Starting phenix.real_space_refine on Fri Mar 6 18:00:55 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6psn_20459/03_2026/6psn_20459.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psn_20459/03_2026/6psn_20459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6psn_20459/03_2026/6psn_20459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psn_20459/03_2026/6psn_20459.map" model { file = "/net/cci-nas-00/data/ceres_data/6psn_20459/03_2026/6psn_20459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psn_20459/03_2026/6psn_20459.cif" } resolution = 4.6 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= 0.004 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 45 5.16 5 C 20537 2.51 5 N 5641 2.21 5 O 6593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 32830 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "D" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "E" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "F" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "G" Number of atoms: 4431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 562, 4431 Classifications: {'peptide': 562} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "L" Number of atoms: 1799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 1799 Classifications: {'peptide': 220} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 213} 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: 6.95, per 1000 atoms: 0.21 Number of scatterers: 32830 At special positions: 0 Unit cell: (173.34, 175.48, 228.98, 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 45 16.00 O 6593 8.00 N 5641 7.00 C 20537 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.66 Conformation dependent library (CDL) restraints added in 1.3 seconds 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7900 Finding SS restraints... Secondary structure from input PDB file: 111 helices and 76 sheets defined 21.4% alpha, 45.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.37 Creating SS restraints... Processing helix chain 'A' and resid 184 through 191 Processing helix chain 'A' and resid 210 through 215 Processing helix chain 'A' and resid 234 through 241 Processing helix chain 'A' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS A 253 " --> pdb=" O GLU A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 401 removed outlier: 3.683A 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 486 Processing helix chain 'A' and resid 514 through 518 removed outlier: 3.613A pdb=" N LYS A 518 " --> pdb=" O GLU A 515 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 532 Processing helix chain 'A' and resid 555 through 570 Processing helix chain 'A' and resid 573 through 577 removed outlier: 3.586A pdb=" N THR A 576 " --> pdb=" O ASN A 573 " (cutoff:3.500A) Processing helix chain 'A' and resid 608 through 615 removed outlier: 3.589A pdb=" N GLU A 614 " --> pdb=" O SER A 610 " (cutoff:3.500A) Processing helix chain 'A' and resid 632 through 637 removed outlier: 3.855A pdb=" N LYS A 637 " --> pdb=" O LYS A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 679 through 682 Processing helix chain 'B' and resid 184 through 191 Processing helix chain 'B' and resid 210 through 215 Processing helix chain 'B' and resid 234 through 241 Processing helix chain 'B' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS B 253 " --> pdb=" O GLU B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 401 removed outlier: 3.682A 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 486 Processing helix chain 'B' and resid 514 through 518 removed outlier: 3.612A pdb=" N LYS B 518 " --> pdb=" O GLU B 515 " (cutoff:3.500A) Processing helix chain 'B' and resid 522 through 532 Processing helix chain 'B' and resid 555 through 570 Processing helix chain 'B' and resid 573 through 577 removed outlier: 3.586A pdb=" N THR B 576 " --> pdb=" O ASN B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 608 through 615 removed outlier: 3.590A pdb=" N GLU B 614 " --> pdb=" O SER B 610 " (cutoff:3.500A) Processing helix chain 'B' and resid 632 through 637 removed outlier: 3.856A pdb=" N LYS B 637 " --> pdb=" O LYS B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 682 Processing helix chain 'C' and resid 184 through 191 Processing helix chain 'C' and resid 210 through 215 Processing helix chain 'C' and resid 234 through 241 Processing helix chain 'C' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS C 253 " --> pdb=" O GLU C 250 " (cutoff:3.500A) Processing helix chain 'C' and resid 397 through 401 removed outlier: 3.683A pdb=" N LEU C 401 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 435 through 446 Processing helix chain 'C' and resid 480 through 486 Processing helix chain 'C' and resid 514 through 518 removed outlier: 3.612A pdb=" N LYS C 518 " --> pdb=" O GLU C 515 " (cutoff:3.500A) Processing helix chain 'C' and resid 522 through 532 Processing helix chain 'C' and resid 555 through 570 Processing helix chain 'C' and resid 573 through 577 removed outlier: 3.586A pdb=" N THR C 576 " --> pdb=" O ASN C 573 " (cutoff:3.500A) Processing helix chain 'C' and resid 608 through 615 removed outlier: 3.589A pdb=" N GLU C 614 " --> pdb=" O SER C 610 " (cutoff:3.500A) Processing helix chain 'C' and resid 632 through 637 removed outlier: 3.855A pdb=" N LYS C 637 " --> pdb=" O LYS C 633 " (cutoff:3.500A) Processing helix chain 'C' and resid 679 through 682 Processing helix chain 'D' and resid 184 through 191 Processing helix chain 'D' and resid 210 through 215 Processing helix chain 'D' and resid 234 through 241 Processing helix chain 'D' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS D 253 " --> pdb=" O GLU D 250 " (cutoff:3.500A) Processing helix chain 'D' and resid 397 through 401 removed outlier: 3.683A 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 514 through 518 removed outlier: 3.612A pdb=" N LYS D 518 " --> pdb=" O GLU D 515 " (cutoff:3.500A) Processing helix chain 'D' and resid 522 through 532 Processing helix chain 'D' and resid 555 through 570 Processing helix chain 'D' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR D 576 " --> pdb=" O ASN D 573 " (cutoff:3.500A) Processing helix chain 'D' and resid 608 through 615 removed outlier: 3.589A pdb=" N GLU D 614 " --> pdb=" O SER D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 632 through 637 removed outlier: 3.856A pdb=" N LYS D 637 " --> pdb=" O LYS D 633 " (cutoff:3.500A) Processing helix chain 'D' and resid 679 through 682 Processing helix chain 'E' and resid 184 through 191 Processing helix chain 'E' and resid 210 through 215 Processing helix chain 'E' and resid 234 through 241 Processing helix chain 'E' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS E 253 " --> pdb=" O GLU E 250 " (cutoff:3.500A) Processing helix chain 'E' and resid 397 through 401 removed outlier: 3.683A 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: 3.612A pdb=" N LYS E 518 " --> pdb=" O GLU E 515 " (cutoff:3.500A) Processing helix chain 'E' and resid 522 through 532 Processing helix chain 'E' and resid 555 through 570 Processing helix chain 'E' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR E 576 " --> pdb=" O ASN E 573 " (cutoff:3.500A) Processing helix chain 'E' and resid 608 through 615 removed outlier: 3.590A pdb=" N GLU E 614 " --> pdb=" O SER E 610 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 637 removed outlier: 3.856A pdb=" N LYS E 637 " --> pdb=" O LYS E 633 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 682 Processing helix chain 'F' and resid 184 through 191 Processing helix chain 'F' and resid 210 through 215 Processing helix chain 'F' and resid 234 through 241 Processing helix chain 'F' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS F 253 " --> pdb=" O GLU F 250 " (cutoff:3.500A) Processing helix chain 'F' and resid 397 through 401 removed outlier: 3.683A pdb=" N LEU F 401 " --> pdb=" O GLU F 398 " (cutoff:3.500A) Processing helix chain 'F' and resid 435 through 446 Processing helix chain 'F' and resid 480 through 486 Processing helix chain 'F' and resid 514 through 518 removed outlier: 3.612A pdb=" N LYS F 518 " --> pdb=" O GLU F 515 " (cutoff:3.500A) Processing helix chain 'F' and resid 522 through 532 Processing helix chain 'F' and resid 555 through 570 Processing helix chain 'F' and resid 573 through 577 removed outlier: 3.585A pdb=" N THR F 576 " --> pdb=" O ASN F 573 " (cutoff:3.500A) Processing helix chain 'F' and resid 608 through 615 removed outlier: 3.589A pdb=" N GLU F 614 " --> pdb=" O SER F 610 " (cutoff:3.500A) Processing helix chain 'F' and resid 632 through 637 removed outlier: 3.856A pdb=" N LYS F 637 " --> pdb=" O LYS F 633 " (cutoff:3.500A) Processing helix chain 'F' and resid 679 through 682 Processing helix chain 'G' and resid 184 through 191 Processing helix chain 'G' and resid 210 through 215 Processing helix chain 'G' and resid 234 through 241 Processing helix chain 'G' and resid 248 through 253 removed outlier: 3.946A pdb=" N HIS G 253 " --> pdb=" O GLU G 250 " (cutoff:3.500A) Processing helix chain 'G' and resid 397 through 401 removed outlier: 3.682A 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 486 Processing helix chain 'G' and resid 514 through 518 removed outlier: 3.612A pdb=" N LYS G 518 " --> pdb=" O GLU G 515 " (cutoff:3.500A) Processing helix chain 'G' and resid 522 through 532 Processing helix chain 'G' and resid 555 through 570 Processing helix chain 'G' and resid 573 through 577 removed outlier: 3.587A pdb=" N THR G 576 " --> pdb=" O ASN G 573 " (cutoff:3.500A) Processing helix chain 'G' and resid 608 through 615 removed outlier: 3.589A pdb=" N GLU G 614 " --> pdb=" O SER G 610 " (cutoff:3.500A) Processing helix chain 'G' and resid 632 through 637 removed outlier: 3.856A pdb=" N LYS G 637 " --> pdb=" O LYS G 633 " (cutoff:3.500A) Processing helix chain 'G' and resid 679 through 682 Processing helix chain 'L' and resid 32 through 44 Processing helix chain 'L' and resid 50 through 66 removed outlier: 3.658A pdb=" N LYS L 65 " --> pdb=" O LYS L 61 