Starting phenix.real_space_refine on Tue Sep 15 07:30:04 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.cif Found real_map, /net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.cif" restraint_files = "/net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6uzb_20955/09_2026/6uzb_20955.map" } resolution = 3.2 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= 0.006 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 48 5.16 5 C 23153 2.51 5 N 6330 2.21 5 O 7406 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.04s 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: 36951 Number of models: 1 Model: "" Number of chains: 15 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: "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: 7.88, per 1000 atoms: 0.21 Number of scatterers: 36951 At special positions: 0 Unit cell: (174.41, 175.48, 296.39, 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 48 16.00 O 7406 8.00 N 6330 7.00 C 23153 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.90 Conformation dependent library (CDL) restraints added in 1.4 seconds 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8838 Finding SS restraints... Secondary structure from input PDB file: 123 helices and 80 sheets defined 23.0% alpha, 35.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.57 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 209 through 214 removed outlier: 4.055A pdb=" N LYS A 213 " --> pdb=" O ASN A 209 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS A 214 " --> pdb=" O ILE A 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 209 through 214' Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.832A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.851A 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 487 removed outlier: 3.650A pdb=" N GLU A 486 " --> pdb=" O PRO A 482 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N THR A 487 " --> pdb=" O GLN A 483 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 569 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.601A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 614 removed outlier: 3.662A pdb=" N VAL A 612 " --> pdb=" O ASP A 608 " (cutoff:3.500A) Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 209 through 214 removed outlier: 4.403A pdb=" N LYS B 213 " --> pdb=" O ASN B 209 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS B 214 " --> pdb=" O ILE B 210 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 209 through 214' Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 252 Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.574A pdb=" N LEU B 401 " --> pdb=" O GLU B 398 " (cutoff:3.500A) Processing helix chain 'B' and resid 435 through 446 Processing helix chain 'B' and resid 480 through 485 Processing helix chain 'B' and resid 522 through 531 Processing helix chain 'B' and resid 555 through 570 Processing helix chain 'B' and resid 573 through 581 removed outlier: 3.692A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N LEU B 578 " --> pdb=" O TYR B 575 " (cutoff:3.500A) removed outlier: 5.681A pdb=" N ASP B 579 " --> pdb=" O THR B 576 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N ILE B 581 " --> pdb=" O LEU B 578 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 614 Processing helix chain 'B' and resid 615 through 617 No H-bonds generated for 'chain 'B' and resid 615 through 617' Processing helix chain 'B' and resid 632 through 637 Processing helix chain 'B' and resid 659 through 663 removed outlier: 4.088A pdb=" N LEU B 663 " --> pdb=" O TYR B 660 " (cutoff:3.500A) Processing helix chain 'B' and resid 704 through 706 No H-bonds generated for 'chain 'B' and resid 704 through 706' Processing helix chain 'B' and resid 730 through 734 removed outlier: 3.606A pdb=" N ILE B 734 " --> pdb=" O GLY B 731 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 191 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: 3.633A 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 487 removed outlier: 3.816A pdb=" N THR C 487 " --> pdb=" O GLN C 483 " (cutoff:3.500A) Processing helix chain 'C' and resid 513 through 517 Processing helix chain 'C' and resid 522 through 531 removed outlier: 3.500A pdb=" N PHE C 531 " --> pdb=" O LEU C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 570 Processing helix chain 'C' and resid 608 through 614 Processing helix chain 'C' and resid 717 through 721 removed outlier: 4.101A pdb=" N GLY C 720 " --> pdb=" O SER C 717 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 252 Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.685A 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 513 through 518 removed outlier: 3.778A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 531 removed outlier: 3.513A 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 569 Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.836A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 614 removed outlier: 3.586A pdb=" N VAL D 612 " --> pdb=" O ASP D 608 " (cutoff:3.500A) Processing helix chain 'D' and resid 615 through 617 No H-bonds generated for 'chain 'D' and resid 615 through 617' Processing helix chain 'D' and resid 634 through 638 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 207 through 215 removed outlier: 4.165A pdb=" N LYS E 213 " --> pdb=" O ASN E 209 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LYS E 214 " --> pdb=" O ILE E 210 " (cutoff:3.500A) Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 252 Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.763A 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 486 Processing helix chain 'E' and resid 514 through 518 removed outlier: 3.622A pdb=" N THR E 517 " --> pdb=" O LEU E 514 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 removed outlier: 3.575A pdb=" N PHE E 531 " --> pdb=" O LEU E 527 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N GLY E 532 " --> pdb=" O LYS E 528 " (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 570 Processing helix chain 'E' and resid 573 through 581 removed outlier: 3.776A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL E 577 " --> pdb=" O ILE E 574 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N LEU E 578 " --> pdb=" O TYR E 575 " (cutoff:3.500A) removed outlier: 5.548A pdb=" N ASP E 579 " --> pdb=" O THR E 576 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 4.073A pdb=" N VAL E 612 " --> pdb=" O ASP E 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 207 through 215 removed outlier: 3.773A pdb=" N HIS F 211 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLU F 212 " --> pdb=" O SER F 208 " (cutoff:3.500A) removed outlier: 4.705A pdb=" N LYS F 213 " --> pdb=" O ASN F 209 " (cutoff:3.500A) removed outlier: 3.657A 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 248 through 252 Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 480 through 485 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.657A pdb=" N THR F 517 " --> pdb=" O LEU F 514 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 531 removed outlier: 3.618A pdb=" N PHE F 531 " --> pdb=" O LEU F 527 " (cutoff:3.500A) Processing helix chain 'F' and resid 555 through 568 Processing helix chain 'F' and resid 577 through 581 removed outlier: 3.937A pdb=" N ILE F 581 " --> pdb=" O LEU F 578 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 614 removed outlier: 4.195A pdb=" N VAL F 612 " --> pdb=" O ASP F 608 " (cutoff:3.500A) Processing helix chain 'F' and resid 732 through 734 No H-bonds generated for 'chain 'F' and resid 732 through 734' Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.812A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 removed outlier: 3.684A pdb=" N LEU G 401 " --> pdb=" O GLU G 398 " (cutoff:3.500A) Processing helix chain 'G' and resid 435 through 446 Processing helix chain 'G' and resid 480 through 485 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.516A pdb=" N THR G 517 " --> pdb=" O LEU G 514 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 514 through 518' Processing helix chain 'G' and resid 522 through 530 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 569 Processing helix chain 'G' and resid 608 through 614 Processing helix chain 'G' and resid 632 through 637 removed outlier: 4.181A pdb=" N LYS G 637 " --> pdb=" O LYS G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 660 through 664 removed outlier: 3.958A pdb=" N LEU G 663 " --> pdb=" O TYR G 660 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N ASN G 664 " --> pdb=" O ASP G 661 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 660 through 664' Processing helix chain 'H' and resid 21 through 30 Processing helix chain 'H' and resid 43 through 54 Processing helix chain 'H' and resid 57 through 67 removed outlier: 3.697A pdb=" N LEU H 61 " --> pdb=" O PRO H 57 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N LEU H 67 " --> pdb=" O ILE H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 81 through 85 removed outlier: 3.532A pdb=" N LEU H 84 " --> pdb=" O HIS H 81 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N GLN H 85 " --> pdb=" O LYS H 82 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 81 through 85' Processing helix chain 'H' and resid 88 through 93 removed outlier: 3.522A pdb=" N ASN H 93 " --> pdb=" O GLU H 89 " (cutoff:3.500A) Processing helix chain 'H' and resid 131 through 144 removed outlier: 3.846A pdb=" N GLU H 135 " --> pdb=" O GLU H 131 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N VAL H 136 " --> pdb=" O GLN H 132 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR H 137 " --> pdb=" O SER H 133 " (cutoff:3.500A) Processing helix chain 'H' and resid 144 through 150 removed outlier: 3.736A pdb=" N ILE H 148 " --> pdb=" O ILE H 144 " (cutoff:3.500A) Processing helix chain 'H' and resid 156 through 169 removed outlier: 3.899A pdb=" N ASP H 169 " --> pdb=" O SER H 165 " (cutoff:3.500A) Processing helix chain 'H' and resid 170 through 177 Processing helix chain 'H' and resid 178 through 188 removed outlier: 3.767A pdb=" N GLU H 186 " --> pdb=" O LYS H 182 " (cutoff:3.500A) Processing helix chain 'H' and resid 192 through 200 Processing helix