_final: 0.5587 (t80) outliers start: 51 outliers final: 17 residues processed: 216 average time/residue: 0.2420 time to fit residues: 88.4506 Evaluate side-chains 150 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 131 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 203 LEU Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 383 ASN Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 191 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 245 optimal weight: 4.9990 chunk 198 optimal weight: 2.9990 chunk 431 optimal weight: 30.0000 chunk 387 optimal weight: 0.0030 chunk 164 optimal weight: 6.9990 chunk 252 optimal weight: 3.9990 chunk 177 optimal weight: 7.9990 chunk 286 optimal weight: 6.9990 chunk 530 optimal weight: 20.0000 overall best weight: 2.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 326 ASN A 328 ASN B 336 HIS ** B 463 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 509 ASN C 682 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN E 409 ASN ** E 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN G 557 GLN G 719 ASN H 726 GLN I 81 HIS ** I 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4206 r_free = 0.4206 target = 0.157954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.100401 restraints weight = 89842.470| |-----------------------------------------------------------------------------| r_work (start): 0.3207 rms_B_bonded: 2.37 r_work: 0.3035 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.1633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 43557 Z= 0.149 Angle : 0.536 10.219 58937 Z= 0.289 Chirality : 0.046 0.168 6645 Planarity : 0.004 0.058 7701 Dihedral : 5.333 35.438 5777 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.72 % Favored : 94.28 % Rotamer: Outliers : 1.39 % Allowed : 14.22 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.39 (0.11), residues: 5348 helix: -0.65 (0.15), residues: 1173 sheet: -1.41 (0.13), residues: 1323 loop : -2.09 (0.11), residues: 2852 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 659 TYR 0.023 0.001 TYR H 593 PHE 0.017 0.001 PHE H 655 TRP 0.012 0.001 TRP E 226 HIS 0.005 0.001 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00350 / 0.15 (43557) covalent geometry : angle 0.53615 / 0.29 (58937) hydrogen bonds : bond 0.03593 / 2.45 ( 1369) hydrogen bonds : angle 5.83916 / 4.02 ( 3942) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 142 time to evaluate : 1.676 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.9032 (OUTLIER) cc_final: 0.8575 (p0) REVERT: A 340 LEU cc_start: 0.8495 (mp) cc_final: 0.8157 (mt) REVERT: A 356 ASP cc_start: 0.8439 (t70) cc_final: 0.8106 (t70) REVERT: C 496 LYS cc_start: 0.9031 (tttt) cc_final: 0.8820 (tptp) REVERT: D 356 ASP cc_start: 0.8782 (t0) cc_final: 0.8452 (t70) REVERT: E 287 ARG cc_start: 0.7823 (ttp-170) cc_final: 0.7135 (mtp85) REVERT: E 595 ARG cc_start: 0.7827 (mtm110) cc_final: 0.7196 (ptt-90) REVERT: F 350 MET cc_start: 0.8564 (mmt) cc_final: 0.8323 (mmm) REVERT: F 662 MET cc_start: 0.2531 (mtp) cc_final: 0.1078 (ppp) REVERT: G 338 LEU cc_start: 0.8021 (mp) cc_final: 0.7699 (tt) REVERT: H 558 ASN cc_start: 0.6374 (p0) cc_final: 0.6040 (m-40) REVERT: H 630 PHE cc_start: 0.5350 (t80) cc_final: 0.4474 (m-10) REVERT: H 634 LEU cc_start: 0.4056 (OUTLIER) cc_final: 0.3676 (tp) REVERT: H 753 GLU cc_start: 0.5143 (pt0) cc_final: 0.4381 (tt0) REVERT: I 370 LEU cc_start: 0.3196 (OUTLIER) cc_final: 0.2829 (mm) REVERT: I 671 TYR cc_start: 0.5825 (t80) cc_final: 0.5586 (t80) outliers start: 67 outliers final: 38 residues processed: 207 average time/residue: 0.2444 time to fit residues: 86.8683 Evaluate side-chains 170 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 129 time to evaluate : 1.596 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 328 ASN Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 611 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain G residue 719 ASN Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 330 TYR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 562 ILE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 193 ASP Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 238 LEU Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 254 optimal weight: 0.4980 chunk 259 optimal weight: 0.6980 chunk 24 optimal weight: 3.9990 chunk 476 optimal weight: 0.7980 chunk 236 