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N VAL L 66 " --> pdb=" O LEU L 62 " (cutoff:3.500A) Processing helix chain 'L' and resid 67 through 77 removed outlier: 3.898A pdb=" N LEU L 71 " --> pdb=" O PRO L 67 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N MET L 73 " --> pdb=" O ASP L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 101 Processing helix chain 'L' and resid 115 through 117 No H-bonds generated for 'chain 'L' and resid 115 through 117' Processing helix chain 'L' and resid 135 through 140 removed outlier: 3.959A pdb=" N GLU L 139 " --> pdb=" O GLU L 135 " (cutoff:3.500A) Processing helix chain 'L' and resid 140 through 157 Processing helix chain 'L' and resid 167 through 179 removed outlier: 4.681A pdb=" N VAL L 173 " --> pdb=" O LYS L 169 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N ASN L 175 " --> pdb=" O LEU L 171 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE L 177 " --> pdb=" O VAL L 173 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS L 178 " --> pdb=" O LEU L 174 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 190 Processing helix chain 'L' and resid 204 through 209 Processing helix chain 'L' and resid 209 through 226 removed outlier: 3.580A pdb=" N PHE L 217 " --> pdb=" O VAL L 213 " (cutoff:3.500A) Processing helix chain 'L' and resid 229 through 237 Processing helix chain 'L' and resid 237 through 250 removed outlier: 3.793A pdb=" N ASN L 248 " --> pdb=" O MET L 244 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N GLU L 249 " --> pdb=" O ASP L 245 " (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: 6.640A pdb=" N ASN A 363 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE A 269 " --> pdb=" O ASN A 361 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ASN A 361 " --> pdb=" O ILE A 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU A 271 " --> pdb=" O ARG A 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG A 359 " --> pdb=" O LEU A 271 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 409 through 411 removed outlier: 3.627A pdb=" N ASN A 409 " --> pdb=" O ASN A 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 432 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 275 through 311 removed outlier: 3.951A pdb=" N GLY A 318 " --> pdb=" O ALA B 311 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA B 311 " --> pdb=" O GLY A 318 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 320 " --> pdb=" O VAL B 309 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL B 309 " --> pdb=" O VAL A 320 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA A 322 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N HIS A 336 " --> pdb=" O THR B 293 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N GLY B 318 " --> pdb=" O ALA C 311 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ALA C 311 " --> pdb=" O GLY B 318 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N VAL B 320 " --> pdb=" O VAL C 309 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N VAL C 309 " --> pdb=" O VAL B 320 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N ALA B 322 " --> pdb=" O ALA C 307 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N ALA C 307 " --> pdb=" O ALA B 322 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N PHE B 324 " --> pdb=" O GLY C 305 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 328 " --> pdb=" O SER C 301 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N SER B 330 " --> pdb=" O HIS C 299 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 316 through 353 removed outlier: 3.771A pdb=" N ALA C 322 " --> pdb=" O ALA D 307 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ALA D 307 " --> pdb=" O ALA C 322 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N PHE C 324 " --> pdb=" O GLY D 305 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ASN C 328 " --> pdb=" O SER D 301 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N HIS D 299 " --> pdb=" O SER C 330 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ILE C 334 " --> pdb=" O THR D 295 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N HIS C 336 " --> pdb=" O THR D 293 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N ALA D 322 " --> pdb=" O ALA E 307 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N PHE D 324 " --> pdb=" O GLY E 305 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ASN D 328 " --> pdb=" O SER E 301 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N HIS E 299 " --> pdb=" O SER D 330 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE D 334 " --> pdb=" O THR E 295 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N HIS D 336 " --> pdb=" O THR E 293 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA E 322 " --> pdb=" O ALA F 307 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N PHE E 324 " --> pdb=" O GLY F 305 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN E 328 " --> pdb=" O SER F 301 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N HIS F 299 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N ILE E 334 " --> pdb=" O THR F 295 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR F 295 " --> pdb=" O ILE E 334 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N HIS E 336 " --> pdb=" O THR F 293 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N LEU E 338 " --> pdb=" O LYS F 291 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLY F 318 " --> pdb=" O ALA G 311 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N ALA G 311 " --> pdb=" O GLY F 318 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N VAL F 320 " --> pdb=" O VAL G 309 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N VAL G 309 " --> pdb=" O VAL F 320 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N ALA F 322 " --> pdb=" O ALA G 307 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA G 307 " --> pdb=" O ALA F 322 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE F 324 " --> pdb=" O GLY G 305 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE F 334 " --> pdb=" O THR G 295 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS F 336 " --> pdb=" O THR G 293 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 275 through 311 removed outlier: 3.742A pdb=" N PHE G 324 " --> pdb=" O GLY A 305 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ASN G 328 " --> pdb=" O SER A 301 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N SER A 301 " --> pdb=" O ASN G 328 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N SER G 330 " --> pdb=" O HIS A 299 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N HIS A 299 " --> pdb=" O SER G 330 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N THR A 279 " --> pdb=" O MET G 350 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N GLN A 285 " --> pdb=" O ARG G 344 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N ARG G 344 " --> pdb=" O GLN A 285 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ARG A 287 " --> pdb=" O GLY G 342 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N GLY G 342 " --> pdb=" O ARG A 287 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ILE A 289 " --> pdb=" O LEU G 340 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N LEU G 340 " --> pdb=" O ILE A 289 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 275 through 311 removed outlier: 3.589A pdb=" N ARG A 297 " --> pdb=" O VAL G 332 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N ILE G 334 " --> pdb=" O THR A 295 " (cutoff:3.500A) removed outlier: 3.833A pdb=" N THR A 295 " --> pdb=" O ILE G 334 " (cutoff:3.500A) removed outlier: 4.480A pdb=" N HIS G 336 " --> pdb=" O THR A 293 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N THR A 293 " --> pdb=" O HIS G 336 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG A 344 " --> pdb=" O GLN B 285 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N GLN B 285 " --> pdb=" O ARG A 344 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N THR B 279 " --> pdb=" O MET A 350 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR A 375 " --> pdb=" O ILE A 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE A 404 " --> pdb=" O TYR A 375 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU A 383 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR A 393 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR A 381 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS A 395 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 377 " --> pdb=" O TYR A 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR A 456 " --> pdb=" O VAL A 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN A 454 " --> pdb=" O PRO A 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR A 381 " --> pdb=" O THR A 452 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR A 452 " --> pdb=" O THR A 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU A 383 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU A 450 " --> pdb=" O LEU A 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU A 385 " --> pdb=" O LEU A 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU A 448 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL A 455 " --> pdb=" O ASN A 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN A 476 " --> pdb=" O VAL A 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY A 457 " --> pdb=" O GLY A 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY A 474 " --> pdb=" O GLY A 457 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE A 459 " --> pdb=" O ASP A 472 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE A 589 " --> pdb=" O THR A 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG A 490 " --> pdb=" O ILE A 589 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE A 591 " --> pdb=" O ARG A 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE A 492 " --> pdb=" O ILE A 591 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP A 593 " --> pdb=" O ILE A 492 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 541 through 542 Processing sheet with id=AB3, first strand: chain 'A' and resid 597 through 598 removed outlier: 