chain 'H' and resid 200 through 217 removed outlier: 3.958A pdb=" N PHE H 204 " --> pdb=" O ASN H 200 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 220 No H-bonds generated for 'chain 'H' and resid 218 through 220' Processing helix chain 'H' and resid 221 through 228 Processing helix chain 'H' and resid 230 through 240 Processing helix chain 'H' and resid 241 through 255 removed outlier: 4.093A pdb=" N GLU H 253 " --> pdb=" O SER H 249 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N VAL H 255 " --> pdb=" O LYS H 251 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 272 removed outlier: 3.594A pdb=" N LEU H 269 " --> pdb=" O GLY H 265 " (cutoff:3.500A) Processing helix chain 'H' and resid 275 through 290 Processing helix chain 'H' and resid 299 through 307 removed outlier: 4.007A pdb=" N LEU H 305 " --> pdb=" O LEU H 301 " (cutoff:3.500A) Processing helix chain 'H' and resid 334 through 338 removed outlier: 3.713A pdb=" N LEU H 337 " --> pdb=" O ASP H 334 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 361 removed outlier: 3.916A pdb=" N HIS H 361 " --> pdb=" O SER H 357 " (cutoff:3.500A) Processing helix chain 'H' and resid 375 through 382 Processing helix chain 'H' and resid 467 through 473 removed outlier: 3.615A pdb=" N LYS H 473 " --> pdb=" O THR H 469 " (cutoff:3.500A) Processing helix chain 'H' and resid 479 through 484 Processing helix chain 'H' and resid 488 through 504 Processing helix chain 'H' and resid 517 through 530 Processing helix chain 'H' and resid 574 through 585 Processing helix chain 'H' and resid 626 through 637 removed outlier: 3.609A pdb=" N ILE H 637 " --> pdb=" O ASN H 633 " (cutoff:3.500A) Processing helix chain 'H' and resid 651 through 672 removed outlier: 3.526A pdb=" N PHE H 655 " --> pdb=" O ASP H 651 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N SER H 669 " --> pdb=" O ALA H 665 " (cutoff:3.500A) Processing helix chain 'H' and resid 680 through 703 removed outlier: 3.784A pdb=" N LYS H 684 " --> pdb=" O SER H 680 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU H 703 " --> pdb=" O ILE H 699 " (cutoff:3.500A) Processing helix chain 'H' and resid 709 through 733 Processing helix chain 'H' and resid 739 through 747 removed outlier: 3.552A pdb=" N LEU H 743 " --> pdb=" O GLU H 739 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N LEU H 747 " --> pdb=" O LEU H 743 " (cutoff:3.500A) Processing helix chain 'H' and resid 755 through 766 removed outlier: 3.940A pdb=" N ILE H 763 " --> pdb=" O VAL H 759 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ILE H 764 " --> pdb=" O PHE H 760 " (cutoff:3.500A) 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 273 removed outlier: 6.674A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.807A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.646A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 410 through 411 removed outlier: 3.552A pdb=" N ALA A 358 " --> pdb=" O MET A 434 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 276 through 304 removed outlier: 3.546A pdb=" N ASN B 306 " --> pdb=" O SER B 321 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N GLU B 302 " --> pdb=" O SER B 325 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR B 298 " --> pdb=" O SER B 329 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ASN B 292 " --> pdb=" O ASP B 335 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N THR B 288 " --> pdb=" O SER B 339 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N GLN B 280 " --> pdb=" O ALA B 347 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 311 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 318 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY A 318 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA B 311 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR B 279 " --> pdb=" O MET A 350 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N LEU A 340 " --> pdb=" O ILE B 289 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LEU A 338 " --> pdb=" O LYS B 291 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ILE A 334 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ARG B 297 " --> pdb=" O VAL A 332 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL A 332 " --> pdb=" O ARG B 297 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LEU G 340 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N ASN G 292 " --> pdb=" O ASP G 335 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N SER G 290 " --> pdb=" O SER G 337 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N THR G 282 " --> pdb=" O THR G 345 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N THR G 298 " --> pdb=" O SER G 329 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N GLY G 323 " --> pdb=" O HIS G 304 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 323 through 324 removed outlier: 3.528A pdb=" N ASP C 276 " --> pdb=" O GLY C 351 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N SER C 290 " --> pdb=" O SER C 337 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N THR D 293 " --> pdb=" O HIS C 336 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N LEU C 340 " --> pdb=" O ILE D 289 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N GLY C 342 " --> pdb=" O ARG D 287 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 329 through 332 removed outlier: 3.703A pdb=" N ASP D 276 " --> pdb=" O GLY D 351 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 284 " --> pdb=" O GLU D 343 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N THR D 286 " --> pdb=" O ALA D 341 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N ASP F 276 " --> pdb=" O GLY F 351 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL F 320 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N VAL G 309 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N ALA F 322 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N ALA G 307 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL G 320 " --> pdb=" O VAL A 309 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLY A 305 " --> pdb=" O PHE G 324 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ASN G 326 " --> pdb=" O VAL A 303 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 334 through 353 removed outlier: 3.758A pdb=" N LYS F 291 " --> pdb=" O LEU E 338 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N THR F 298 " --> pdb=" O SER F 329 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N GLU F 302 " --> pdb=" O SER F 325 " (cutoff:3.500A) removed outlier: 4.262A pdb=" N PHE F 324 " --> pdb=" O GLY G 305 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLY G 305 " --> pdb=" O PHE F 324 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N VAL F 332 " --> pdb=" O ARG G 297 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ARG G 297 " --> pdb=" O VAL F 332 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 291 through 311 removed outlier: 4.630A pdb=" N VAL F 303 " --> pdb=" O ASN E 326 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ASN E 326 " --> pdb=" O VAL F 303 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLY F 305 " --> pdb=" O PHE E 324 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA F 307 " --> pdb=" O ALA E 322 " (cutoff:3.500A) removed outlier: 4.824A pdb=" N ALA E 322 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER E 319 " --> pdb=" O GLU E 308 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLU E 308 " --> pdb=" O SER E 319 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N SER E 321 " --> pdb=" O ASN E 306 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N ASN E 306 " --> pdb=" O SER E 321 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N GLY E 323 " --> pdb=" O HIS E 304 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N HIS E 304 " --> pdb=" O GLY E 323 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N SER E 325 " --> pdb=" O GLU E 302 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU E 302 " --> pdb=" O SER E 325 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N VAL E 309 " --> pdb=" O VAL D 320 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N VAL D 320 " --> pdb=" O VAL E 309 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA E 311 " --> pdb=" O GLY D 318 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY D 318 " --> pdb=" O ALA E 311 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 395 removed outlier: 3.624A pdb=" N GLN A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR A 375 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N ILE A 404 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 389 through 395 removed outlier: 3.624A pdb=" N GLN A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 4.239A pdb=" N VAL A 377 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TYR A 456 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N GLN A 454 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N THR A 381 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.789A pdb=" N THR A 452 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU A 383 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 7.108A pdb=" N LEU A 450 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N LEU A 385 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N LEU A 448 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 11.038A pdb=" N VAL A 455 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 8.869A pdb=" N ASN A 476 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 10.250A pdb=" N GLY A 457 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 8.337A pdb=" N GLY A 474 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.427A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.770A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.155A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.533A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.121A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.057A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB4, first strand: chain 'A' and resid 596 through 598 removed outlier: 6.825A pdb=" N HIS A 597 " --> pdb=" O VAL A 605 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 628 through 