optimal weight: 20.0000 chunk 361 optimal weight: 8.9990 chunk 36 optimal weight: 0.8980 chunk 255 optimal weight: 1.9990 chunk 305 optimal weight: 3.9990 chunk 176 optimal weight: 0.8980 chunk 413 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 682 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN E 409 ASN E 616 HIS G 463 ASN I 81 HIS ** I 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 574 ASN I 676 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4229 r_free = 0.4229 target = 0.159934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.102492 restraints weight = 89395.448| |-----------------------------------------------------------------------------| r_work (start): 0.3243 rms_B_bonded: 2.30 r_work: 0.3089 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 43557 Z= 0.087 Angle : 0.485 12.445 58937 Z= 0.260 Chirality : 0.044 0.164 6645 Planarity : 0.003 0.053 7701 Dihedral : 4.833 35.757 5775 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 1.23 % Allowed : 15.24 % Favored : 83.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.11), residues: 5348 helix: -0.27 (0.15), residues: 1208 sheet: -1.04 (0.14), residues: 1253 loop : -1.91 (0.11), residues: 2887 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 287 TYR 0.020 0.001 TYR H 593 PHE 0.012 0.001 PHE H 655 TRP 0.010 0.001 TRP E 226 HIS 0.003 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00192 / 0.09 (43557) covalent geometry : angle 0.48450 / 0.26 (58937) hydrogen bonds : bond 0.02864 / 1.94 ( 1369) hydrogen bonds : angle 5.38046 / 3.70 ( 3942) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 151 time to evaluate : 2.122 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.8904 (OUTLIER) cc_final: 0.8432 (p0) REVERT: A 340 LEU cc_start: 0.8320 (mp) cc_final: 0.7974 (mt) REVERT: A 356 ASP cc_start: 0.8220 (t70) cc_final: 0.7655 (t0) REVERT: B 470 ARG cc_start: 0.8399 (mtt90) cc_final: 0.8192 (mtt-85) REVERT: C 496 LYS cc_start: 0.9064 (tttt) cc_final: 0.8837 (tptp) REVERT: E 259 TYR cc_start: 0.9382 (p90) cc_final: 0.9145 (p90) REVERT: E 287 ARG cc_start: 0.7705 (ttp-170) cc_final: 0.6921 (mtp85) REVERT: E 595 ARG cc_start: 0.7744 (mtm110) cc_final: 0.7121 (ptt180) REVERT: F 183 ILE cc_start: 0.9243 (tt) cc_final: 0.8949 (mt) REVERT: F 662 MET cc_start: 0.2445 (mtp) cc_final: 0.1144 (ppp) REVERT: G 335 ASP cc_start: 0.6758 (m-30) cc_final: 0.6472 (t70) REVERT: G 338 LEU cc_start: 0.7899 (mp) cc_final: 0.7643 (tt) REVERT: H 269 LEU cc_start: 0.1280 (OUTLIER) cc_final: 0.1004 (mp) REVERT: H 558 ASN cc_start: 0.6374 (p0) cc_final: 0.5829 (m-40) REVERT: H 634 LEU cc_start: 0.4040 (OUTLIER) cc_final: 0.3571 (tp) REVERT: H 753 GLU cc_start: 0.4916 (pt0) cc_final: 0.3889 (tt0) REVERT: I 370 LEU cc_start: 0.3510 (OUTLIER) cc_final: 0.3167 (mm) REVERT: I 671 TYR cc_start: 0.5912 (t80) cc_final: 0.5654 (t80) outliers start: 59 outliers final: 28 residues processed: 207 average time/residue: 0.2408 time to fit residues: 85.6067 Evaluate side-chains 165 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 133 time to evaluate : 1.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 635 ILE Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 269 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 676 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 187 optimal weight: 7.9990 chunk 535 optimal weight: 0.0980 chunk 328 optimal weight: 10.0000 chunk 329 optimal weight: 40.0000 chunk 377 optimal weight: 5.9990 chunk 174 optimal weight: 0.7980 chunk 452 optimal weight: 0.5980 chunk 319 optimal weight: 10.0000 chunk 361 optimal weight: 8.9990 chunk 263 optimal weight: 10.0000 chunk 375 optimal weight: 10.0000 overall best weight: 3.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN D 494 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 389 GLN E 409 ASN F 630 ASN H 335 GLN H 493 GLN H 681 GLN I 81 HIS ** I 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 676 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.157767 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099566 restraints weight = 89602.922| |-----------------------------------------------------------------------------| r_work (start): 0.3165 rms_B_bonded: 2.39 r_work: 0.2996 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.2885 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2885 