3.655A pdb=" N GLY A 606 " --> pdb=" O HIS A 597 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 619 through 622 removed outlier: 6.603A pdb=" N LEU A 628 " --> pdb=" O ILE A 620 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER A 622 " --> pdb=" O GLY A 626 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY A 626 " --> pdb=" O SER A 622 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 654 through 655 removed outlier: 3.543A pdb=" N GLU A 654 " --> pdb=" O ILE A 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY A 641 " --> pdb=" O VAL A 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS A 729 " --> pdb=" O VAL A 696 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA A 700 " --> pdb=" O LEU A 725 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A 725 " --> pdb=" O ALA A 700 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 192 through 196 Processing sheet with id=AB7, first strand: chain 'B' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN B 363 " --> pdb=" O GLU B 267 " (cutoff:3.500A) removed outlier: 4.661A pdb=" N ILE B 269 " --> pdb=" O ASN B 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN B 361 " --> pdb=" O ILE B 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU B 271 " --> pdb=" O ARG B 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG B 359 " --> pdb=" O LEU B 271 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN B 409 " --> pdb=" O ASN B 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE B 432 " --> pdb=" O LEU B 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR B 375 " --> pdb=" O ILE B 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE B 404 " --> pdb=" O TYR B 375 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU B 383 " --> pdb=" O LEU B 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR B 393 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR B 381 " --> pdb=" O THR B 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS B 395 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL B 377 " --> pdb=" O TYR B 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR B 456 " --> pdb=" O VAL B 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN B 454 " --> pdb=" O PRO B 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR B 381 " --> pdb=" O THR B 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR B 452 " --> pdb=" O THR B 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU B 383 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU B 450 " --> pdb=" O LEU B 383 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU B 385 " --> pdb=" O LEU B 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU B 448 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL B 455 " --> pdb=" O ASN B 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN B 476 " --> pdb=" O VAL B 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY B 457 " --> pdb=" O GLY B 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY B 474 " --> pdb=" O GLY B 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE B 459 " --> pdb=" O ASP B 472 " (cutoff:3.500A) Processing sheet with id=AC2, 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: 6.747A pdb=" N ARG B 490 " --> pdb=" O ILE B 589 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE B 591 " --> pdb=" O ARG B 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE B 492 " --> pdb=" O ILE B 591 " (cutoff:3.500A) removed outlier: 8.416A pdb=" N ASP B 593 " --> pdb=" O ILE B 492 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'B' and resid 541 through 542 Processing sheet with id=AC4, first strand: chain 'B' and resid 597 through 598 removed outlier: 3.655A pdb=" N GLY B 606 " --> pdb=" O HIS B 597 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'B' and resid 619 through 622 removed outlier: 6.603A pdb=" N LEU B 628 " --> pdb=" O ILE B 620 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER B 622 " --> pdb=" O GLY B 626 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY B 626 " --> pdb=" O SER B 622 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'B' and resid 654 through 655 removed outlier: 3.543A pdb=" N GLU B 654 " --> pdb=" O ILE B 646 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY B 641 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS B 729 " --> pdb=" O VAL B 696 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA B 700 " --> pdb=" O LEU B 725 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU B 725 " --> pdb=" O ALA B 700 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'C' and resid 192 through 196 Processing sheet with id=AC8, first strand: chain 'C' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN C 363 " --> pdb=" O GLU C 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE C 269 " --> pdb=" O ASN C 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN C 361 " --> pdb=" O ILE C 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU C 271 " --> pdb=" O ARG C 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG C 359 " --> pdb=" O LEU C 271 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'C' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN C 409 " --> pdb=" O ASN C 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE C 432 " --> pdb=" O LEU C 360 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR C 375 " --> pdb=" O ILE C 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE C 404 " --> pdb=" O TYR C 375 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'C' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU C 383 " --> pdb=" O LEU C 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR C 393 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR C 381 " --> pdb=" O THR C 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS C 395 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL C 377 " --> pdb=" O TYR C 456 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR C 456 " --> pdb=" O VAL C 377 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N GLN C 454 " --> pdb=" O PRO C 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR C 381 " --> pdb=" O THR C 452 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N THR C 452 " --> pdb=" O THR C 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU C 383 " --> pdb=" O LEU C 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU C 450 " --> pdb=" O LEU C 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU C 385 " --> pdb=" O LEU C 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU C 448 " --> pdb=" O LEU C 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL C 455 " --> pdb=" O ASN C 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN C 476 " --> pdb=" O VAL C 455 " (cutoff:3.500A) removed outlier: 8.873A pdb=" N GLY C 457 " --> pdb=" O GLY C 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY C 474 " --> pdb=" O GLY C 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE C 459 " --> pdb=" O ASP C 472 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'C' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE C 589 " --> pdb=" O THR C 488 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG C 490 " --> pdb=" O ILE C 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE C 591 " --> pdb=" O ARG C 490 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE C 492 " --> pdb=" O ILE C 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP C 593 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'C' and resid 541 through 542 Processing sheet with id=AD5, first strand: chain 'C' and resid 597 through 598 removed outlier: 3.655A pdb=" N GLY C 606 " --> pdb=" O HIS C 597 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'C' and resid 619 through 622 removed outlier: 6.604A pdb=" N LEU C 628 " --> pdb=" O ILE C 620 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER C 622 " --> pdb=" O GLY C 626 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY C 626 " --> pdb=" O SER C 622 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'C' and resid 654 through 655 removed outlier: 3.542A pdb=" N GLU C 654 " --> pdb=" O ILE C 646 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N GLY C 641 " --> pdb=" O VAL C 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS C 729 " --> pdb=" O VAL C 696 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA C 700 " --> pdb=" O LEU C 725 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU C 725 " --> pdb=" O ALA C 700 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'D' and resid 192 through 196 Processing sheet with id=AD9, first strand: chain 'D' and resid 262 through 273 removed outlier: 6.639A pdb=" N ASN D 363 " --> pdb=" O GLU D 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE D 269 " --> pdb=" O ASN D 361 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N ASN D 361 " --> pdb=" O ILE D 269 " (cutoff:3.500A) removed outlier: 4.343A pdb=" N LEU D 271 " --> pdb=" O ARG D 359 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N ARG D 359 " --> pdb=" O LEU D 271 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'D' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN D 409 " --> pdb=" O ASN D 368 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N ILE D 432 " --> pdb=" O LEU D 360 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR D 375 " --> pdb=" O ILE D 404 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE D 404 " --> pdb=" O TYR D 375 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'D' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU D 383 " --> pdb=" O LEU D 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR D 393 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR D 381 " --> pdb=" O THR D 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS D 395 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL D 377 " --> pdb=" O TYR D 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR D 456 " --> pdb=" O VAL D 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN D 454 " --> pdb=" O PRO D 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR D 381 " --> pdb=" O THR D 