629 Processing sheet with id=AB6, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.561A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLU A 645 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ASN A 697 " --> pdb=" O GLU A 645 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB8, first strand: chain 'B' and resid 262 through 269 removed outlier: 6.495A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 262 through 269 removed outlier: 6.495A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 272 through 273 removed outlier: 4.724A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.852A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N TYR B 375 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N ILE B 404 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.852A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.659A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.799A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL B 377 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TYR B 456 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N GLN B 454 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N THR B 381 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N THR B 452 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N LEU B 383 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N LEU B 450 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU B 385 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N LEU B 448 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 10.895A pdb=" N VAL B 455 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 9.165A pdb=" N ASN B 476 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 8.821A pdb=" N GLY B 457 " --> pdb=" O GLY B 474 " (cutoff:3.500A) removed outlier: 8.403A pdb=" N GLY B 474 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'B' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE B 589 " --> pdb=" O THR B 488 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.827A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 541 through 542 removed outlier: 3.754A pdb=" N LYS B 545 " --> pdb=" O TYR B 542 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 597 through 598 removed outlier: 6.885A pdb=" N HIS B 597 " --> pdb=" O VAL B 605 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'B' and resid 628 through 629 removed outlier: 3.601A pdb=" N THR B 674 " --> pdb=" O LEU B 629 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N SER B 667 " --> pdb=" O PHE B 675 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'B' and resid 639 through 643 removed outlier: 7.116A pdb=" N VAL B 696 " --> pdb=" O SER B 728 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N SER B 728 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.596A pdb=" N VAL B 698 " --> pdb=" O ILE B 726 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 645 through 646 removed outlier: 3.622A pdb=" N GLU B 654 " --> pdb=" O ILE B 646 " (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: 6.587A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 3.658A 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: 6.587A 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: 3.566A pdb=" N ALA C 358 " --> pdb=" O MET C 434 " (cutoff:3.500A) removed outlier: 4.715A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'C' and resid 310 through 311 Processing sheet with id=AD6, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.605A pdb=" N GLN C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TYR C 375 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N ILE C 404 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 389 through 395 removed outlier: 3.605A pdb=" N GLN C 389 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 4.283A pdb=" N VAL C 377 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.635A pdb=" N TYR C 456 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N GLN C 454 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N THR C 381 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N THR C 452 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N LEU C 383 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N LEU C 450 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N LEU C 385 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N LEU C 448 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 10.951A pdb=" N VAL C 455 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 8.914A pdb=" N ASN C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 9.915A pdb=" N GLY C 457 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N GLY C 474 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.658A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AE1, first strand: chain 'C' and resid 596 through 598 removed outlier: 6.532A pdb=" N HIS C 597 " --> pdb=" O VAL C 605 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'C' and resid 619 through 622 removed outlier: 7.173A pdb=" N LEU C 628 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N SER C 622 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 7.479A pdb=" N GLY C 626 " --> pdb=" O SER C 622 " (cutoff:3.500A) removed outlier: 5.140A pdb=" N LEU C 629 " --> pdb=" O THR C 674 " (cutoff:3.500A) removed outlier: 5.432A pdb=" N THR C 674 " --> pdb=" O LEU C 629 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'C' and resid 652 through 655 removed outlier: 3.803A pdb=" N LEU C 652 " --> pdb=" O ASP C 648 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL C 701 " --> pdb=" O SER C 640 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N TYR C 642 " --> pdb=" O TYR C 699 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N TYR C 699 " --> pdb=" O TYR C 642 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N VAL C 644 " --> pdb=" O ASN C 697 " (cutoff:3.500A) removed outlier: 6.710A pdb=" N ASN C 697 " --> pdb=" O VAL C 644 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE C 646 " --> pdb=" O LYS C 695 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LYS C 695 " --> pdb=" O ILE C 646 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AE5, first strand: chain 'D' and resid 262 through 273 removed outlier: 6.733A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.334A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.789A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.956A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N TYR D 375 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ILE D 404 " --> pdb=" O TYR D 375 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.956A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.685A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N VAL D 377 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TYR D 456 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN D 454 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N THR D 381 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR D 452 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 383 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU D 450 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N LEU D 385 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N LEU D 448 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 10.808A pdb=" N VAL D 455 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 8.933A pdb=" N ASN D 476 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 9.659A pdb=" N GLY D 457 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 8.397A pdb=" N GLY D 474 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.819A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.546A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'D' and resid 596 through 598 removed outlier: 5.945A pdb=" N HIS D 597 " --> pdb=" O VAL D 605 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'D' and resid 618 through 621 removed outlier: 4.418A pdb=" N GLU D 618 " --> pdb=" O ASN D 630 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N LEU D 628 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LEU D 627 " --> pdb=" O ILE D 676 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'D' and resid 643 through 646 removed outlier: 3.970A pdb=" N ILE D 643 " --> pdb=" O TYR D 699 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AF5, first strand: chain 'E' and resid 262 through 273 removed outlier: 6.691A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.660A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ALA E 358 " --> pdb=" O MET E 434 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.945A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.797A pdb=" N TYR E 375 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N ILE E 404 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.945A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.797A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N VAL E 377 " --> pdb=" O TYR E 456 " (cutoff:3.500A) removed outlier: 6.652A pdb=" N TYR E 456 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLN E 454 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N THR E 381 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.869A pdb=" N THR E 452 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU E 383 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 6.904A pdb=" N LEU E 450 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N LEU E 385 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 6.995A pdb=" N LEU E 448 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 4.275A 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: 7.474A pdb=" N THR E 488 " --> pdb=" O MET E 587 " (cutoff:3.500A) removed outlier: 8.984A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.613A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.387A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'E' and resid 597 through 598 Processing sheet with id=AG2, first strand: chain 'E' and resid 628 through 629 Processing sheet with id=AG3, first strand: chain 'E' and resid 643 through 645 removed outlier: 3.809A pdb=" N ASN E 697 " --> pdb=" O GLU E 645 " (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 269 removed