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 43557 Z= 0.176 Angle : 0.528 8.555 58937 Z= 0.284 Chirality : 0.046 0.168 6645 Planarity : 0.004 0.051 7701 Dihedral : 4.936 32.194 5772 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.57 % Favored : 94.43 % Rotamer: Outliers : 1.71 % Allowed : 16.22 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.11), residues: 5348 helix: -0.11 (0.15), residues: 1215 sheet: -1.07 (0.14), residues: 1288 loop : -1.84 (0.11), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 287 TYR 0.018 0.001 TYR H 593 PHE 0.012 0.001 PHE E 596 TRP 0.010 0.001 TRP E 226 HIS 0.005 0.001 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (43557) covalent geometry : angle 0.52817 / 0.28 (58937) hydrogen bonds : bond 0.03332 / 2.27 ( 1369) hydrogen bonds : angle 5.36657 / 3.70 ( 3942) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 133 time to evaluate : 1.707 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.9344 (OUTLIER) cc_final: 0.9035 (tp) REVERT: A 276 ASP cc_start: 0.8942 (OUTLIER) cc_final: 0.8484 (p0) REVERT: A 340 LEU cc_start: 0.8403 (mp) cc_final: 0.8040 (mt) REVERT: A 356 ASP cc_start: 0.8323 (t70) cc_final: 0.7780 (t0) REVERT: B 470 ARG cc_start: 0.8514 (mtt90) cc_final: 0.8272 (mtt-85) REVERT: C 496 LYS cc_start: 0.9060 (tttt) cc_final: 0.8828 (tptp) REVERT: D 350 MET cc_start: 0.8091 (OUTLIER) cc_final: 0.7773 (mmt) REVERT: D 356 ASP cc_start: 0.8860 (t0) cc_final: 0.8250 (t70) REVERT: E 287 ARG cc_start: 0.7716 (ttp-170) cc_final: 0.7196 (ttm-80) REVERT: E 356 ASP cc_start: 0.8730 (t0) cc_final: 0.8445 (t0) REVERT: F 662 MET cc_start: 0.2287 (mtp) cc_final: 0.1128 (ppp) REVERT: G 335 ASP cc_start: 0.6729 (m-30) cc_final: 0.6411 (t0) REVERT: G 338 LEU cc_start: 0.7870 (mp) cc_final: 0.7593 (tt) REVERT: H 634 LEU cc_start: 0.3831 (OUTLIER) cc_final: 0.3412 (tp) REVERT: H 714 ASN cc_start: 0.7058 (t0) cc_final: 0.6785 (p0) REVERT: H 753 GLU cc_start: 0.4981 (pt0) cc_final: 0.3894 (tt0) REVERT: I 671 TYR cc_start: 0.5980 (t80) cc_final: 0.5613 (t80) outliers start: 82 outliers final: 57 residues processed: 208 average time/residue: 0.2214 time to fit residues: 81.0239 Evaluate side-chains 188 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 127 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 381 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 330 TYR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 630 PHE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 743 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 676 ASN Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 300 optimal weight: 2.9990 chunk 405 optimal weight: 9.9990 chunk 265 optimal weight: 0.0270 chunk 290 optimal weight: 5.9990 chunk 336 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 528 optimal weight: 10.0000 chunk 140 optimal weight: 6.9990 chunk 403 optimal weight: 0.1980 chunk 236 optimal weight: 50.0000 chunk 224 optimal weight: 10.0000 overall best weight: 2.6444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN G 376 ASN G 557 GLN I 81 HIS I 205 GLN ** I 354 ASN ** 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 = 0.4208 r_free = 0.4208 target = 0.158589 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.101394 restraints weight = 90229.407| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.34 r_work: 0.3027 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.2916 rms_B_bonded: 4.41 restraints_weight: 0.2500 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.2038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 43557 Z= 0.155 Angle : 0.514 8.684 58937 Z= 0.276 Chirality : 0.045 0.168 6645 Planarity : 0.004 0.050 7701 Dihedral : 4.878 32.667 5772 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 1.79 % Allowed : 17.13 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.74 (0.11), residues: 5348 helix: 0.03 (0.15), residues: 1215 sheet: -0.99 (0.14), residues: 1288 loop : -1.79 (0.11), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 287 TYR 0.034 0.001 TYR H 593 PHE 0.012 0.001 PHE E 596 TRP 0.010 0.001 TRP E 226 HIS 0.006 0.001 HIS E 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.15 (43557) covalent geometry : angle 0.51444 / 0.28 (58937) hydrogen bonds : bond 0.03192 / 2.17 ( 1369) hydrogen bonds : angle 5.28213 / 3.64 ( 3942) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 