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR D 452 " --> pdb=" O THR D 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU D 383 " --> pdb=" O LEU D 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU D 450 " --> pdb=" O LEU D 383 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU D 385 " --> pdb=" O LEU D 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU D 448 " --> pdb=" O LEU D 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL D 455 " --> pdb=" O ASN D 476 " (cutoff:3.500A) removed outlier: 8.961A pdb=" N ASN D 476 " --> pdb=" O VAL D 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY D 457 " --> pdb=" O GLY D 474 " (cutoff:3.500A) removed outlier: 8.603A pdb=" N GLY D 474 " --> pdb=" O GLY D 457 " (cutoff:3.500A) removed outlier: 4.477A pdb=" N ILE D 459 " --> pdb=" O ASP D 472 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'D' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE D 589 " --> pdb=" O THR D 488 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG D 490 " --> pdb=" O ILE D 589 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N ILE D 591 " --> pdb=" O ARG D 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE D 492 " --> pdb=" O ILE D 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP D 593 " --> pdb=" O ILE D 492 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'D' and resid 541 through 542 Processing sheet with id=AE6, first strand: chain 'D' and resid 597 through 598 removed outlier: 3.655A pdb=" N GLY D 606 " --> pdb=" O HIS D 597 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'D' and resid 619 through 622 removed outlier: 6.603A pdb=" N LEU D 628 " --> pdb=" O ILE D 620 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N SER D 622 " --> pdb=" O GLY D 626 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N GLY D 626 " --> pdb=" O SER D 622 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'D' and resid 654 through 655 removed outlier: 3.543A pdb=" N GLU D 654 " --> pdb=" O ILE D 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY D 641 " --> pdb=" O VAL D 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS D 729 " --> pdb=" O VAL D 696 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA D 700 " --> pdb=" O LEU D 725 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU D 725 " --> pdb=" O ALA D 700 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'E' and resid 192 through 196 Processing sheet with id=AF1, first strand: chain 'E' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN E 363 " --> pdb=" O GLU E 267 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N ILE E 269 " --> pdb=" O ASN E 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN E 361 " --> pdb=" O ILE E 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU E 271 " --> pdb=" O ARG E 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG E 359 " --> pdb=" O LEU E 271 " (cutoff:3.500A) Processing sheet with id=AF2, first strand: chain 'E' and resid 409 through 411 removed outlier: 3.627A pdb=" N ASN E 409 " --> pdb=" O ASN E 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE E 432 " --> pdb=" O LEU E 360 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N TYR E 375 " --> pdb=" O ILE E 404 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N ILE E 404 " --> pdb=" O TYR E 375 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'E' and resid 389 through 395 removed outlier: 6.607A pdb=" N LEU E 383 " --> pdb=" O LEU E 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR E 393 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N THR E 381 " --> pdb=" O THR E 393 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N LYS E 395 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N VAL E 377 " --> pdb=" O TYR E 456 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N TYR E 456 " --> pdb=" O VAL E 377 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN E 454 " --> pdb=" O PRO E 379 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N THR E 381 " --> pdb=" O THR E 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR E 452 " --> pdb=" O THR E 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU E 383 " --> pdb=" O LEU E 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU E 450 " --> pdb=" O LEU E 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU E 385 " --> pdb=" O LEU E 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU E 448 " --> pdb=" O LEU E 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL E 455 " --> pdb=" O ASN E 476 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ASN E 476 " --> pdb=" O VAL E 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY E 457 " --> pdb=" O GLY E 474 " (cutoff:3.500A) removed outlier: 8.601A pdb=" N GLY E 474 " --> pdb=" O GLY E 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE E 459 " --> pdb=" O ASP E 472 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'E' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE E 589 " --> pdb=" O THR E 488 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG E 490 " --> pdb=" O ILE E 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE E 591 " --> pdb=" O ARG E 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE E 492 " --> pdb=" O ILE E 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP E 593 " --> pdb=" O ILE E 492 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'E' and resid 541 through 542 Processing sheet with id=AF7, first strand: chain 'E' and resid 597 through 598 removed outlier: 3.655A pdb=" N GLY E 606 " --> pdb=" O HIS E 597 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'E' and resid 619 through 622 removed outlier: 6.604A pdb=" N LEU E 628 " --> pdb=" O ILE E 620 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N SER E 622 " --> pdb=" O GLY E 626 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY E 626 " --> pdb=" O SER E 622 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'E' and resid 654 through 655 removed outlier: 3.543A pdb=" N GLU E 654 " --> pdb=" O ILE E 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY E 641 " --> pdb=" O VAL E 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS E 729 " --> pdb=" O VAL E 696 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA E 700 " --> pdb=" O LEU E 725 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU E 725 " --> pdb=" O ALA E 700 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'F' and resid 192 through 196 Processing sheet with id=AG2, first strand: chain 'F' and resid 262 through 273 removed outlier: 6.641A pdb=" N ASN F 363 " --> pdb=" O GLU F 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE F 269 " --> pdb=" O ASN F 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN F 361 " --> pdb=" O ILE F 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU F 271 " --> pdb=" O ARG F 359 " (cutoff:3.500A) removed outlier: 6.389A pdb=" N ARG F 359 " --> pdb=" O LEU F 271 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'F' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN F 409 " --> pdb=" O ASN F 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE F 432 " --> pdb=" O LEU F 360 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR F 375 " --> pdb=" O ILE F 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE F 404 " --> pdb=" O TYR F 375 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'F' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU F 383 " --> pdb=" O LEU F 391 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N THR F 393 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR F 381 " --> pdb=" O THR F 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS F 395 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL F 377 " --> pdb=" O TYR F 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR F 456 " --> pdb=" O VAL F 377 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N GLN F 454 " --> pdb=" O PRO F 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR F 381 " --> pdb=" O THR F 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR F 452 " --> pdb=" O THR F 381 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N LEU F 383 " --> pdb=" O LEU F 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU F 450 " --> pdb=" O LEU F 383 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N LEU F 385 " --> pdb=" O LEU F 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU F 448 " --> pdb=" O LEU F 385 " (cutoff:3.500A) removed outlier: 10.813A pdb=" N VAL F 455 " --> pdb=" O ASN F 476 " (cutoff:3.500A) removed outlier: 8.960A pdb=" N ASN F 476 " --> pdb=" O VAL F 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY F 457 " --> pdb=" O GLY F 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY F 474 " --> pdb=" O GLY F 457 " (cutoff:3.500A) removed outlier: 4.476A pdb=" N ILE F 459 " --> pdb=" O ASP F 472 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'F' and resid 501 through 506 removed outlier: 8.838A pdb=" N ILE F 589 " --> pdb=" O THR F 488 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N ARG F 490 " --> pdb=" O ILE F 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE F 591 " --> pdb=" O ARG F 490 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ILE F 492 " --> pdb=" O ILE F 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP F 593 " --> pdb=" O ILE F 492 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'F' and resid 541 through 542 Processing sheet with id=AG8, first strand: chain 'F' and resid 597 through 598 removed outlier: 3.655A pdb=" N GLY F 606 " --> pdb=" O HIS F 597 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'F' and resid 619 through 622 removed outlier: 6.603A pdb=" N LEU F 628 " --> pdb=" O ILE F 620 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER F 622 " --> pdb=" O GLY F 626 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY F 626 " --> pdb=" O SER F 622 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'F' and resid 654 through 655 removed outlier: 3.542A pdb=" N GLU F 654 " --> pdb=" O ILE F 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY F 641 " --> pdb=" O VAL F 701 