outlier: 6.608A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 262 through 269 removed outlier: 6.608A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 272 through 273 removed outlier: 4.753A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.938A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N GLN F 403 " --> pdb=" O ASN F 376 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.938A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.742A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N VAL F 377 " --> pdb=" O TYR F 456 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TYR F 456 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N GLN F 454 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N THR F 381 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.971A pdb=" N THR F 452 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU F 383 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N LEU F 450 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N LEU F 385 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N LEU F 448 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 11.084A pdb=" N VAL F 455 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 9.127A pdb=" N ASN F 476 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 9.353A pdb=" N GLY F 457 " --> pdb=" O GLY F 474 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N GLY F 474 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.940A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.757A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AH3, first strand: chain 'F' and resid 596 through 598 removed outlier: 6.939A pdb=" N HIS F 597 " --> pdb=" O VAL F 605 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'F' and resid 627 through 629 removed outlier: 3.659A pdb=" N LEU F 629 " --> pdb=" O THR F 674 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR F 674 " --> pdb=" O LEU F 629 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'F' and resid 639 through 647 removed outlier: 3.516A pdb=" N ASN F 697 " --> pdb=" O GLU F 645 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AH7, first strand: chain 'G' and resid 262 through 273 removed outlier: 5.612A pdb=" N VAL G 264 " --> pdb=" O VAL G 367 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL G 367 " --> pdb=" O VAL G 264 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N MET G 266 " --> pdb=" O ARG G 365 " (cutoff:3.500A) removed outlier: 7.056A pdb=" N ARG G 365 " --> pdb=" O MET G 266 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N ASN G 268 " --> pdb=" O ASN G 363 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.634A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'G' and resid 389 through 395 removed outlier: 3.694A pdb=" N GLN G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N TYR G 375 " --> pdb=" O ILE G 404 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N ILE G 404 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 389 through 395 removed outlier: 3.694A pdb=" N GLN G 389 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.716A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.860A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N VAL G 377 " --> pdb=" O TYR G 456 " (cutoff:3.500A) removed outlier: 6.621A pdb=" N TYR G 456 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N GLN G 454 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR G 381 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N THR G 452 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N LEU G 383 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N LEU G 450 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 7.061A pdb=" N LEU G 385 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LEU G 448 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 10.909A pdb=" N VAL G 455 " --> pdb=" O ASN G 476 " (cutoff:3.500A) removed outlier: 9.002A pdb=" N ASN G 476 " --> pdb=" O VAL G 455 " (cutoff:3.500A) removed outlier: 9.119A pdb=" N GLY G 457 " --> pdb=" O GLY G 474 " (cutoff:3.500A) removed outlier: 8.328A pdb=" N GLY G 474 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 4.389A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.824A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.679A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'G' and resid 596 through 598 removed outlier: 3.617A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'G' and resid 639 through 647 removed outlier: 3.599A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE G 727 " --> pdb=" O VAL G 698 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N ALA G 700 " --> pdb=" O LEU G 725 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N LEU G 725 " --> pdb=" O ALA G 700 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'H' and resid 70 through 74 removed outlier: 6.123A pdb=" N GLU H 70 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N ILE H 121 " --> pdb=" O GLU H 70 " (cutoff:3.500A) removed outlier: 6.122A pdb=" N TYR H 72 " --> pdb=" O ILE H 121 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'H' and resid 291 through 295 removed outlier: 3.702A pdb=" N LEU H 294 " --> pdb=" O ALA H 463 " (cutoff:3.500A) removed outlier: 4.367A pdb=" N ALA H 463 " --> pdb=" O LEU H 294 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'H' and resid 393 through 394 Processing sheet with id=AI8, first strand: chain 'H' and resid 562 through 563 1280 hydrogen bonds defined for protein. 3495 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 9.65 Time building geometry restraints manager: 3.86 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: 7843 1.32 - 1.44: 8217 1.44 - 1.57: 21423 1.57 - 1.69: 2 1.69 - 1.81: 96 Bond restraints: 37581 Sorted by residual: bond pdb=" N SER C 711 " pdb=" CA SER C 711 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.25e-02 6.40e+03 1.02e+01 bond pdb=" N ILE H 192 " pdb=" CA ILE H 192 " ideal model delta sigma weight residual 1.459 1.499 -0.040 1.25e-02 6.40e+03 1.00e+01 bond pdb=" N SER B 711 " pdb=" CA SER B 711 " ideal model delta sigma weight residual 1.453 1.493 -0.039 1.27e-02 6.20e+03 9.66e+00 bond pdb=" N ASP B 599 " pdb=" CA ASP B 599 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.37e+00 bond pdb=" N GLU B 712 " pdb=" CA GLU B 712 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.17e-02 7.31e+03 8.90e+00 ... (remaining 37576 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.23: 49217 2.23 - 4.47: 1496 4.47 - 6.70: 151 6.70 - 8.94: 43 8.94 - 11.17: 6 Bond angle restraints: 50913 Sorted by residual: angle pdb=" N ASP C 683 " pdb=" CA ASP C 683 " pdb=" C ASP C 683 " ideal model delta sigma weight residual 111.90 103.16 8.74 1.32e+00 5.74e-01 4.39e+01 angle pdb=" O PHE H 38 " pdb=" C PHE H 38 " pdb=" N THR H 39 " ideal model delta sigma weight residual 120.83 124.86 -4.03 7.40e-01 1.83e+00 2.97e+01 angle pdb=" C SER C 711 " pdb=" CA SER C 711 " pdb=" CB SER C 711 " ideal model delta sigma weight residual 111.78 100.61 11.17 2.20e+00 2.07e-01 2.58e+01 angle pdb=" C LYS A 496 " pdb=" N ASP A 497 " pdb=" CA ASP A 497 " ideal model delta sigma weight residual 122.08 129.48 -7.40 1.47e+00 4.63e-01 2.54e+01 angle pdb=" C SER D 711 " pdb=" N GLU D 712 " pdb=" CA GLU D 712 " ideal model delta sigma weight residual 121.19 128.85 -7.66 1.59e+00 3.96e-01 2.32e+01 ... (remaining 50908 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 20329 17.77 - 35.54: 2167 35.54 - 53.30: 389 53.30 - 71.07: 77 71.07 - 88.84: 30 Dihedral angle restraints: 22992 sinusoidal: 9332 harmonic: 13660 Sorted by residual: dihedral pdb=" CA ASP G 608 " pdb=" C ASP G 608 " pdb=" N GLU G 609 " pdb=" CA GLU G 609 " ideal model delta harmonic sigma weight residual -180.00 -150.61 -29.39 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ASP D 608 " pdb=" C ASP D 608 " pdb=" N GLU D 609 " pdb=" CA GLU D 609 " ideal model delta harmonic sigma weight residual -180.00 -153.37 -26.63 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" C ILE H 192 " pdb=" N ILE H 192 " pdb=" CA ILE H 192 " pdb=" CB ILE H 192 " ideal model delta harmonic sigma weight residual -122.00 -134.47 12.47 0 2.50e+00 1.60e-01 2.49e+01 ... (remaining 22989 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 5063 0.095 - 0.190: 677 0.190 - 0.286: 30 0.286 - 0.381: 5 0.381 - 0.476: 1 Chirality restraints: 5776 Sorted by residual: chirality pdb=" CB ILE C 689 " pdb=" CA ILE C 689 " pdb=" CG1 ILE C 689 " pdb=" CG2 ILE C 689 " both_signs ideal model delta sigma weight residual False 2.64 2.17 0.48 2.00e-01 2.50e+01 5.67e+00 chirality pdb=" CB ILE D 183 " pdb=" CA ILE D 183 " pdb=" CG1 ILE D 183 " pdb=" CG2 ILE D 183 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.87e+00 chirality pdb=" CB ILE E 269 " pdb=" CA ILE E 269 " pdb=" CG1 ILE E 269 " pdb=" CG2 ILE E 269 " both_signs ideal model delta sigma weight residual False 2.64 2.32 0.33 2.00e-01 2.50e+01 2.64e+00 ... (remaining 5773 not shown) Planarity restraints: 6668 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA F 607 " -0.024 2.00e-02 2.50e+03 4.89e-02 2.39e+01 pdb=" C ALA F 607 " 0.085 2.00e-02 2.50e+03 pdb=" O ALA F 607 " -0.032 2.00e-02 2.50e+03 pdb=" N ASP F 608 " -0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU G 712 " -0.019 2.00e-02 2.50e+03 3.80e-02 1.44e+01 pdb=" C GLU G 712 " 0.066 2.00e-02 2.50e+03 pdb=" O GLU G 712 " -0.025 2.00e-02 2.50e+03 pdb=" N ASN G 713 " -0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE H 624 " -0.054 5.00e-02 4.00e+02 8.21e-02 1.08e+01 pdb=" N PRO H 625 " 0.142 5.00e-02 4.00e+02 pdb=" CA PRO H 625 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO H 625 " -0.045 5.00e-02 4.00e+02 ... (remaining 6665 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 7031 2.77 - 3.30: 31997 3.30 - 3.83: 60096 3.83 - 4.37: 70620 4.37 - 4.90: 124921 Nonbonded interactions: 294665 Sorted by model distance: nonbonded pdb=" CD1 LEU H 294 " pdb=" CD1 ILE H 562 " model vdw 2.236 3.880 nonbonded pdb=" O ILE B 484 " pdb=" OG1 THR B 488 " model vdw 2.248 3.040 nonbonded pdb=" O ILE C 484 " pdb=" OG1 THR C 488 " model vdw 2.249 3.040 nonbonded pdb=" O PHE D 236 " pdb=" OG1 THR D 240 " model vdw 2.251 3.040 nonbonded pdb=" OE2 GLU H 479 " pdb=" OH TYR H 503 " model vdw 2.253 3.040 ... (remaining 294660 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' } 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.020 Extract box with map and model: 0.710 Check model and map are aligned: 0.120 Set scattering table: 0.100 Process input model: 35.720 Find NCS groups from input model: 0.870 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:1.