136 time to evaluate : 1.737 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.9335 (OUTLIER) cc_final: 0.9058 (tp) REVERT: A 276 ASP cc_start: 0.8944 (OUTLIER) cc_final: 0.8493 (p0) REVERT: A 340 LEU cc_start: 0.8527 (mp) cc_final: 0.8178 (mt) REVERT: A 356 ASP cc_start: 0.8329 (t70) cc_final: 0.7850 (t0) REVERT: B 470 ARG cc_start: 0.8519 (mtt90) cc_final: 0.8272 (mtt-85) REVERT: D 350 MET cc_start: 0.8110 (OUTLIER) cc_final: 0.7819 (mmt) REVERT: D 356 ASP cc_start: 0.8844 (t0) cc_final: 0.8256 (t70) REVERT: E 287 ARG cc_start: 0.7669 (ttp-170) cc_final: 0.6906 (mtp85) REVERT: E 356 ASP cc_start: 0.8713 (t0) cc_final: 0.8477 (t0) REVERT: F 662 MET cc_start: 0.2092 (mtp) cc_final: 0.1166 (ppp) REVERT: G 335 ASP cc_start: 0.6740 (m-30) cc_final: 0.6482 (t0) REVERT: G 338 LEU cc_start: 0.7922 (mp) cc_final: 0.7675 (tt) REVERT: H 714 ASN cc_start: 0.7008 (t0) cc_final: 0.6787 (p0) REVERT: H 753 GLU cc_start: 0.4920 (pt0) cc_final: 0.3868 (tt0) REVERT: I 671 TYR cc_start: 0.6037 (t80) cc_final: 0.5771 (t80) outliers start: 86 outliers final: 60 residues processed: 215 average time/residue: 0.2366 time to fit residues: 89.7316 Evaluate side-chains 189 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 126 time to evaluate : 1.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 630 PHE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 676 ASN Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 317 optimal weight: 9.9990 chunk 73 optimal weight: 6.9990 chunk 213 optimal weight: 30.0000 chunk 404 optimal weight: 0.4980 chunk 357 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 420 optimal weight: 30.0000 chunk 463 optimal weight: 9.9990 chunk 435 optimal weight: 10.0000 chunk 452 optimal weight: 5.9990 chunk 146 optimal weight: 1.9990 overall best weight: 2.2988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 584 ASN C 682 ASN ** D 409 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN G 557 GLN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** I 278 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 676 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.159110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.101353 restraints weight = 88698.065| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.34 r_work: 0.3045 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2929 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 43557 Z= 0.139 Angle : 0.504 10.242 58937 Z= 0.270 Chirality : 0.045 0.166 6645 Planarity : 0.004 0.055 7701 Dihedral : 4.782 33.414 5772 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.77 % Allowed : 17.97 % Favored : 80.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.61 (0.11), residues: 5348 helix: 0.15 (0.16), residues: 1215 sheet: -0.86 (0.14), residues: 1274 loop : -1.73 (0.11), residues: 2859 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG D 287 TYR 0.030 0.001 TYR H 593 PHE 0.012 0.001 PHE I 760 TRP 0.009 0.001 TRP E 226 HIS 0.005 0.001 HIS E 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00331 / 0.14 (43557) covalent geometry : angle 0.50445 / 0.27 (58937) hydrogen bonds : bond 0.03066 / 2.09 ( 1369) hydrogen bonds : angle 5.18292 / 3.57 ( 3942) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 137 time to evaluate : 1.789 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ILE cc_start: 0.9321 (OUTLIER) cc_final: 0.9043 (tp) REVERT: A 276 ASP cc_start: 0.8921 (OUTLIER) cc_final: 0.8445 (p0) REVERT: A 340 LEU cc_start: 0.8474 (mp) cc_final: 0.8091 (mt) REVERT: A 350 MET cc_start: 0.8450 (tmm) cc_final: 0.8054 (tmm) REVERT: A 356 ASP cc_start: 0.8297 (t70) cc_final: 0.7829 (t0) REVERT: A 662 MET cc_start: 0.1569 (tmm) cc_final: 0.0256 (mmt) REVERT: B 470 ARG cc_start: 0.8564 (mtt90) cc_final: 0.8297 (mtt-85) REVERT: D 350 MET cc_start: 0.8024 (OUTLIER) cc_final: 0.7775 (mmt) REVERT: D 356 ASP cc_start: 0.8861 (t0) cc_final: 0.8277 (t70) REVERT: D 521 MET cc_start: 0.9050 (tpp) cc_final: 0.8768 (tpt) REVERT: E 259 TYR cc_start: 0.9384 (p90) cc_final: 0.9111 (p90) REVERT: E 287 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.6913 (mtp85) REVERT: E 356 ASP cc_start: 0.8735 (t0) cc_final: 0.8524 (t0) REVERT: F 183 ILE cc_start: 0.9286 (tt) cc_final: 0.8930 (mt) REVERT: F 569 LEU cc_start: 0.9119 (OUTLIER) cc_final: 0.8898 (tt) REVERT: F 597 HIS cc_start: 0.7248 (m90) cc_final: 0.6575 (m90) REVERT: F 662 MET cc_start: 0.2440 (mtp) cc_final: 0.1074 (ppp) REVERT: G 335 ASP cc_start: 0.6888 (m-30) cc_final: 0.6592 (t0) REVERT: G 338 LEU cc_start: 0.8043 (mp) cc_final: 0.7738 (tt) REVERT: H 62 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7937 (tp30) REVERT: H 714 ASN cc_start: 0.6939 (t0) cc_final: 0.6730 (p0) REVERT: H 753 GLU cc_start: 0.5255 (pt0) cc_final: 0.4031 (tt0) REVERT: I 370 LEU cc_start: 0.3597 (OUTLIER) cc_final: 0.3185 (mm) outliers start: 85 outliers final: 66 residues processed: 215 average time/residue: 0.2339 time to fit residues: 88.6634 Evaluate side-chains 200 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 129 time to evaluate : 1.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 269 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 304 HIS Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 350 MET Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 694 TYR Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 569 LEU Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 330 TYR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 486 THR Chi-restraints excluded: chain H residue 630 PHE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 298 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 676 ASN Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 522 optimal weight: 6.9990 chunk 374 optimal weight: 6.9990 chunk 271 optimal weight: 9.9990 chunk 525 optimal weight: 9.9990 chunk 417 optimal weight: 30.0000 chunk 98 optimal weight: 5.9990 chunk 205 optimal weight: 8.9990 chunk 468 optimal weight: 3.9990 chunk 369 optimal weight: 6.9990 chunk 460 optimal weight: 5.9990 chunk 404 optimal weight: 4.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN E 560 GLN F 389 GLN G 557 GLN ** G 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 189 ASN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 518 ASN I 676 ASN I 737 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4180 r_free = 0.4180 target = 0.156224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.097919 restraints weight = 91022.497| |-----------------------------------------------------------------------------| r_work (start): 0.3160 rms_B_bonded: 2.36 r_work: 0.2997 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8631 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.127 43557 Z= 0.300 Angle : 0.623 8.317 58937 Z= 0.333 Chirality : 0.049 0.178 6645 Planarity : 0.004 0.059 7701 Dihedral : 5.307 36.129 5772 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 1.98 % Allowed : 18.24 % Favored : 79.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.87 (0.11), residues: 5348 helix: -0.09 (0.15), residues: 1215 sheet: -1.06 (0.14), residues: 1288 loop : -1.87 (0.11), residues: 2845 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG D 287 TYR 0.031 0.002 TYR H 593 PHE 0.018 0.002 PHE B 554 TRP 0.012 0.002 TRP C 226 HIS 0.009 0.001 HIS E 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00723 / 0.30 (43557) covalent geometry : angle 0.62286 / 0.33 (58937) hydrogen bonds : bond 0.03919 / 2.67 ( 1369) hydrogen bonds : angle 5.50286 / 3.79 ( 3942) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 130 time to evaluate : 1.753 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.8946 (OUTLIER) cc_final: 0.8500 (p0) REVERT: A 350 MET cc_start: 0.8501 (tmm) cc_final: 0.8136 (tmm) REVERT: A 356 ASP cc_start: 0.8428 (t70) cc_final: 0.8089 (t70) REVERT: C 263 HIS cc_start: 0.8895 (OUTLIER) cc_final: 0.8576 (p-80) REVERT: D 521 MET cc_start: 0.9044 (tpp) cc_final: 0.8830 (tpt) REVERT: E 287 ARG cc_start: 0.7806 (ttp-170) cc_final: 0.7095 (mtp85) REVERT: E 356 ASP cc_start: 0.8818 (t0) cc_final: 0.8589 (t0) REVERT: F 662 MET cc_start: 0.2437 (mtp) cc_final: 0.1194 (ppp) REVERT: G 338 LEU cc_start: 0.8083 (mp) cc_final: 0.7789 (tt) REVERT: H 62 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7939 (tp30) REVERT: H 753 GLU cc_start: 0.5169 (pt0) cc_final: 0.4317 (tt0) REVERT: I 33 LEU cc_start: 0.9308 (OUTLIER) cc_final: 0.9088 (tt) REVERT: I 370 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.3310 (mm) REVERT: I 671 TYR cc_start: 0.7167 (t80) cc_final: 0.6961 (t80) outliers start: 95 outliers final: 72 residues processed: 216 average time/residue: 0.2372 time to fit residues: 90.1618 Evaluate side-chains 199 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 123 time to evaluate : 1.