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS F 729 " --> pdb=" O VAL F 696 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ALA F 700 " --> pdb=" O LEU F 725 " (cutoff:3.500A) removed outlier: 6.048A pdb=" N LEU F 725 " --> pdb=" O ALA F 700 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'G' and resid 192 through 196 Processing sheet with id=AH3, first strand: chain 'G' and resid 262 through 273 removed outlier: 6.640A pdb=" N ASN G 363 " --> pdb=" O GLU G 267 " (cutoff:3.500A) removed outlier: 4.662A pdb=" N ILE G 269 " --> pdb=" O ASN G 361 " (cutoff:3.500A) removed outlier: 6.679A pdb=" N ASN G 361 " --> pdb=" O ILE G 269 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N LEU G 271 " --> pdb=" O ARG G 359 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ARG G 359 " --> pdb=" O LEU G 271 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'G' and resid 409 through 411 removed outlier: 3.628A pdb=" N ASN G 409 " --> pdb=" O ASN G 368 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE G 432 " --> pdb=" O LEU G 360 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 7.014A pdb=" N TYR G 375 " --> pdb=" O ILE G 404 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N ILE G 404 " --> pdb=" O TYR G 375 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'G' and resid 389 through 395 removed outlier: 6.606A pdb=" N LEU G 383 " --> pdb=" O LEU G 391 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N THR G 393 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 6.637A pdb=" N THR G 381 " --> pdb=" O THR G 393 " (cutoff:3.500A) removed outlier: 4.873A pdb=" N LYS G 395 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL G 377 " --> pdb=" O TYR G 456 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N TYR G 456 " --> pdb=" O VAL G 377 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N GLN G 454 " --> pdb=" O PRO G 379 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N THR G 381 " --> pdb=" O THR G 452 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N THR G 452 " --> pdb=" O THR G 381 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N LEU G 383 " --> pdb=" O LEU G 450 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LEU G 450 " --> pdb=" O LEU G 383 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU G 385 " --> pdb=" O LEU G 448 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N LEU G 448 " --> pdb=" O LEU G 385 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N VAL G 455 " --> pdb=" O ASN G 476 " (cutoff:3.500A) removed outlier: 8.962A pdb=" N ASN G 476 " --> pdb=" O VAL G 455 " (cutoff:3.500A) removed outlier: 8.874A pdb=" N GLY G 457 " --> pdb=" O GLY G 474 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N GLY G 474 " --> pdb=" O GLY G 457 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N ILE G 459 " --> pdb=" O ASP G 472 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'G' and resid 501 through 506 removed outlier: 8.839A pdb=" N ILE G 589 " --> pdb=" O THR G 488 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N ARG G 490 " --> pdb=" O ILE G 589 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N ILE G 591 " --> pdb=" O ARG G 490 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N ILE G 492 " --> pdb=" O ILE G 591 " (cutoff:3.500A) removed outlier: 8.415A pdb=" N ASP G 593 " --> pdb=" O ILE G 492 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'G' and resid 541 through 542 Processing sheet with id=AH9, first strand: chain 'G' and resid 597 through 598 removed outlier: 3.654A pdb=" N GLY G 606 " --> pdb=" O HIS G 597 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'G' and resid 619 through 622 removed outlier: 6.603A pdb=" N LEU G 628 " --> pdb=" O ILE G 620 " (cutoff:3.500A) removed outlier: 5.191A pdb=" N SER G 622 " --> pdb=" O GLY G 626 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N GLY G 626 " --> pdb=" O SER G 622 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'G' and resid 654 through 655 removed outlier: 3.542A pdb=" N GLU G 654 " --> pdb=" O ILE G 646 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLY G 641 " --> pdb=" O VAL G 701 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS G 729 " --> pdb=" O VAL G 696 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ALA G 700 " --> pdb=" O LEU G 725 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU G 725 " --> pdb=" O ALA G 700 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'L' and resid 80 through 84 removed outlier: 5.814A pdb=" N LYS L 80 " --> pdb=" O LEU L 129 " (cutoff:3.500A) removed outlier: 7.700A pdb=" N ILE L 131 " --> pdb=" O LYS L 80 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N TYR L 82 " --> pdb=" O ILE L 131 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N VAL L 128 " --> pdb=" O LYS L 122 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'L' and resid 103 through 105 1306 hydrogen bonds defined for protein. 3528 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: 7.51 Time building geometry restraints manager: 3.54 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 10414 1.33 - 1.46: 6093 1.46 - 1.58: 16792 1.58 - 1.70: 0 1.70 - 1.82: 90 Bond restraints: 33389 Sorted by residual: bond pdb=" CA SER B 301 " pdb=" C SER B 301 " ideal model delta sigma weight residual 1.524 1.562 -0.039 1.25e-02 6.40e+03 9.60e+00 bond pdb=" CG1 ILE L 39 " pdb=" CD1 ILE L 39 " ideal model delta sigma weight residual 1.513 1.401 0.112 3.90e-02 6.57e+02 8.29e+00 bond pdb=" CA THR B 300 " pdb=" C THR B 300 " ideal model delta sigma weight residual 1.523 1.554 -0.031 1.23e-02 6.61e+03 6.48e+00 bond pdb=" CA HIS L 42 " pdb=" CB HIS L 42 " ideal model delta sigma weight residual 1.528 1.494 0.034 1.59e-02 3.96e+03 4.69e+00 bond pdb=" CD2 TYR L 118 " pdb=" CE2 TYR L 118 " ideal model delta sigma weight residual 1.382 1.324 0.058 3.00e-02 1.11e+03 3.76e+00 ... (remaining 33384 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.95: 44591 2.95 - 5.91: 644 5.91 - 8.86: 50 8.86 - 11.82: 11 11.82 - 14.77: 1 Bond angle restraints: 45297 Sorted by residual: angle pdb=" N THR B 300 " pdb=" CA THR B 300 " pdb=" C THR B 300 " ideal model delta sigma weight residual 108.52 123.29 -14.77 1.63e+00 3.76e-01 8.21e+01 angle pdb=" N VAL L 138 " pdb=" CA VAL L 138 " pdb=" C VAL L 138 " ideal model delta sigma weight residual 113.43 105.64 7.79 1.09e+00 8.42e-01 5.11e+01 angle pdb=" N TYR D 542 " pdb=" CA TYR D 542 " pdb=" C TYR D 542 " ideal model delta sigma weight residual 108.52 98.53 9.99 1.63e+00 3.76e-01 3.76e+01 angle pdb=" N TYR A 542 " pdb=" CA TYR A 542 " pdb=" C TYR A 542 " ideal model delta sigma weight residual 108.52 98.55 9.97 1.63e+00 3.76e-01 3.74e+01 angle pdb=" N TYR B 542 " pdb=" CA TYR B 542 " pdb=" C TYR B 542 " ideal model delta sigma weight residual 108.52 98.55 9.97 1.63e+00 3.76e-01 3.74e+01 ... (remaining 45292 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.83: 19591 16.83 - 33.67: 682 33.67 - 50.50: 107 50.50 - 67.34: 7 67.34 - 84.17: 21 Dihedral angle restraints: 20408 sinusoidal: 8201 harmonic: 12207 Sorted by residual: dihedral pdb=" CA SER D 294 " pdb=" C SER D 294 " pdb=" N THR D 295 " pdb=" CA THR D 295 " ideal model delta harmonic sigma weight residual 180.00 157.68 22.32 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER A 294 " pdb=" C SER A 294 " pdb=" N THR A 295 " pdb=" CA THR A 295 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER E 294 " pdb=" C SER E 294 " pdb=" N THR E 295 " pdb=" CA THR E 295 " ideal model delta harmonic sigma weight residual 180.00 157.69 22.31 0 5.00e+00 4.00e-02 1.99e+01 ... (remaining 20405 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.094: 4675 0.094 - 0.189: 478 0.189 - 0.283: 22 0.283 - 0.377: 1 0.377 - 0.471: 2 Chirality restraints: 5178 Sorted by residual: chirality pdb=" CA THR B 300 " pdb=" N THR B 300 " pdb=" C THR B 300 " pdb=" CB THR B 300 " both_signs ideal model delta sigma weight residual False 2.53 2.05 0.47 2.00e-01 2.50e+01 5.55e+00 chirality pdb=" CB VAL L 147 " pdb=" CA VAL L 147 " pdb=" CG1 VAL L 147 " pdb=" CG2 VAL L 147 " both_signs ideal model delta sigma weight residual False -2.63 -2.21 -0.42 2.00e-01 2.50e+01 4.47e+00 chirality pdb=" CB ILE L 163 " pdb=" CA ILE L 163 " pdb=" CG1 ILE L 163 " pdb=" CG2 ILE L 163 " both_signs ideal model delta sigma weight residual False 2.64 2.96 -0.31 2.00e-01 2.50e+01 2.47e+00 ... (remaining 5175 not shown) Planarity restraints: 5940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE L 163 " 0.016 2.00e-02 2.50e+03 3.19e-02 1.02e+01 pdb=" C ILE L 163 " -0.055 2.00e-02 2.50e+03 pdb=" O ILE L 163 " 0.021 2.00e-02 2.50e+03 pdb=" N ASN L 164 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU L 51 " 0.015 2.00e-02 2.50e+03 3.04e-02 9.25e+00 pdb=" C GLU L 51 " -0.053 2.00e-02 2.50e+03 pdb=" O GLU L 51 " 0.020 2.00e-02 2.50e+03 pdb=" N GLU L 52 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 694 " 0.027 2.00e-02 2.50e+03 1.99e-02 7.95e+00 pdb=" CG TYR C 694 " -0.048 2.00e-02 2.50e+03 pdb=" CD1 TYR C 694 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR C 694 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR C 694 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 694 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 694 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR C 694 " 0.008 2.00e-02 2.50e+03 ... (remaining 5937 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 619 2.67 - 3.22: 29719 3.22 - 3.78: 50506 3.78 - 4.34: 69665 4.34 - 4.90: 114689 Nonbonded interactions: 265198 Sorted by model distance: nonbonded pdb=" O ILE E 183 " pdb="CA CA E 801 " model vdw 2.107 2.510 nonbonded pdb=" O ILE G 183 " pdb="CA CA G 801 " model vdw 2.107 2.510 nonbonded pdb=" O ILE F 183 " pdb="CA CA F 801 " model vdw 2.108 2.510 nonbonded pdb=" O ILE A 183 " pdb="CA CA A 801 " model vdw 2.108 2.510 nonbonded pdb=" O ILE C 183 " pdb="CA CA C 801 " model vdw 2.108 2.510 ... (remaining 265193 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 group one per residue 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: 2.