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.970 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 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 0.101 37581 Z= 0.429 Angle : 0.919 11.172 50913 Z= 0.519 Chirality : 0.063 0.476 5776 Planarity : 0.007 0.082 6668 Dihedral : 15.212 88.841 14154 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.04 % Allowed : 6.34 % Favored : 93.61 % Rotamer: Outliers : 0.84 % Allowed : 8.56 % Favored : 90.60 % Cbeta Deviations : 0.05 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.78 (0.10), residues: 4634 helix: -2.81 (0.13), residues: 858 sheet: -1.94 (0.14), residues: 1107 loop : -2.73 (0.10), residues: 2669 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 600 TYR 0.045 0.002 TYR A 366 PHE 0.034 0.003 PHE B 727 TRP 0.020 0.002 TRP G 226 HIS 0.013 0.002 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.01017 / 0.43 (37581) covalent geometry : angle 0.91876 / 0.52 (50913) hydrogen bonds : bond 0.24370 / 16.42 ( 1247) hydrogen bonds : angle 9.88724 / 6.90 ( 3495) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 209 time to evaluate : 1.369 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 662 MET cc_start: 0.5314 (ptp) cc_final: 0.4459 (pmm) REVERT: A 680 LYS cc_start: 0.6204 (OUTLIER) cc_final: 0.5900 (pttm) REVERT: C 597 HIS cc_start: 0.7083 (m90) cc_final: 0.6737 (m90) REVERT: C 681 TYR cc_start: -0.0124 (OUTLIER) cc_final: -0.0420 (t80) REVERT: D 356 ASP cc_start: 0.7905 (t0) cc_final: 0.7299 (t0) REVERT: D 541 GLN cc_start: 0.7816 (mt0) cc_final: 0.7578 (mt0) REVERT: D 561 ASN cc_start: 0.8359 (t0) cc_final: 0.7833 (t0) REVERT: F 591 ILE cc_start: 0.8592 (mt) cc_final: 0.8297 (tt) REVERT: G 285 GLN cc_start: 0.7670 (mt0) cc_final: 0.7452 (pt0) REVERT: G 662 MET cc_start: 0.1249 (ptt) cc_final: 0.0318 (tpt) REVERT: H 77 ASP cc_start: 0.8199 (OUTLIER) cc_final: 0.7827 (p0) REVERT: H 196 PHE cc_start: 0.8376 (OUTLIER) cc_final: 0.7220 (t80) REVERT: H 713 LYS cc_start: 0.8966 (tttm) cc_final: 0.8391 (mttm) REVERT: H 765 ASP cc_start: 0.8115 (OUTLIER) cc_final: 0.7909 (t0) outliers start: 35 outliers final: 10 residues processed: 241 average time/residue: 0.2638 time to fit residues: 98.9419 Evaluate side-chains 159 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 144 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain B residue 600 ARG Chi-restraints excluded: chain C residue 681 TYR Chi-restraints excluded: chain H residue 77 ASP Chi-restraints excluded: chain H residue 164 LYS Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 194 ILE Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 294 LEU Chi-restraints excluded: chain H residue 760 PHE Chi-restraints excluded: chain H residue 764 ILE Chi-restraints excluded: chain H residue 765 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 432 optimal weight: 8.9990 chunk 197 optimal weight: 0.8980 chunk 388 optimal weight: 30.0000 chunk 455 optimal weight: 5.9990 chunk 215 optimal weight: 0.0170 chunk 20 optimal weight: 0.8980 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 0.1980 chunk 207 optimal weight: 7.9990 chunk 401 optimal weight: 7.9990 overall best weight: 1.2020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 363 ASN A 389 GLN A 437 ASN A 630 ASN A 697 ASN B 277 GLN B 281 ASN B 304 HIS B 363 ASN B 389 GLN B 399 ASN B 437 ASN C 363 ASN C 389 GLN C 499 ASN C 553 ASN C 601 ASN C 657 ASN C 697 ASN C 713 ASN D 353 ASN D 389 GLN D 553 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 292 ASN E 389 GLN E 424 GLN E 494 ASN E 541 GLN E 584 ASN E 602 ASN E 682 ASN E 691 ASN E 693 ASN E 697 ASN E 719 ASN F 363 ASN F 389 GLN F 543 GLN F 697 ASN F 719 ASN G 389 GLN G 437 ASN G 584 ASN H 188 ASN H 205 GLN H 316 ASN H 343 GLN H 354 ASN H 406 ASN H 493 GLN H 528 ASN H 642 ASN H 677 HIS Total number of N/Q/H flips: 53 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.157986 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3116 r_free = 0.3116 target = 0.095529 restraints weight = 69741.739| |-----------------------------------------------------------------------------| r_work (start): 0.3021 rms_B_bonded: 3.59 r_work: 0.2733 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work: 0.2606 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8884 moved from start: 0.1315 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 37581 Z= 0.131 Angle : 0.556 7.871 50913 Z= 0.303 Chirality : 0.046 0.179 5776 Planarity : 0.005 0.064 6668 Dihedral : 6.088 56.534 5041 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.27 % Favored : 95.71 % Rotamer: Outliers : 0.89 % Allowed : 11.04 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % 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: -2.58 (0.11), residues: 4634 helix: -1.04 (0.17), residues: 873 sheet: -1.41 (0.14), residues: 1176 loop : -2.13 (0.11), residues: 2585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG G 287 TYR 0.016 0.001 TYR A 366 PHE 0.014 0.001 PHE B 727 TRP 0.014 0.001 TRP H 519 HIS 0.005 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 (37581) covalent geometry : angle 0.55607 / 0.30 (50913) hydrogen bonds : bond 0.04358 / 3.00 ( 1247) hydrogen bonds : angle 6.56748 / 4.61 ( 3495) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 161 time to evaluate : 1.432 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8323 (tmt170) cc_final: 0.8026 (ttp80) REVERT: A 662 MET cc_start: 0.5065 (ptp) cc_final: 0.4480 (pmm) REVERT: A 680 LYS cc_start: 0.6251 (OUTLIER) cc_final: 0.5849 (pttm) REVERT: A 694 TYR cc_start: 0.2106 (OUTLIER) cc_final: 0.0382 (p90) REVERT: B 350 MET cc_start: 0.8414 (tmm) cc_final: 0.8194 (tmm) REVERT: C 597 HIS cc_start: 0.7257 (m90) cc_final: 0.6857 (m90) REVERT: C 681 TYR cc_start: 0.0811 (OUTLIER) cc_final: 0.0327 (t80) REVERT: D 197 LYS cc_start: 0.8675 (tttm) cc_final: 0.8443 (ttmm) REVERT: D 541 GLN cc_start: 0.7549 (mt0) cc_final: 0.7306 (mt0) REVERT: D 561 ASN cc_start: 0.8506 (t0) cc_final: 0.7987 (t0) REVERT: E 465 GLU cc_start: 0.8837 (mp0) cc_final: 0.8406 (mp0) REVERT: F 287 ARG cc_start: 0.8371 (mtp180) cc_final: 0.8117 (mtp85) REVERT: F 591 ILE cc_start: 0.8851 (mt) cc_final: 0.8519 (tt) REVERT: G 662 MET cc_start: 0.0585 (ptt) cc_final: -0.0239 (tpt) REVERT: H 196 PHE cc_start: 0.8712 (OUTLIER) cc_final: 0.7862 (t80) REVERT: H 582 ILE cc_start: 0.8160 (OUTLIER) cc_final: 0.7875 (tp) REVERT: H 713 LYS cc_start: 0.8905 (tttm) cc_final: 0.8251 (mttm) REVERT: H 765 ASP cc_start: 0.8236 (OUTLIER) cc_final: 0.7825 (m-30) outliers start: 37 outliers final: 13 residues processed: 194 average time/residue: 0.2389 time to fit residues: 75.9784 Evaluate side-chains 157 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 138 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 680 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 681 TYR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain E residue 693 ASN Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 582 ILE Chi-restraints excluded: chain H residue 765 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 430 optimal weight: 50.0000 chunk 199 optimal weight: 0.9980 chunk 153 optimal weight: 9.9990 chunk 207 optimal weight: 10.0000 chunk 458 optimal weight: 0.7980 chunk 346 optimal weight: 6.9990 chunk 269 optimal weight: 8.9990 chunk 174 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 329 optimal weight: 30.0000 chunk 55 optimal weight: 10.0000 overall best weight: 2.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 336 HIS C 556 GLN C 570 ASN ** D 602 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 363 ASN E 424 GLN E 541 GLN E 682 ASN F 304 HIS F 697 ASN G 363 ASN H 200 ASN H 421 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4115 r_free = 0.4115 target = 0.157017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.093671 restraints weight = 69906.777| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.22 r_work: 0.2714 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work: 0.2588 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.2588 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 37581 Z= 0.174 Angle : 0.544 7.854 50913 Z= 0.294 Chirality : 0.047 0.218 5776 Planarity : 0.004 0.066 6668 Dihedral : 5.629 57.233 5021 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.03 % Favored : 94.95 % Rotamer: Outliers : 1.54 % Allowed : 13.08 % Favored : 85.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % 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: -2.08 (0.12), residues: 4634 helix: -0.32 (0.18), residues: 876 sheet: -1.14 (0.14), residues: 1148 loop : -1.91 (0.11), residues: 2610 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 595 TYR 0.019 0.001 TYR A 366 PHE 0.016 0.001 PHE B 727 TRP 0.011 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (37581) covalent geometry : angle 0.54365 / 0.29 (50913) hydrogen bonds : bond 0.03876 / 2.66 ( 1247) hydrogen bonds : angle 5.94394 / 4.18 ( 3495) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 144 time to evaluate : 1.399 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8290 (tmt170) cc_final: 0.7965 (ttp80) REVERT: A 346 TRP cc_start: 0.8658 (OUTLIER) cc_final: 0.8318 (t60) REVERT: A 662 MET cc_start: 0.5140 (ptp) cc_final: 0.4486 (pmm) REVERT: B 287 ARG cc_start: 0.8320 (mtm110) cc_final: 0.7991 (ttp80) REVERT: C 597 HIS cc_start: 0.7281 (m90) cc_final: 0.6896 (m90) REVERT: D 197 LYS cc_start: 0.8746 (tttm) cc_final: 0.8544 (ttmm) REVERT: D 541 GLN cc_start: 0.7564 (mt0) cc_final: 0.7190 (mt0) REVERT: D 561 ASN cc_start: 0.8508 (t0) cc_final: 0.7988 (t0) REVERT: E 263 HIS cc_start: 0.8456 (OUTLIER) cc_final: 0.7488 (p-80) REVERT: F 591 ILE cc_start: 0.8838 (mt) cc_final: 0.8470 (tt) REVERT: G 481 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9306 (mp) REVERT: G 497 ASP cc_start: 0.8724 (m-30) cc_final: 0.8377 (t0) REVERT: G 662 MET cc_start: 0.0334 (ptt) cc_final: -0.0550 (tpt) REVERT: H 75 ASP cc_start: 0.8912 (p0) cc_final: 0.8658 (p0) REVERT: H 196 PHE cc_start: 0.8705 (OUTLIER) cc_final: 0.7991 (t80) REVERT: H 713 LYS cc_start: 0.8878 (tttm) cc_final: 0.8318 (mmtt) outliers start: 64 outliers final: 27 residues processed: 201 average time/residue: 0.2164 time to fit residues: 72.2423 Evaluate side-chains 171 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 140 time to evaluate : 1.