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 183 ILE Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 304 HIS Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 263 HIS Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 694 TYR Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 608 ASP Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 359 THR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 577 MET Chi-restraints excluded: chain H residue 630 PHE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain I residue 33 LEU Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 219 ASP Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 443 VAL Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 707 GLN Chi-restraints excluded: chain I residue 730 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 512 optimal weight: 0.8980 chunk 271 optimal weight: 8.9990 chunk 297 optimal weight: 6.9990 chunk 326 optimal weight: 10.0000 chunk 402 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 419 optimal weight: 5.9990 chunk 168 optimal weight: 6.9990 chunk 178 optimal weight: 2.9990 chunk 217 optimal weight: 0.5980 chunk 72 optimal weight: 40.0000 overall best weight: 2.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 682 ASN ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN F 389 GLN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 ASN ** 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 = 0.4202 r_free = 0.4202 target = 0.157934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.099816 restraints weight = 89204.710| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 2.41 r_work: 0.3022 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.2169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 43557 Z= 0.133 Angle : 0.525 14.466 58937 Z= 0.279 Chirality : 0.045 0.171 6645 Planarity : 0.004 0.059 7701 Dihedral : 4.931 34.202 5772 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 1.77 % Allowed : 18.76 % Favored : 79.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.63 (0.11), residues: 5348 helix: 0.12 (0.16), residues: 1215 sheet: -0.89 (0.14), residues: 1276 loop : -1.73 (0.11), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 287 TYR 0.037 0.001 TYR H 593 PHE 0.013 0.001 PHE A 493 TRP 0.010 0.001 TRP B 346 HIS 0.005 0.001 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (43557) covalent geometry : angle 0.52504 / 0.28 (58937) hydrogen bonds : bond 0.03147 / 2.15 ( 1369) hydrogen bonds : angle 5.26191 / 3.62 ( 3942) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 130 time to evaluate : 2.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.8986 (OUTLIER) cc_final: 0.8567 (p0) REVERT: A 350 MET cc_start: 0.8508 (tmm) cc_final: 0.8213 (tmm) REVERT: A 356 ASP cc_start: 0.8400 (t70) cc_final: 0.8100 (t70) REVERT: B 470 ARG cc_start: 0.8544 (mtt90) cc_final: 0.8267 (mtt-85) REVERT: D 521 MET cc_start: 0.9023 (tpp) cc_final: 0.8813 (tpt) REVERT: E 287 ARG cc_start: 0.7726 (ttp-170) cc_final: 0.7266 (mtm110) REVERT: E 356 ASP cc_start: 0.8805 (t0) cc_final: 0.8564 (t0) REVERT: F 662 MET cc_start: 0.2497 (mtp) cc_final: 0.1210 (ppp) REVERT: G 335 ASP cc_start: 0.6650 (m-30) cc_final: 0.6420 (t0) REVERT: G 338 LEU cc_start: 0.7976 (mp) cc_final: 0.7699 (tt) REVERT: H 62 GLU cc_start: 0.8232 (mm-30) cc_final: 0.7950 (tp30) REVERT: H 753 GLU cc_start: 0.5075 (pt0) cc_final: 0.3979 (tt0) REVERT: I 370 LEU cc_start: 0.3675 (OUTLIER) cc_final: 0.3262 (mm) REVERT: I 671 TYR cc_start: 0.7137 (t80) cc_final: 0.6859 (t80) outliers start: 85 outliers final: 67 residues processed: 209 average time/residue: 0.2309 time to fit residues: 86.1367 Evaluate side-chains 195 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 126 time to evaluate : 1.701 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 694 TYR Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 330 TYR Chi-restraints excluded: chain H residue 359 THR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 630 PHE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 759 VAL Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 443 VAL Chi-restraints excluded: chain I residue 541 VAL Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 129 optimal weight: 10.0000 chunk 276 optimal