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.660 Check model and map are aligned: 0.110 Set scattering table: 0.120 Process input model: 30.160 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 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 : 0.006 0.112 33389 Z= 0.301 Angle : 0.931 14.772 45297 Z= 0.546 Chirality : 0.056 0.471 5178 Planarity : 0.006 0.070 5940 Dihedral : 9.419 84.174 12508 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.65 % Allowed : 1.90 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.98 (0.12), residues: 4138 helix: -2.15 (0.16), residues: 647 sheet: -0.45 (0.13), residues: 1357 loop : -1.59 (0.13), residues: 2134 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG D 592 TYR 0.048 0.003 TYR C 694 PHE 0.023 0.003 PHE B 202 TRP 0.016 0.003 TRP F 226 HIS 0.012 0.003 HIS L 91 Details of bonding type rmsd covalent geometry : bond 0.00612 (33389) covalent geometry : angle 0.93067 (45297) hydrogen bonds : bond 0.22736 ( 1285) hydrogen bonds : angle 9.73061 ( 3528) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 253 time to evaluate : 0.937 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.8894 (m-80) cc_final: 0.8558 (m-80) REVERT: A 434 MET cc_start: 0.8798 (ttm) cc_final: 0.8214 (mmt) REVERT: B 233 TYR cc_start: 0.9420 (m-80) cc_final: 0.9212 (m-80) REVERT: B 479 GLU cc_start: 0.8463 (mt-10) cc_final: 0.8260 (mt-10) REVERT: B 509 ASN cc_start: 0.8840 (t0) cc_final: 0.8590 (t0) REVERT: C 243 ILE cc_start: 0.9068 (tt) cc_final: 0.8729 (mm) REVERT: C 299 HIS cc_start: 0.8826 (m90) cc_final: 0.8505 (p-80) REVERT: C 434 MET cc_start: 0.9018 (ttm) cc_final: 0.8653 (ttm) REVERT: C 496 LYS cc_start: 0.8185 (tttt) cc_final: 0.7663 (tppt) REVERT: D 515 GLU cc_start: 0.8586 (tp30) cc_final: 0.8138 (tp30) REVERT: F 426 ASP cc_start: 0.8683 (m-30) cc_final: 0.8195 (t70) REVERT: F 527 LEU cc_start: 0.9861 (mt) cc_final: 0.9634 (pp) REVERT: G 434 MET cc_start: 0.9132 (ttm) cc_final: 0.8792 (tmm) REVERT: G 515 GLU cc_start: 0.9109 (tp30) cc_final: 0.8621 (tp30) REVERT: G 521 MET cc_start: 0.8041 (tpp) cc_final: 0.7098 (tpp) REVERT: G 636 ARG cc_start: 0.6911 (ppp-140) cc_final: 0.6580 (tpp-160) REVERT: G 726 ILE cc_start: 0.2915 (OUTLIER) cc_final: 0.2375 (pt) REVERT: L 73 MET cc_start: 0.9086 (mtm) cc_final: 0.8760 (mmp) REVERT: L 217 PHE cc_start: 0.9195 (t80) cc_final: 0.8855 (t80) REVERT: L 221 PHE cc_start: 0.9524 (t80) cc_final: 0.8928 (t80) outliers start: 24 outliers final: 0 residues processed: 277 average time/residue: 0.2269 time to fit residues: 98.8018 Evaluate side-chains 110 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 109 time to evaluate : 1.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 197 optimal weight: 3.9990 chunk 388 optimal weight: 30.0000 chunk 215 optimal weight: 7.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 6.9990 chunk 261 optimal weight: 10.0000 chunk 248 optimal weight: 0.0070 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 6.9990 chunk 155 optimal weight: 20.0000 chunk 244 optimal weight: 3.9990 overall best weight: 4.4006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 263 HIS A 336 HIS A 389 GLN A 483 GLN A 584 ASN B 424 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 499 ASN B 553 ASN B 584 ASN C 198 ASN C 424 GLN C 553 ASN C 584 ASN C 705 ASN D 198 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 ASN D 584 ASN E 198 ASN E 299 HIS E 304 HIS ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 483 GLN E 543 GLN E 553 ASN E 584 ASN F 198 ASN F 389 GLN F 553 ASN F 584 ASN G 198 ASN G 336 HIS ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 553 ASN G 584 ASN L 186 GLN L 250 GLN Total number of N/Q/H flips: 35 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.086877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058162 restraints weight = 279074.746| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3076 r_free = 0.3076 target = 0.058922 restraints weight = 166238.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.059318 restraints weight = 118020.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.059723 restraints weight = 98546.624| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.059931 restraints weight = 86389.188| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.2614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 33389 Z= 0.183 Angle : 0.599 9.494 45297 Z= 0.320 Chirality : 0.044 0.166 5178 Planarity : 0.004 0.056 5940 Dihedral : 5.103 23.056 4470 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.05 % Allowed : 1.35 % Favored : 98.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.07 (0.13), residues: 4138 helix: -0.31 (0.21), residues: 690 sheet: -0.04 (0.14), residues: 1231 loop : -1.22 (0.12), residues: 2217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 470 TYR 0.026 0.002 TYR L 148 PHE 0.019 0.002 PHE A 202 TRP 0.012 0.002 TRP A 206 HIS 0.012 0.001 HIS A 336 Details of bonding type rmsd covalent geometry : bond 0.00378 (33389) covalent geometry : angle 0.59877 (45297) hydrogen bonds : bond 0.03572 ( 1285) hydrogen bonds : angle 6.26432 ( 3528) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 131 time to evaluate : 1.221 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: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.9308 (m-80) cc_final: 0.8884 (m-10) REVERT: A 434 MET cc_start: 0.9000 (ttm) cc_final: 0.8530 (mmt) REVERT: B 346 TRP cc_start: 0.8731 (t-100) cc_final: 0.8240 (t60) REVERT: B 405 LEU cc_start: 0.8554 (tp) cc_final: 0.8046 (tp) REVERT: B 434 MET cc_start: 0.9366 (ttp) cc_final: 0.9054 (ttp) REVERT: B 509 ASN cc_start: 0.8973 (t0) cc_final: 0.8706 (t0) REVERT: B 520 ASP cc_start: 0.8693 (p0) cc_final: 0.8471 (t70) REVERT: C 299 HIS cc_start: 0.8739 (m90) cc_final: 0.7855 (t70) REVERT: C 434 MET cc_start: 0.9011 (ttm) cc_final: 0.8749 (ttm) REVERT: C 587 MET cc_start: 0.7989 (mmp) cc_final: 0.7775 (mmm) REVERT: D 515 GLU cc_start: 0.8644 (tp30) cc_final: 0.8096 (tp30) REVERT: E 543 GLN cc_start: 0.9322 (OUTLIER) cc_final: 0.9084 (mp10) REVERT: F 426 ASP cc_start: 0.9014 (m-30) cc_final: 0.8389 (t70) REVERT: G 515 GLU cc_start: 0.9254 (tp30) cc_final: 0.8589 (tp30) REVERT: L 40 MET cc_start: 0.8117 (ppp) cc_final: 0.7834 (ppp) REVERT: L 73 MET cc_start: 0.9144 (mtm) cc_final: 0.8733 (mmp) REVERT: L 217 PHE cc_start: 0.9298 (t80) cc_final: 0.8947 (t80) REVERT: L 221 PHE cc_start: 0.9478 (t80) cc_final: 0.8954 (t80) REVERT: L 244 MET cc_start: 0.9355 (mmm) cc_final: 0.9081 (mmm) outliers start: 2 outliers final: 0 residues processed: 133 average time/residue: 0.2035 time to fit residues: 44.8891 Evaluate side-chains 89 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 88 time to evaluate : 1.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 0.6980 chunk 18 optimal weight: 5.9990 chunk 268 optimal weight: 6.9990 chunk 113 optimal weight: 2.9990 chunk 47 optimal weight: 10.0000 chunk 251 optimal weight: 8.9990 chunk 163 optimal weight: 10.0000 chunk 301 optimal weight: 3.9990 chunk 77 optimal weight: 0.9980 chunk 176 optimal weight: 10.0000 chunk 142 optimal weight: 4.9990 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 ASN A 616 HIS B 299 HIS B 424 GLN ** B 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 250 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3775 r_free = 0.3775 target = 0.086386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.058314 restraints weight = 284286.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.059271 restraints weight = 165065.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.059958 restraints weight = 117204.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060236 restraints weight = 94160.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.060578 restraints weight = 83760.168| |-----------------------------------------------------------------------------| r_work (final): 0.2931 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 33389 Z= 0.119 Angle : 0.503 6.975 45297 Z= 0.269 Chirality : 0.043 0.158 5178 Planarity : 0.003 0.042 5940 Dihedral : 4.633 19.641 4470 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer: Outliers : 0.00 % Allowed : 1.25 % Favored : 98.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.46 (0.13), residues: 4138 helix: -0.03 (0.21), residues: 725 sheet: 0.81 (0.15), residues: 1203 loop : -1.04 (0.13), residues: 2210 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 470 TYR 0.017 0.001 TYR C 542 PHE 0.019 0.001 PHE A 727 TRP 0.010 0.001 TRP E 206 HIS 0.004 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00253 (33389) covalent geometry : angle 0.50316 (45297) hydrogen bonds : bond 0.03003 ( 1285) hydrogen bonds : angle 5.58259 ( 3528) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 108 time to evaluate : 1.111 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 233 TYR cc_start: 0.9390 (m-80) cc_final: 0.8970 (m-10) REVERT: A 350 MET cc_start: 0.9250 (ppp) cc_final: 0.9024 (ppp) REVERT: A 434 MET cc_start: 0.9092 (ttm) cc_final: 0.8597 (mmt) REVERT: B 346 TRP cc_start: 0.8770 (t-100) cc_final: 0.8293 (t60) REVERT: B 405 LEU cc_start: 0.8686 (tp) cc_final: 0.8203 (tp) REVERT: B 434 MET cc_start: 0.9349 (ttp) cc_final: 0.9038 (ttp) REVERT: B 509 ASN cc_start: 0.9001 (t0) cc_final: 0.8746 (t0) REVERT: C 299 HIS cc_start: 0.8705 (m90) cc_final: 0.7835 (t-170) REVERT: C 434 MET cc_start: 0.8999 (ttm) cc_final: 0.8753 (ttm) REVERT: C 587 MET cc_start: 0.7930 (mmp) cc_final: 0.7718 (mmm) REVERT: D 515 GLU cc_start: 0.8706 (tp30) cc_final: 0.8060 (tp30) REVERT: F 426 ASP cc_start: 0.9023 (m-30) cc_final: 0.8450 (t70) REVERT: G 515 GLU cc_start: 0.9208 (tp30) cc_final: 0.8440 (tp30) REVERT: L 73 MET cc_start: 0.9092 (mtm) cc_final: 0.8674 (mmp) REVERT: L 217 PHE cc_start: 0.9342 (t80) cc_final: 0.9054 (t80) REVERT: L 221 PHE cc_start: 0.9430 (t80) cc_final: 0.8991 (t80) REVERT: L 244 MET cc_start: 0.9390 (mmm) cc_final: 0.8885 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1987 time to fit residues: 35.7158 Evaluate side-chains 81 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 81 optimal weight: 0.0000 chunk 352 optimal weight: 40.0000 chunk 10 optimal weight: 10.0000 chunk 232 optimal weight: 1.9990 chunk 195 optimal weight: 10.0000 chunk 287 optimal weight: 7.9990 chunk 14 optimal weight: 20.0000 chunk 28 optimal weight: 9.9990 chunk 310 optimal weight: 7.9990 chunk 215 optimal weight: 0.2980 chunk 222 optimal weight: 1.9990 overall best weight: 2.4590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 616 HIS A 705 ASN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN E 304 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 32 GLN L 186 GLN L 250 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.086502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.058987 restraints weight = 284294.