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 265 ASP Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 481 LEU Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 197 ILE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 702 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 5 optimal weight: 1.9990 chunk 168 optimal weight: 10.0000 chunk 197 optimal weight: 4.9990 chunk 237 optimal weight: 50.0000 chunk 356 optimal weight: 0.8980 chunk 134 optimal weight: 0.9980 chunk 384 optimal weight: 0.0970 chunk 69 optimal weight: 40.0000 chunk 448 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 99 optimal weight: 7.9990 overall best weight: 0.9780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 280 GLN C 403 GLN C 556 GLN D 310 HIS D 602 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 541 GLN E 682 ASN F 657 ASN F 697 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.158642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.095094 restraints weight = 69527.183| |-----------------------------------------------------------------------------| r_work (start): 0.3029 rms_B_bonded: 2.93 r_work: 0.2760 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2637 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2637 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.046 37581 Z= 0.098 Angle : 0.490 11.355 50913 Z= 0.263 Chirality : 0.045 0.215 5776 Planarity : 0.003 0.062 6668 Dihedral : 5.074 53.367 5013 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.19 % Favored : 95.79 % Rotamer: Outliers : 1.64 % Allowed : 14.09 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % 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: -1.64 (0.12), residues: 4634 helix: 0.15 (0.19), residues: 872 sheet: -0.84 (0.14), residues: 1148 loop : -1.66 (0.11), residues: 2614 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG F 595 TYR 0.014 0.001 TYR F 411 PHE 0.014 0.001 PHE H 295 TRP 0.012 0.001 TRP H 519 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00222 / 0.10 (37581) covalent geometry : angle 0.49035 / 0.26 (50913) hydrogen bonds : bond 0.03037 / 2.10 ( 1247) hydrogen bonds : angle 5.48722 / 3.87 ( 3495) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 147 time to evaluate : 1.370 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8235 (tmt170) cc_final: 0.7965 (ttp80) REVERT: A 346 TRP cc_start: 0.8580 (OUTLIER) cc_final: 0.8309 (t60) REVERT: A 662 MET cc_start: 0.5082 (ptp) cc_final: 0.4875 (ptp) REVERT: B 287 ARG cc_start: 0.8212 (mtm110) cc_final: 0.7951 (ttp80) REVERT: C 595 ARG cc_start: 0.8463 (OUTLIER) cc_final: 0.7824 (ttp-110) REVERT: D 539 ASN cc_start: 0.8088 (m110) cc_final: 0.7566 (p0) REVERT: D 541 GLN cc_start: 0.7480 (mt0) cc_final: 0.6413 (mt0) REVERT: D 561 ASN cc_start: 0.8512 (t0) cc_final: 0.7979 (t0) REVERT: D 602 ASN cc_start: 0.6448 (OUTLIER) cc_final: 0.6145 (m-40) REVERT: E 263 HIS cc_start: 0.8312 (OUTLIER) cc_final: 0.7489 (p-80) REVERT: F 591 ILE cc_start: 0.8797 (mt) cc_final: 0.8435 (tt) REVERT: F 595 ARG cc_start: 0.7485 (mtm110) cc_final: 0.7237 (mtm110) REVERT: G 497 ASP cc_start: 0.8702 (m-30) cc_final: 0.8386 (t0) REVERT: G 662 MET cc_start: 0.0322 (ptt) cc_final: -0.0628 (tpt) REVERT: H 196 PHE cc_start: 0.8696 (OUTLIER) cc_final: 0.7975 (t80) REVERT: H 372 LEU cc_start: 0.1837 (OUTLIER) cc_final: 0.1584 (pp) REVERT: H 713 LYS cc_start: 0.8858 (tttm) cc_final: 0.8337 (mmtt) outliers start: 68 outliers final: 29 residues processed: 208 average time/residue: 0.2261 time to fit residues: 77.4864 Evaluate side-chains 175 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 140 time to evaluate : 1.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 290 SER Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 595 ARG Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 602 ASN Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 303 VAL Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 702 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 258 optimal weight: 4.9990 chunk 255 optimal weight: 1.9990 chunk 157 optimal weight: 30.0000 chunk 65 optimal weight: 3.9990 chunk 123 optimal weight: 5.9990 chunk 424 optimal weight: 7.9990 chunk 132 optimal weight: 0.9980 chunk 252 optimal weight: 4.9990 chunk 212 optimal weight: 30.0000 chunk 428 optimal weight: 50.0000 chunk 254 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN C 556 GLN C 570 ASN D 602 ASN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN H 726 GLN H 756 ASN H 761 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4117 r_free = 0.4117 target = 0.156847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.092811 restraints weight = 69415.698| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 2.93 r_work: 0.2720 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work: 0.2595 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2595 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8893 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 37581 Z= 0.183 Angle : 0.528 9.300 50913 Z= 0.282 Chirality : 0.046 0.201 5776 Planarity : 0.004 0.062 6668 Dihedral : 5.074 51.458 5013 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.83 % Favored : 95.14 % Rotamer: Outliers : 1.71 % Allowed : 15.03 % Favored : 83.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % 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: -1.52 (0.12), residues: 4634 helix: 0.01 (0.18), residues: 930 sheet: -0.66 (0.14), residues: 1190 loop : -1.59 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG E 669 TYR 0.017 0.001 TYR H 292 PHE 0.014 0.001 PHE B 493 TRP 0.011 0.001 TRP G 226 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00440 / 0.18 (37581) covalent geometry : angle 0.52802 / 0.28 (50913) hydrogen bonds : bond 0.03380 / 2.33 ( 1247) hydrogen bonds : angle 5.40465 / 3.80 ( 3495) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 143 time to evaluate : 1.407 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8289 (tmt170) cc_final: 0.8001 (ttp80) REVERT: A 346 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.8330 (t60) REVERT: A 662 MET cc_start: 0.5049 (ptp) cc_final: 0.4828 (ptp) REVERT: B 287 ARG cc_start: 0.8262 (mtm110) cc_final: 0.8001 (ttp80) REVERT: C 595 ARG cc_start: 0.8518 (ttm110) cc_final: 0.8155 (ttp-110) REVERT: D 539 ASN cc_start: 0.8093 (m110) cc_final: 0.7596 (p0) REVERT: D 541 GLN cc_start: 0.7589 (mt0) cc_final: 0.6544 (mt0) REVERT: D 561 ASN cc_start: 0.8533 (t0) cc_final: 0.8009 (t0) REVERT: E 263 HIS cc_start: 0.8406 (OUTLIER) cc_final: 0.7446 (p-80) REVERT: E 629 LEU cc_start: 0.2839 (OUTLIER) cc_final: 0.2250 (tp) REVERT: F 591 ILE cc_start: 0.8833 (mt) cc_final: 0.8441 (tt) REVERT: G 497 ASP cc_start: 0.8690 (m-30) cc_final: 0.8401 (t0) REVERT: H 196 PHE cc_start: 0.8729 (OUTLIER) cc_final: 0.8005 (t80) REVERT: H 713 LYS cc_start: 0.8862 (tttm) cc_final: 0.8339 (mmtt) outliers start: 71 outliers final: 40 residues processed: 206 average time/residue: 0.2270 time to fit residues: 77.2794 Evaluate side-chains 183 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 139 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 646 ILE Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 756 ASN Chi-restraints excluded: chain H residue 761 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 444 optimal weight: 7.9990 chunk 424 optimal weight: 7.9990 chunk 49 optimal weight: 30.0000 chunk 190 optimal weight: 2.9990 chunk 45 optimal weight: 9.9990 chunk 283 optimal weight: 0.9980 chunk 123 optimal weight: 5.9990 chunk 456 optimal weight: 4.9990 chunk 272 optimal weight: 40.0000 chunk 122 optimal weight: 2.9990 chunk 391 optimal weight: 0.2980 overall best weight: 2.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 281 ASN A 389 GLN C 556 GLN D 389 GLN ** D 616 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 682 ASN H 761 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4120 r_free = 0.4120 target = 0.157287 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.093207 restraints weight = 69621.678| |-----------------------------------------------------------------------------| r_work (start): 0.3013 rms_B_bonded: 3.03 r_work: 0.2716 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work: 0.2592 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8890 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 37581 Z= 0.175 Angle : 0.529 8.841 50913 Z= 0.282 Chirality : 0.046 0.269 5776 Planarity : 0.004 0.062 6668 Dihedral : 5.022 50.019 5013 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.01 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.57 % Favored : 95.40 % Rotamer: Outliers : 1.68 % Allowed : 15.75 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % 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: -1.41 (0.12), residues: 4634 helix: 0.10 (0.18), residues: 930 sheet: -0.56 (0.14), residues: 1190 loop : -1.53 (0.12), residues: 2514 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG F 595 TYR 0.015 0.001 TYR A 366 PHE 0.039 0.001 PHE B 727 TRP 0.011 0.001 TRP G 226 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 (37581) covalent geometry : angle 0.52863 / 0.28 (50913) hydrogen bonds : bond 0.03333 / 2.30 ( 1247) hydrogen bonds : angle 5.33320 / 3.75 ( 3495) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 141 time to evaluate : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8312 (tmt170) cc_final: 0.8021 (ttp80) REVERT: A 346 TRP cc_start: 0.8640 (OUTLIER) cc_final: 0.8322 (t60) REVERT: B 287 ARG cc_start: 0.8278 (mtm110) cc_final: 0.8015 (ttp80) REVERT: C 556 GLN cc_start: 0.8247 (OUTLIER) cc_final: 0.7861 (tm-30) REVERT: C 595 ARG cc_start: 0.8526 (ttm110) cc_final: 0.7937 (ttp-110) REVERT: D 539 ASN cc_start: 0.7947 (m110) cc_final: 0.7486 (p0) REVERT: D 541 GLN cc_start: 0.7600 (mt0) cc_final: 0.6587 (mt0) REVERT: D 561 ASN cc_start: 0.8528 (t0) cc_final: 0.8007 (t0) REVERT: E 263 HIS cc_start: 0.8416 (OUTLIER) cc_final: 0.7451 (p-80) REVERT: E 629 LEU cc_start: 0.2899 (OUTLIER) cc_final: 0.2303 (tp) REVERT: F 591 ILE cc_start: 0.8835 (mt) cc_final: 0.8444 (tt) REVERT: F 595 ARG cc_start: 0.7564 (mtm110) cc_final: 0.7330 (mtm110) REVERT: G 497 ASP cc_start: 0.8748 (m-30) cc_final: 0.8440 (t0) REVERT: G 600 ARG cc_start: 0.7235 (OUTLIER) cc_final: 0.6081 (mmt180) REVERT: G 662 MET cc_start: 0.0450 (ptt) cc_final: -0.0434 (tpt) REVERT: H 196 PHE cc_start: 0.8692 (OUTLIER) cc_final: 0.7969 (t80) REVERT: H 372 LEU cc_start: 0.1707 (OUTLIER) cc_final: 0.1449 (pp) REVERT: H 713 LYS cc_start: 0.8853 (tttm) cc_final: 0.8339 (mmtt) outliers start: 70 outliers final: 41 residues processed: 203 average time/residue: 0.2151 time to fit residues: 72.8607 Evaluate side-chains 183 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 135 time to evaluate : 1.