weight: 50.0000 chunk 481 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 20.0000 chunk 488 optimal weight: 2.9990 chunk 377 optimal weight: 9.9990 chunk 286 optimal weight: 5.9990 chunk 391 optimal weight: 0.0070 chunk 520 optimal weight: 6.9990 chunk 363 optimal weight: 0.9980 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.158427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3287 r_free = 0.3287 target = 0.102230 restraints weight = 89614.852| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.45 r_work: 0.3026 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.47 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 43557 Z= 0.155 Angle : 0.527 13.639 58937 Z= 0.281 Chirality : 0.045 0.186 6645 Planarity : 0.004 0.062 7701 Dihedral : 4.854 34.063 5772 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.71 % Allowed : 18.84 % Favored : 79.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.55 (0.11), residues: 5348 helix: 0.22 (0.16), residues: 1214 sheet: -0.85 (0.14), residues: 1304 loop : -1.69 (0.11), residues: 2830 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 287 TYR 0.035 0.001 TYR H 593 PHE 0.013 0.001 PHE A 493 TRP 0.010 0.001 TRP B 346 HIS 0.006 0.001 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00370 / 0.15 (43557) covalent geometry : angle 0.52739 / 0.28 (58937) hydrogen bonds : bond 0.03181 / 2.17 ( 1369) hydrogen bonds : angle 5.19515 / 3.57 ( 3942) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10696 Ramachandran restraints generated. 5348 Oldfield, 0 Emsley, 5348 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 128 time to evaluate : 1.527 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 276 ASP cc_start: 0.9004 (OUTLIER) cc_final: 0.8605 (p0) REVERT: A 356 ASP cc_start: 0.8396 (t70) cc_final: 0.8028 (t70) REVERT: A 662 MET cc_start: 0.1742 (tmm) cc_final: -0.0627 (tpp) REVERT: B 470 ARG cc_start: 0.8566 (mtt90) cc_final: 0.8314 (mtt-85) REVERT: D 521 MET cc_start: 0.9045 (tpp) cc_final: 0.8675 (tpt) REVERT: E 287 ARG cc_start: 0.7899 (ttp-170) cc_final: 0.7024 (mtp85) REVERT: E 356 ASP cc_start: 0.8824 (t0) cc_final: 0.8605 (t0) REVERT: F 662 MET cc_start: 0.2530 (mtp) cc_final: 0.1126 (ppp) REVERT: G 335 ASP cc_start: 0.6622 (m-30) cc_final: 0.6416 (t0) REVERT: G 338 LEU cc_start: 0.8036 (mp) cc_final: 0.7690 (tt) REVERT: H 62 GLU cc_start: 0.8126 (mm-30) cc_final: 0.7863 (tp30) REVERT: H 753 GLU cc_start: 0.5135 (pt0) cc_final: 0.3979 (tt0) REVERT: I 370 LEU cc_start: 0.3667 (OUTLIER) cc_final: 0.3253 (mm) REVERT: I 671 TYR cc_start: 0.7161 (t80) cc_final: 0.6925 (t80) REVERT: I 707 GLN cc_start: 0.6932 (OUTLIER) cc_final: 0.5891 (tm-30) outliers start: 82 outliers final: 73 residues processed: 205 average time/residue: 0.2311 time to fit residues: 83.7723 Evaluate side-chains 201 residues out of total 4815 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 125 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 175 VAL Chi-restraints excluded: chain A residue 276 ASP Chi-restraints excluded: chain A residue 309 VAL Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 723 LYS Chi-restraints excluded: chain B residue 175 VAL Chi-restraints excluded: chain B residue 196 VAL Chi-restraints excluded: chain B residue 217 THR Chi-restraints excluded: chain B residue 338 LEU Chi-restraints excluded: chain B residue 346 TRP Chi-restraints excluded: chain B residue 349 THR Chi-restraints excluded: chain B residue 357 THR Chi-restraints excluded: chain B residue 434 MET Chi-restraints excluded: chain C residue 374 ILE Chi-restraints excluded: chain C residue 381 THR Chi-restraints excluded: chain C residue 404 ILE Chi-restraints excluded: chain C residue 464 PHE Chi-restraints excluded: chain C residue 469 VAL Chi-restraints excluded: chain C residue 590 LEU Chi-restraints excluded: chain C residue 658 ASP Chi-restraints excluded: chain D residue 183 ILE Chi-restraints excluded: chain D residue 185 ASP Chi-restraints excluded: chain D residue 203 LEU Chi-restraints excluded: chain D residue 263 HIS Chi-restraints excluded: chain D residue 328 ASN Chi-restraints excluded: chain D residue 337 SER Chi-restraints excluded: chain D residue 404 ILE Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 572 THR Chi-restraints excluded: chain D residue 663 LEU Chi-restraints excluded: chain E residue 286 THR