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.059809 restraints weight = 168371.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.060401 restraints weight = 119899.499| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.060694 restraints weight = 97008.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.061070 restraints weight = 85958.148| |-----------------------------------------------------------------------------| r_work (final): 0.2927 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.055 33389 Z= 0.109 Angle : 0.484 6.998 45297 Z= 0.257 Chirality : 0.043 0.165 5178 Planarity : 0.003 0.033 5940 Dihedral : 4.432 16.762 4470 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.16 (0.13), residues: 4138 helix: 0.09 (0.21), residues: 740 sheet: 1.19 (0.15), residues: 1161 loop : -0.90 (0.13), residues: 2237 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 659 TYR 0.013 0.001 TYR G 233 PHE 0.012 0.001 PHE A 202 TRP 0.009 0.001 TRP E 206 HIS 0.004 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00233 (33389) covalent geometry : angle 0.48394 (45297) hydrogen bonds : bond 0.02644 ( 1285) hydrogen bonds : angle 5.19548 ( 3528) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 1.314 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: A 350 MET cc_start: 0.9360 (ppp) cc_final: 0.9128 (ppp) REVERT: A 434 MET cc_start: 0.9085 (ttm) cc_final: 0.8603 (mmt) REVERT: B 405 LEU cc_start: 0.8652 (tp) cc_final: 0.8156 (tp) REVERT: B 434 MET cc_start: 0.9361 (ttp) cc_final: 0.9089 (ttp) REVERT: B 447 GLN cc_start: 0.9220 (mt0) cc_final: 0.8883 (tm-30) REVERT: B 465 GLU cc_start: 0.9622 (tt0) cc_final: 0.9392 (tm-30) REVERT: B 509 ASN cc_start: 0.9032 (t0) cc_final: 0.8768 (t0) REVERT: C 299 HIS cc_start: 0.8742 (m90) cc_final: 0.7890 (t-170) REVERT: C 587 MET cc_start: 0.7966 (mmp) cc_final: 0.7755 (mmm) REVERT: D 515 GLU cc_start: 0.8717 (tp30) cc_final: 0.8029 (tp30) REVERT: D 587 MET cc_start: 0.8906 (mtt) cc_final: 0.8609 (mtm) REVERT: F 426 ASP cc_start: 0.9006 (m-30) cc_final: 0.8677 (p0) REVERT: G 515 GLU cc_start: 0.9227 (tp30) cc_final: 0.8497 (tp30) REVERT: L 73 MET cc_start: 0.9095 (mtm) cc_final: 0.8798 (ptp) REVERT: L 217 PHE cc_start: 0.9340 (t80) cc_final: 0.9052 (t80) REVERT: L 221 PHE cc_start: 0.9460 (t80) cc_final: 0.9042 (t80) REVERT: L 244 MET cc_start: 0.9397 (mmm) cc_final: 0.8874 (mmm) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.2245 time to fit residues: 38.9423 Evaluate side-chains 82 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 225 optimal weight: 6.9990 chunk 170 optimal weight: 0.5980 chunk 297 optimal weight: 20.0000 chunk 257 optimal weight: 0.0670 chunk 6 optimal weight: 0.9990 chunk 330 optimal weight: 20.0000 chunk 114 optimal weight: 2.9990 chunk 191 optimal weight: 3.9990 chunk 405 optimal weight: 10.0000 chunk 406 optimal weight: 8.9990 chunk 199 optimal weight: 9.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 299 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS E 705 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 250 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3765 r_free = 0.3765 target = 0.086858 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.060173 restraints weight = 290312.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.061120 restraints weight = 165307.453| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.061755 restraints weight = 115628.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.062052 restraints weight = 92971.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.062416 restraints weight = 82187.326| |-----------------------------------------------------------------------------| r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 33389 Z= 0.089 Angle : 0.464 6.050 45297 Z= 0.246 Chirality : 0.043 0.151 5178 Planarity : 0.003 0.035 5940 Dihedral : 4.226 17.609 4470 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 6.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4138 helix: 0.11 (0.21), residues: 740 sheet: 1.08 (0.16), residues: 1056 loop : -0.83 (0.13), residues: 2342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG E 659 TYR 0.013 0.001 TYR G 233 PHE 0.011 0.001 PHE A 202 TRP 0.008 0.001 TRP E 206 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00189 (33389) covalent geometry : angle 0.46397 (45297) hydrogen bonds : bond 0.02488 ( 1285) hydrogen bonds : angle 5.02073 ( 3528) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 106 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.9375 (ppp) cc_final: 0.9129 (ppp) REVERT: A 434 MET cc_start: 0.9057 (ttm) cc_final: 0.8587 (mmt) REVERT: B 405 LEU cc_start: 0.8623 (tp) cc_final: 0.8106 (tp) REVERT: B 434 MET cc_start: 0.9361 (ttp) cc_final: 0.9044 (ttp) REVERT: B 447 GLN cc_start: 0.9254 (mt0) cc_final: 0.8912 (tm-30) REVERT: B 465 GLU cc_start: 0.9598 (tt0) cc_final: 0.9354 (tm-30) REVERT: B 509 ASN cc_start: 0.9043 (t0) cc_final: 0.8786 (t0) REVERT: C 299 HIS cc_start: 0.8774 (m90) cc_final: 0.7973 (t-170) REVERT: C 434 MET cc_start: 0.9080 (ttm) cc_final: 0.8870 (ttm) REVERT: C 587 MET cc_start: 0.7864 (mmp) cc_final: 0.7664 (mmm) REVERT: D 515 GLU cc_start: 0.8699 (tp30) cc_final: 0.8006 (tp30) REVERT: D 587 MET cc_start: 0.8960 (mtt) cc_final: 0.8684 (mtm) REVERT: F 426 ASP cc_start: 0.8962 (m-30) cc_final: 0.8629 (p0) REVERT: G 515 GLU cc_start: 0.9227 (tp30) cc_final: 0.8475 (tp30) REVERT: L 73 MET cc_start: 0.9076 (mtm) cc_final: 0.8819 (ptp) REVERT: L 217 PHE cc_start: 0.9354 (t80) cc_final: 0.9080 (t80) REVERT: L 221 PHE cc_start: 0.9482 (t80) cc_final: 0.9056 (t80) REVERT: L 244 MET cc_start: 0.9395 (mmm) cc_final: 0.8877 (mmm) outliers start: 0 outliers final: 0 residues processed: 106 average time/residue: 0.2139 time to fit residues: 37.1671 Evaluate side-chains 83 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 210 optimal weight: 7.9990 chunk 300 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 86 optimal weight: 2.9990 chunk 157 optimal weight: 50.0000 chunk 219 optimal weight: 40.0000 chunk 89 optimal weight: 9.9990 chunk 49 optimal weight: 0.0070 chunk 359 optimal weight: 9.9990 chunk 83 optimal weight: 7.9990 chunk 153 optimal weight: 1.9990 overall best weight: 3.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS B 403 GLN B 499 ASN B 541 GLN C 363 ASN C 693 ASN E 304 HIS E 403 GLN F 389 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.085877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.058116 restraints weight = 282999.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.059045 restraints weight = 165314.258| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059595 restraints weight = 117471.603| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.060024 restraints weight = 96006.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060184 restraints weight = 84660.367| |-----------------------------------------------------------------------------| r_work (final): 0.2912 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 33389 Z= 0.123 Angle : 0.496 7.415 45297 Z= 0.262 Chirality : 0.043 0.153 5178 Planarity : 0.003 0.032 5940 Dihedral : 4.355 19.966 4470 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.00 % Allowed : 0.98 % Favored : 99.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.05 (0.13), residues: 4138 helix: 0.18 (0.21), residues: 733 sheet: 1.31 (0.15), residues: 1112 loop : -0.80 (0.13), residues: 2293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 359 TYR 0.020 0.001 TYR B 542 PHE 0.011 0.001 PHE A 727 TRP 0.009 0.001 TRP E 206 HIS 0.010 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00264 (33389) covalent geometry : angle 0.49648 (45297) hydrogen bonds : bond 0.02592 ( 1285) hydrogen bonds : angle 5.01436 ( 3528) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.9425 (ppp) cc_final: 0.9215 (ppp) REVERT: A 434 MET cc_start: 0.9089 (ttm) cc_final: 0.8605 (mmt) REVERT: B 405 LEU cc_start: 0.8645 (tp) cc_final: 0.8066 (tp) REVERT: B 434 MET cc_start: 0.9372 (ttp) cc_final: 0.9079 (ttp) REVERT: B 447 GLN cc_start: 0.9182 (mt0) cc_final: 0.8877 (tm-30) REVERT: B 465 GLU cc_start: 0.9634 (tt0) cc_final: 0.9355 (tm-30) REVERT: B 509 ASN cc_start: 0.9060 (t0) cc_final: 0.8804 (t0) REVERT: C 299 HIS cc_start: 0.8669 (m90) cc_final: 0.7866 (t-170) REVERT: C 300 THR cc_start: 0.8253 (m) cc_final: 0.8052 (p) REVERT: C 434 MET cc_start: 0.9118 (ttm) cc_final: 0.8850 (ttm) REVERT: D 233 TYR cc_start: 0.9069 (m-80) cc_final: 0.8634 (m-80) REVERT: D 515 GLU cc_start: 0.8733 (tp30) cc_final: 0.8072 (tp30) REVERT: D 587 MET cc_start: 0.9055 (mtt) cc_final: 0.8792 (mtm) REVERT: F 426 ASP cc_start: 0.8941 (m-30) cc_final: 0.8672 (p0) REVERT: G 233 TYR cc_start: 0.9002 (m-80) cc_final: 0.8801 (m-80) REVERT: G 515 GLU cc_start: 0.9258 (tp30) cc_final: 0.8371 (tp30) REVERT: L 73 MET cc_start: 0.9086 (mtm) cc_final: 0.8801 (ptp) REVERT: L 221 PHE cc_start: 0.9475 (t80) cc_final: 0.9058 (t80) REVERT: L 244 MET cc_start: 0.9395 (mmm) cc_final: 0.8940 (mmm) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.2066 time to fit residues: 33.8144 Evaluate side-chains 81 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 81 time to evaluate : 1.208 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 173 optimal weight: 0.8980 chunk 208 optimal weight: 10.0000 chunk 53 optimal weight: 50.0000 chunk 125 optimal weight: 10.0000 chunk 172 optimal weight: 7.9990 chunk 241 optimal weight: 20.0000 chunk 395 optimal weight: 3.9990 chunk 49 optimal weight: 30.0000 chunk 101 optimal weight: 50.0000 chunk 62 optimal weight: 0.0570 chunk 63 optimal weight: 8.9990 overall best weight: 4.3904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 458 ASN A 564 ASN B 198 ASN B 299 HIS B 565 GLN C 280 GLN ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 280 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN D 693 ASN D 705 ASN E 304 HIS F 389 GLN F 403 GLN ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 165 GLN L 186 GLN L 250 GLN Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.084721 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058495 restraints weight = 261277.