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 481 LEU Chi-restraints excluded: chain A residue 678 PHE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 685 LEU Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 644 VAL Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 289 ILE Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 469 VAL Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain H residue 53 LEU Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 190 LYS Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 402 LEU Chi-restraints excluded: chain H residue 702 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 115 optimal weight: 3.9990 chunk 189 optimal weight: 2.9990 chunk 122 optimal weight: 2.9990 chunk 100 optimal weight: 9.9990 chunk 227 optimal weight: 5.9990 chunk 335 optimal weight: 5.9990 chunk 225 optimal weight: 3.9990 chunk 264 optimal weight: 0.3980 chunk 338 optimal weight: 0.4980 chunk 408 optimal weight: 0.0060 chunk 198 optimal weight: 0.2980 overall best weight: 0.8398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 328 ASN E 281 ASN E 682 ASN F 560 GLN F 564 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4136 r_free = 0.4136 target = 0.158139 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.095254 restraints weight = 69580.238| |-----------------------------------------------------------------------------| r_work (start): 0.3033 rms_B_bonded: 3.39 r_work: 0.2741 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work: 0.2612 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 37581 Z= 0.092 Angle : 0.481 8.029 50913 Z= 0.256 Chirality : 0.044 0.191 5776 Planarity : 0.003 0.060 6668 Dihedral : 4.705 47.911 5013 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.84 % Favored : 96.14 % Rotamer: Outliers : 1.39 % Allowed : 16.19 % Favored : 82.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.15 (0.12), residues: 4634 helix: 0.32 (0.19), residues: 926 sheet: -0.38 (0.14), residues: 1190 loop : -1.38 (0.12), residues: 2518 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG F 595 TYR 0.017 0.001 TYR H 593 PHE 0.026 0.001 PHE B 727 TRP 0.008 0.001 TRP F 226 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00206 / 0.09 (37581) covalent geometry : angle 0.48089 / 0.26 (50913) hydrogen bonds : bond 0.02805 / 1.92 ( 1247) hydrogen bonds : angle 5.12062 / 3.61 ( 3495) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 146 time to evaluate : 1.347 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8334 (tmt170) cc_final: 0.8077 (ttp80) REVERT: A 346 TRP cc_start: 0.8604 (OUTLIER) cc_final: 0.8337 (t60) REVERT: A 662 MET cc_start: 0.5292 (ptp) cc_final: 0.4636 (pmm) REVERT: B 287 ARG cc_start: 0.8257 (mtm110) cc_final: 0.8013 (ttp80) REVERT: C 595 ARG cc_start: 0.8501 (ttm110) cc_final: 0.7869 (ttp-110) REVERT: D 539 ASN cc_start: 0.7981 (m110) cc_final: 0.7612 (p0) REVERT: D 541 GLN cc_start: 0.7415 (mt0) cc_final: 0.6407 (mt0) REVERT: D 561 ASN cc_start: 0.8505 (t0) cc_final: 0.7989 (t0) REVERT: E 263 HIS cc_start: 0.8304 (OUTLIER) cc_final: 0.7659 (p-80) REVERT: F 591 ILE cc_start: 0.8807 (mt) cc_final: 0.8398 (tt) REVERT: F 595 ARG cc_start: 0.7581 (mtm110) cc_final: 0.7333 (mtm110) REVERT: G 497 ASP cc_start: 0.8777 (m-30) cc_final: 0.8424 (t0) REVERT: G 600 ARG cc_start: 0.7110 (OUTLIER) cc_final: 0.6044 (mmt180) REVERT: H 196 PHE cc_start: 0.8656 (OUTLIER) cc_final: 0.7974 (t80) REVERT: H 372 LEU cc_start: 0.1637 (OUTLIER) cc_final: 0.1368 (pp) REVERT: H 624 ILE cc_start: 0.2386 (OUTLIER) cc_final: 0.2167 (tp) REVERT: H 713 LYS cc_start: 0.8857 (tttm) cc_final: 0.8336 (mmtt) outliers start: 58 outliers final: 33 residues processed: 202 average time/residue: 0.2401 time to fit residues: 79.2218 Evaluate side-chains 176 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 137 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 652 LEU Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain H residue 79 VAL Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 624 ILE Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 749 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 355 optimal weight: 3.9990 chunk 241 optimal weight: 8.9990 chunk 310 optimal weight: 2.9990 chunk 103 optimal weight: 0.0870 chunk 52 optimal weight: 50.0000 chunk 382 optimal weight: 10.0000 chunk 219 optimal weight: 0.7980 chunk 157 optimal weight: 30.0000 chunk 265 optimal weight: 0.9990 chunk 259 optimal weight: 2.9990 chunk 416 optimal weight: 7.9990 overall best weight: 1.5764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN C 556 GLN D 553 ASN E 682 ASN H 220 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.157612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.094791 restraints weight = 69258.442| |-----------------------------------------------------------------------------| r_work (start): 0.3036 rms_B_bonded: 3.23 r_work: 0.2732 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work: 0.2605 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.2605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.2237 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 37581 Z= 0.126 Angle : 0.498 10.693 50913 Z= 0.264 Chirality : 0.045 0.218 5776 Planarity : 0.003 0.061 6668 Dihedral : 4.583 46.563 5007 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.29 % Favored : 95.68 % Rotamer: Outliers : 1.37 % Allowed : 16.47 % Favored : 82.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.04 (0.12), residues: 4634 helix: 0.38 (0.19), residues: 934 sheet: -0.14 (0.15), residues: 1155 loop : -1.39 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 595 TYR 0.014 0.001 TYR H 593 PHE 0.023 0.001 PHE B 727 TRP 0.010 0.001 TRP G 226 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00300 / 0.13 (37581) covalent geometry : angle 0.49757 / 0.26 (50913) hydrogen bonds : bond 0.02953 / 2.04 ( 1247) hydrogen bonds : angle 5.03540 / 3.54 ( 3495) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 143 time to evaluate : 1.379 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8318 (tmt170) cc_final: 0.8057 (ttp80) REVERT: A 346 TRP cc_start: 0.8605 (OUTLIER) cc_final: 0.8319 (t60) REVERT: A 662 MET cc_start: 0.5303 (ptp) cc_final: 0.4566 (pmm) REVERT: B 287 ARG cc_start: 0.8216 (mtm110) cc_final: 0.7973 (ttp80) REVERT: C 556 GLN cc_start: 0.8162 (OUTLIER) cc_final: 0.7683 (tm-30) REVERT: C 595 ARG cc_start: 0.8477 (ttm110) cc_final: 0.7834 (ttp-110) REVERT: D 207 ILE cc_start: 0.9364 (OUTLIER) cc_final: 0.9030 (mp) REVERT: D 539 ASN cc_start: 0.7971 (m110) cc_final: 0.7547 (p0) REVERT: D 541 GLN cc_start: 0.7484 (mt0) cc_final: 0.6407 (mt0) REVERT: D 561 ASN cc_start: 0.8496 (t0) cc_final: 0.7987 (t0) REVERT: E 263 HIS cc_start: 0.8326 (OUTLIER) cc_final: 0.7606 (p-80) REVERT: E 629 LEU cc_start: 0.2981 (OUTLIER) cc_final: 0.2417 (tp) REVERT: F 591 ILE cc_start: 0.8835 (mt) cc_final: 0.8393 (tt) REVERT: F 595 ARG cc_start: 0.7634 (mtm110) cc_final: 0.7352 (mtm110) REVERT: G 497 ASP cc_start: 0.8688 (m-30) cc_final: 0.8346 (t0) REVERT: G 600 ARG cc_start: 0.7076 (OUTLIER) cc_final: 0.6073 (mmt180) REVERT: H 196 PHE cc_start: 0.8662 (OUTLIER) cc_final: 0.7983 (t80) REVERT: H 372 LEU cc_start: 0.1635 (OUTLIER) cc_final: 0.1375 (pp) REVERT: H 584 LYS cc_start: 0.8257 (tttp) cc_final: 0.8024 (mtpp) REVERT: H 624 ILE cc_start: 0.2255 (OUTLIER) cc_final: 0.2051 (tp) REVERT: H 713 LYS cc_start: 0.8850 (tttm) cc_final: 0.8338 (mmtt) outliers start: 57 outliers final: 41 residues processed: 194 average time/residue: 0.2266 time to fit residues: 72.7429 Evaluate side-chains 189 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 139 time to evaluate : 1.