Chi-restraints excluded: chain E residue 374 ILE Chi-restraints excluded: chain E residue 473 THR Chi-restraints excluded: chain E residue 694 TYR Chi-restraints excluded: chain F residue 196 VAL Chi-restraints excluded: chain F residue 217 THR Chi-restraints excluded: chain F residue 374 ILE Chi-restraints excluded: chain F residue 382 SER Chi-restraints excluded: chain F residue 548 THR Chi-restraints excluded: chain F residue 620 ILE Chi-restraints excluded: chain F residue 624 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 183 ILE Chi-restraints excluded: chain G residue 349 THR Chi-restraints excluded: chain G residue 404 ILE Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 522 THR Chi-restraints excluded: chain G residue 619 VAL Chi-restraints excluded: chain G residue 671 ASP Chi-restraints excluded: chain G residue 718 THR Chi-restraints excluded: chain H residue 52 LEU Chi-restraints excluded: chain H residue 305 LEU Chi-restraints excluded: chain H residue 312 THR Chi-restraints excluded: chain H residue 330 TYR Chi-restraints excluded: chain H residue 359 THR Chi-restraints excluded: chain H residue 422 TYR Chi-restraints excluded: chain H residue 448 VAL Chi-restraints excluded: chain H residue 452 LEU Chi-restraints excluded: chain H residue 485 ASN Chi-restraints excluded: chain H residue 630 PHE Chi-restraints excluded: chain H residue 634 LEU Chi-restraints excluded: chain H residue 743 LEU Chi-restraints excluded: chain H residue 759 VAL Chi-restraints excluded: chain I residue 51 ASP Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 67 LEU Chi-restraints excluded: chain I residue 109 VAL Chi-restraints excluded: chain I residue 275 VAL Chi-restraints excluded: chain I residue 310 VAL Chi-restraints excluded: chain I residue 322 SER Chi-restraints excluded: chain I residue 331 ILE Chi-restraints excluded: chain I residue 370 LEU Chi-restraints excluded: chain I residue 372 LEU Chi-restraints excluded: chain I residue 443 VAL Chi-restraints excluded: chain I residue 707 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 536 random chunks: chunk 489 optimal weight: 5.9990 chunk 391 optimal weight: 5.9990 chunk 172 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 360 optimal weight: 0.9980 chunk 89 optimal weight: 2.9990 chunk 237 optimal weight: 9.9990 chunk 168 optimal weight: 10.0000 chunk 514 optimal weight: 8.9990 chunk 155 optimal weight: 0.0070 chunk 292 optimal weight: 40.0000 overall best weight: 2.6004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 657 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 304 HIS ** C 682 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 621 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 409 ASN ** H 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 354 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 544 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.158312 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.100255 restraints weight = 90560.861| |-----------------------------------------------------------------------------| r_work (start): 0.3187 rms_B_bonded: 2.33 r_work: 0.3037 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2919 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8568 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 43557 Z= 0.153 Angle : 0.525 13.291 58937 Z= 0.279 Chirality : 0.045 0.177 6645 Planarity : 0.004 0.063 7701 Dihedral : 4.809 31.588 5772 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.37 % Favored : 94.63 % Rotamer: Outliers : 1.81 % Allowed : 18.82 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.61 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.48 (0.11), residues: 5348 helix: 0.28 (0.16), residues: 1216 sheet: -0.80 (0.14), residues: 1283 loop : -1.65 (0.11), residues: 2849 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.000 ARG D 287 TYR 0.034 0.001 TYR H 593 PHE 0.013 0.001 PHE A 493 TRP 0.010 0.001 TRP E 226 HIS 0.007 0.001 HIS C 263 Details of bonding type rmsd/Z covalent geometry : bond 0.00366 / 0.15 (43557) covalent geometry : angle 0.52501 / 0.28 (58937) hydrogen bonds : bond 0.03131 / 2.13 ( 1369) hydrogen bonds : angle 5.15692 / 3.55 ( 3942) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15325.81 seconds wall clock time: 262 minutes 6.74 seconds (15726.74 seconds total)