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 553 ASN Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 624 ILE Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 749 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 248 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 118 optimal weight: 1.9990 chunk 435 optimal weight: 8.9990 chunk 457 optimal weight: 4.9990 chunk 408 optimal weight: 0.9990 chunk 133 optimal weight: 0.9990 chunk 49 optimal weight: 40.0000 chunk 149 optimal weight: 0.6980 chunk 259 optimal weight: 0.9980 chunk 147 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN A 719 ASN C 556 GLN E 682 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.158663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.091075 restraints weight = 69928.297| |-----------------------------------------------------------------------------| r_work (start): 0.2942 rms_B_bonded: 2.90 r_work: 0.2755 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work: 0.2629 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2629 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 37581 Z= 0.102 Angle : 0.482 10.542 50913 Z= 0.255 Chirality : 0.044 0.192 5776 Planarity : 0.003 0.061 6668 Dihedral : 4.493 46.007 5007 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.75 % Favored : 96.22 % Rotamer: Outliers : 1.30 % Allowed : 16.62 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.94 (0.12), residues: 4634 helix: 0.46 (0.19), residues: 934 sheet: -0.06 (0.15), residues: 1155 loop : -1.33 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG F 595 TYR 0.014 0.001 TYR H 593 PHE 0.020 0.001 PHE B 727 TRP 0.008 0.001 TRP G 226 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00237 / 0.10 (37581) covalent geometry : angle 0.48206 / 0.26 (50913) hydrogen bonds : bond 0.02811 / 1.93 ( 1247) hydrogen bonds : angle 4.97232 / 3.50 ( 3495) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 140 time to evaluate : 1.393 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8118 (tmt170) cc_final: 0.7811 (ttp80) REVERT: A 346 TRP cc_start: 0.8498 (OUTLIER) cc_final: 0.8046 (t60) REVERT: A 662 MET cc_start: 0.5067 (ptp) cc_final: 0.4471 (pmm) REVERT: B 287 ARG cc_start: 0.8130 (mtm110) cc_final: 0.7921 (ttp80) REVERT: B 496 LYS cc_start: 0.8484 (ttpt) cc_final: 0.8282 (ttpp) REVERT: C 556 GLN cc_start: 0.7971 (OUTLIER) cc_final: 0.7581 (tm-30) REVERT: C 595 ARG cc_start: 0.8420 (ttm110) cc_final: 0.7732 (ttp-110) REVERT: D 539 ASN cc_start: 0.7769 (m110) cc_final: 0.7287 (p0) REVERT: D 541 GLN cc_start: 0.6981 (mt0) cc_final: 0.5847 (mt0) REVERT: D 561 ASN cc_start: 0.8389 (t0) cc_final: 0.7876 (t0) REVERT: E 263 HIS cc_start: 0.8183 (OUTLIER) cc_final: 0.7560 (p-80) REVERT: E 629 LEU cc_start: 0.2866 (OUTLIER) cc_final: 0.2420 (tp) REVERT: F 591 ILE cc_start: 0.8591 (mt) cc_final: 0.8036 (tt) REVERT: F 595 ARG cc_start: 0.7100 (mtm110) cc_final: 0.6820 (mtm110) REVERT: G 497 ASP cc_start: 0.8767 (m-30) cc_final: 0.8262 (t0) REVERT: G 600 ARG cc_start: 0.7018 (OUTLIER) cc_final: 0.5661 (mtm110) REVERT: H 196 PHE cc_start: 0.8709 (OUTLIER) cc_final: 0.8075 (t80) REVERT: H 372 LEU cc_start: 0.1902 (OUTLIER) cc_final: 0.1646 (pp) REVERT: H 713 LYS cc_start: 0.8763 (tttm) cc_final: 0.8320 (mmtt) outliers start: 54 outliers final: 42 residues processed: 189 average time/residue: 0.2351 time to fit residues: 72.0088 Evaluate side-chains 188 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 139 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 620 ILE Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 749 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 273 optimal weight: 50.0000 chunk 313 optimal weight: 3.9990 chunk 357 optimal weight: 0.9980 chunk 88 optimal weight: 3.9990 chunk 200 optimal weight: 10.0000 chunk 450 optimal weight: 9.9990 chunk 95 optimal weight: 7.9990 chunk 141 optimal weight: 6.9990 chunk 114 optimal weight: 0.4980 chunk 337 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN C 556 GLN E 682 ASN H 200 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4128 r_free = 0.4128 target = 0.157568 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.093543 restraints weight = 69367.475| |-----------------------------------------------------------------------------| r_work (start): 0.3027 rms_B_bonded: 3.00 r_work: 0.2741 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2616 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8888 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37581 Z= 0.130 Angle : 0.494 10.330 50913 Z= 0.262 Chirality : 0.045 0.193 5776 Planarity : 0.003 0.061 6668 Dihedral : 4.497 45.136 5007 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.81 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.12 % Favored : 95.86 % Rotamer: Outliers : 1.32 % Allowed : 16.67 % Favored : 82.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.91 (0.12), residues: 4634 helix: 0.49 (0.19), residues: 934 sheet: -0.03 (0.15), residues: 1155 loop : -1.31 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 595 TYR 0.014 0.001 TYR F 411 PHE 0.018 0.001 PHE B 727 TRP 0.010 0.001 TRP G 226 HIS 0.009 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00310 / 0.13 (37581) covalent geometry : angle 0.49354 / 0.26 (50913) hydrogen bonds : bond 0.02928 / 2.01 ( 1247) hydrogen bonds : angle 4.95044 / 3.48 ( 3495) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 9268 Ramachandran restraints generated. 4634 Oldfield, 0 Emsley, 4634 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 140 time to evaluate : 1.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 344 ARG cc_start: 0.8307 (tmt170) cc_final: 0.8058 (ttp80) REVERT: A 346 TRP cc_start: 0.8577 (OUTLIER) cc_final: 0.8314 (t60) REVERT: B 287 ARG cc_start: 0.8215 (mtm110) cc_final: 0.7993 (ttp80) REVERT: C 556 GLN cc_start: 0.7888 (OUTLIER) cc_final: 0.7372 (tm-30) REVERT: C 595 ARG cc_start: 0.8494 (ttm110) cc_final: 0.7914 (ttp-110) REVERT: D 207 ILE cc_start: 0.9371 (OUTLIER) cc_final: 0.9044 (mp) REVERT: D 539 ASN cc_start: 0.7961 (m110) cc_final: 0.7571 (p0) REVERT: D 541 GLN cc_start: 0.7492 (mt0) cc_final: 0.6442 (mt0) REVERT: D 561 ASN cc_start: 0.8506 (t0) cc_final: 0.7994 (t0) REVERT: E 263 HIS cc_start: 0.8293 (OUTLIER) cc_final: 0.7645 (p-80) REVERT: E 629 LEU cc_start: 0.2834 (OUTLIER) cc_final: 0.2379 (tp) REVERT: F 591 ILE cc_start: 0.8823 (mt) cc_final: 0.8373 (tt) REVERT: F 595 ARG cc_start: 0.7462 (mtm110) cc_final: 0.7174 (mtm110) REVERT: G 497 ASP cc_start: 0.8716 (m-30) cc_final: 0.8395 (t0) REVERT: G 600 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.5750 (mtm110) REVERT: H 196 PHE cc_start: 0.8644 (OUTLIER) cc_final: 0.7952 (t80) REVERT: H 372 LEU cc_start: 0.1636 (OUTLIER) cc_final: 0.1378 (pp) REVERT: H 713 LYS cc_start: 0.8847 (tttm) cc_final: 0.8332 (mmtt) outliers start: 55 outliers final: 43 residues processed: 189 average time/residue: 0.2261 time to fit residues: 70.6584 Evaluate side-chains 188 residues out of total 4161 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 137 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 217 THR Chi-restraints excluded: chain A residue 282 THR Chi-restraints excluded: chain A residue 298 THR Chi-restraints excluded: chain A residue 346 TRP Chi-restraints excluded: chain A residue 679 LYS Chi-restraints excluded: chain A residue 694 TYR Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 295 THR Chi-restraints excluded: chain B residue 605 VAL Chi-restraints excluded: chain B residue 624 THR Chi-restraints excluded: chain B residue 685 LEU Chi-restraints excluded: chain B residue 689 ILE Chi-restraints excluded: chain B residue 724 ILE Chi-restraints excluded: chain C residue 271 LEU Chi-restraints excluded: chain C residue 278 SER Chi-restraints excluded: chain C residue 286 THR Chi-restraints excluded: chain C residue 288 THR Chi-restraints excluded: chain C residue 425 ASP Chi-restraints excluded: chain C residue 434 MET Chi-restraints excluded: chain C residue 556 GLN Chi-restraints excluded: chain D residue 207 ILE Chi-restraints excluded: chain D residue 272 SER Chi-restraints excluded: chain D residue 288 THR Chi-restraints excluded: chain D residue 310 HIS Chi-restraints excluded: chain D residue 434 MET Chi-restraints excluded: chain D residue 508 VAL Chi-restraints excluded: chain D residue 689 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 369 THR Chi-restraints excluded: chain E residue 434 MET Chi-restraints excluded: chain E residue 629 LEU Chi-restraints excluded: chain E residue 696 VAL Chi-restraints excluded: chain F residue 207 ILE Chi-restraints excluded: chain F residue 303 VAL Chi-restraints excluded: chain F residue 401 LEU Chi-restraints excluded: chain F residue 572 THR Chi-restraints excluded: chain F residue 696 VAL Chi-restraints excluded: chain G residue 288 THR Chi-restraints excluded: chain G residue 345 THR Chi-restraints excluded: chain G residue 600 ARG Chi-restraints excluded: chain G residue 631 ILE Chi-restraints excluded: chain G residue 655 VAL Chi-restraints excluded: chain G residue 725 LEU Chi-restraints excluded: chain H residue 196 PHE Chi-restraints excluded: chain H residue 293 ILE Chi-restraints excluded: chain H residue 322 SER Chi-restraints excluded: chain H residue 327 VAL Chi-restraints excluded: chain H residue 372 LEU Chi-restraints excluded: chain H residue 537 THR Chi-restraints excluded: chain H residue 702 VAL Chi-restraints excluded: chain H residue 749 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 464 random chunks: chunk 60 optimal weight: 5.9990 chunk 418 optimal weight: 50.0000 chunk 53 optimal weight: 10.0000 chunk 429 optimal weight: 1.9990 chunk 41 optimal weight: 3.9990 chunk 303 optimal weight: 0.0050 chunk 163 optimal weight: 40.0000 chunk 325 optimal weight: 10.0000 chunk 76 optimal weight: 0.7980 chunk 183 optimal weight: 20.0000 chunk 116 optimal weight: 0.7980 overall best weight: 1.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 389 GLN C 556 GLN E 682 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.157669 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.094753 restraints weight = 69381.962| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 3.36 r_work: 0.2728 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work: 0.2602 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2602 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8879 moved from start: 0.2380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 37581 Z= 0.120 Angle : 0.489 10.142 50913 Z= 0.259 Chirality : 0.045 0.188 5776 Planarity : 0.003 0.062 6668 Dihedral : 4.457 43.448 5007 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.01 % Favored : 95.96 % Rotamer: Outliers : 1.35 % Allowed : 16.74 % Favored : 81.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.02 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.86 (0.12), residues: 4634 helix: 0.53 (0.19), residues: 934 sheet: 0.02 (0.15), residues: 1155 loop : -1.29 (0.12), residues: 2545 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 595 TYR 0.013 0.001 TYR F 411 PHE 0.017 0.001 PHE B 727 TRP 0.009 0.001 TRP G 226 HIS 0.006 0.001 HIS H 544 Details of bonding type rmsd/Z covalent geometry : bond 0.00285 / 0.12 (37581) covalent geometry : angle 0.48871 / 0.26 (50913) hydrogen bonds : bond 0.02875 / 1.97 ( 1247) hydrogen bonds : angle 4.92358 / 3.47 ( 3495) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14257.33 seconds wall clock time: 243 minutes 18.50 seconds (14598.50 seconds total)