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058495 restraints weight = 170964.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058495 restraints weight = 170964.553| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058495 restraints weight = 170964.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.058495 restraints weight = 170964.434| |-----------------------------------------------------------------------------| r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7811 moved from start: 0.5156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.082 33389 Z= 0.169 Angle : 0.570 9.140 45297 Z= 0.301 Chirality : 0.043 0.150 5178 Planarity : 0.003 0.033 5940 Dihedral : 4.800 20.117 4470 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 10.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 0.03 % Allowed : 0.92 % Favored : 99.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.23 (0.13), residues: 4138 helix: -0.15 (0.20), residues: 767 sheet: 1.39 (0.16), residues: 1077 loop : -0.93 (0.13), residues: 2294 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 470 TYR 0.020 0.002 TYR E 233 PHE 0.016 0.002 PHE A 550 TRP 0.012 0.002 TRP E 206 HIS 0.006 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00358 (33389) covalent geometry : angle 0.57030 (45297) hydrogen bonds : bond 0.02945 ( 1285) hydrogen bonds : angle 5.30389 ( 3528) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 92 time to evaluate : 1.216 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 434 MET cc_start: 0.9115 (ttm) cc_final: 0.8652 (mmt) REVERT: A 614 GLU cc_start: 0.8102 (tp30) cc_final: 0.7799 (mm-30) REVERT: B 405 LEU cc_start: 0.8906 (tp) cc_final: 0.8317 (tp) REVERT: B 465 GLU cc_start: 0.9689 (tt0) cc_final: 0.9382 (tm-30) REVERT: C 434 MET cc_start: 0.9211 (ttm) cc_final: 0.8904 (ttm) REVERT: C 587 MET cc_start: 0.8236 (mmp) cc_final: 0.7958 (mmm) REVERT: D 515 GLU cc_start: 0.8911 (tp30) cc_final: 0.8303 (tp30) REVERT: G 233 TYR cc_start: 0.9003 (m-80) cc_final: 0.8766 (m-80) REVERT: G 442 LEU cc_start: 0.9424 (tp) cc_final: 0.8960 (pp) REVERT: L 73 MET cc_start: 0.9058 (mtm) cc_final: 0.8782 (ptp) REVERT: L 217 PHE cc_start: 0.9355 (t80) cc_final: 0.9154 (t80) REVERT: L 221 PHE cc_start: 0.9431 (t80) cc_final: 0.9104 (t80) REVERT: L 244 MET cc_start: 0.9434 (mmm) cc_final: 0.9173 (mmm) outliers start: 1 outliers final: 1 residues processed: 92 average time/residue: 0.1972 time to fit residues: 30.8152 Evaluate side-chains 77 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 76 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 353 optimal weight: 5.9990 chunk 390 optimal weight: 0.8980 chunk 122 optimal weight: 6.9990 chunk 146 optimal weight: 4.9990 chunk 242 optimal weight: 6.9990 chunk 333 optimal weight: 0.9990 chunk 201 optimal weight: 0.0870 chunk 65 optimal weight: 6.9990 chunk 136 optimal weight: 5.9990 chunk 384 optimal weight: 10.0000 chunk 323 optimal weight: 20.0000 overall best weight: 2.5964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 458 ASN B 389 GLN D 541 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.085356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.059013 restraints weight = 268966.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.059789 restraints weight = 155093.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.060087 restraints weight = 112404.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.060222 restraints weight = 96082.255| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3084 r_free = 0.3084 target = 0.060196 restraints weight = 88493.063| |-----------------------------------------------------------------------------| r_work (final): 0.2938 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33389 Z= 0.107 Angle : 0.492 7.200 45297 Z= 0.259 Chirality : 0.043 0.189 5178 Planarity : 0.003 0.032 5940 Dihedral : 4.466 20.247 4470 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.08 (0.13), residues: 4138 helix: 0.07 (0.20), residues: 768 sheet: 1.49 (0.15), residues: 1112 loop : -0.92 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 592 TYR 0.018 0.001 TYR B 233 PHE 0.011 0.001 PHE A 727 TRP 0.010 0.002 TRP E 206 HIS 0.006 0.001 HIS A 304 Details of bonding type rmsd covalent geometry : bond 0.00230 (33389) covalent geometry : angle 0.49204 (45297) hydrogen bonds : bond 0.02562 ( 1285) hydrogen bonds : angle 5.08423 ( 3528) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.215 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 237 GLU cc_start: 0.9357 (pt0) cc_final: 0.9122 (pp20) REVERT: A 350 MET cc_start: 0.9392 (ppp) cc_final: 0.9142 (ppp) REVERT: A 434 MET cc_start: 0.8940 (ttm) cc_final: 0.8534 (mmt) REVERT: B 405 LEU cc_start: 0.8738 (tp) cc_final: 0.8201 (tp) REVERT: B 434 MET cc_start: 0.9429 (ttt) cc_final: 0.9196 (tmm) REVERT: B 465 GLU cc_start: 0.9630 (tt0) cc_final: 0.9312 (tm-30) REVERT: B 509 ASN cc_start: 0.9222 (t0) cc_final: 0.8964 (t0) REVERT: C 360 LEU cc_start: 0.9443 (tp) cc_final: 0.9194 (tp) REVERT: C 434 MET cc_start: 0.9173 (ttm) cc_final: 0.8866 (ttm) REVERT: C 587 MET cc_start: 0.8346 (mmp) cc_final: 0.8113 (mmm) REVERT: D 233 TYR cc_start: 0.9212 (m-80) cc_final: 0.8784 (m-80) REVERT: D 515 GLU cc_start: 0.8719 (tp30) cc_final: 0.8088 (tp30) REVERT: D 587 MET cc_start: 0.9286 (mtt) cc_final: 0.9060 (mtm) REVERT: E 304 HIS cc_start: 0.7164 (m90) cc_final: 0.6926 (m90) REVERT: F 600 ARG cc_start: 0.5929 (tpm170) cc_final: 0.5620 (tpm170) REVERT: G 442 LEU cc_start: 0.9327 (tp) cc_final: 0.8847 (pp) REVERT: L 73 MET cc_start: 0.9033 (mtm) cc_final: 0.8755 (ptp) REVERT: L 217 PHE cc_start: 0.9376 (t80) cc_final: 0.9165 (t80) REVERT: L 221 PHE cc_start: 0.9414 (t80) cc_final: 0.9100 (t80) REVERT: L 244 MET cc_start: 0.9415 (mmm) cc_final: 0.9135 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2182 time to fit residues: 34.8441 Evaluate side-chains 78 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 78 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 124 optimal weight: 40.0000 chunk 154 optimal weight: 5.9990 chunk 135 optimal weight: 7.9990 chunk 193 optimal weight: 9.9990 chunk 215 optimal weight: 3.9990 chunk 275 optimal weight: 0.5980 chunk 334 optimal weight: 0.5980 chunk 246 optimal weight: 6.9990 chunk 136 optimal weight: 9.9990 chunk 190 optimal weight: 7.9990 chunk 138 optimal weight: 1.9990 overall best weight: 2.6386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 328 ASN B 299 HIS B 565 GLN D 541 GLN G 277 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.085189 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058722 restraints weight = 266491.737| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.059469 restraints weight = 157512.308| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059883 restraints weight = 113996.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059883 restraints weight = 93364.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.059883 restraints weight = 93364.377| |-----------------------------------------------------------------------------| r_work (final): 0.2919 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7823 moved from start: 0.5451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.056 33389 Z= 0.110 Angle : 0.493 7.171 45297 Z= 0.260 Chirality : 0.043 0.160 5178 Planarity : 0.003 0.032 5940 Dihedral : 4.400 20.089 4470 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.03 % Allowed : 0.30 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.00 (0.13), residues: 4138 helix: 0.15 (0.20), residues: 768 sheet: 1.57 (0.15), residues: 1112 loop : -0.90 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 659 TYR 0.023 0.001 TYR E 233 PHE 0.011 0.001 PHE A 727 TRP 0.010 0.001 TRP E 206 HIS 0.004 0.001 HIS B 299 Details of bonding type rmsd covalent geometry : bond 0.00237 (33389) covalent geometry : angle 0.49342 (45297) hydrogen bonds : bond 0.02506 ( 1285) hydrogen bonds : angle 4.99852 ( 3528) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 94 time to evaluate : 1.185 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 350 MET cc_start: 0.9360 (ppp) cc_final: 0.9102 (ppp) REVERT: A 434 MET cc_start: 0.8952 (ttm) cc_final: 0.8560 (mmt) REVERT: B 405 LEU cc_start: 0.8670 (tp) cc_final: 0.8060 (tp) REVERT: B 434 MET cc_start: 0.9441 (ttt) cc_final: 0.9235 (tmm) REVERT: B 465 GLU cc_start: 0.9638 (tt0) cc_final: 0.9290 (tm-30) REVERT: C 434 MET cc_start: 0.9182 (ttm) cc_final: 0.8907 (ttm) REVERT: C 587 MET cc_start: 0.8312 (mmp) cc_final: 0.8076 (mmm) REVERT: D 233 TYR cc_start: 0.9237 (m-80) cc_final: 0.8867 (m-80) REVERT: D 515 GLU cc_start: 0.8717 (tp30) cc_final: 0.8091 (tp30) REVERT: D 587 MET cc_start: 0.9316 (mtt) cc_final: 0.9109 (mtm) REVERT: E 304 HIS cc_start: 0.7128 (m90) cc_final: 0.6899 (m90) REVERT: F 600 ARG cc_start: 0.5854 (tpm170) cc_final: 0.5568 (tpm170) REVERT: G 442 LEU cc_start: 0.9358 (tp) cc_final: 0.8879 (pp) REVERT: L 73 MET cc_start: 0.9013 (mtm) cc_final: 0.8741 (ptp) REVERT: L 221 PHE cc_start: 0.9415 (t80) cc_final: 0.9116 (t80) REVERT: L 244 MET cc_start: 0.9410 (mmm) cc_final: 0.9128 (mmm) outliers start: 1 outliers final: 1 residues processed: 94 average time/residue: 0.1883 time to fit residues: 29.9798 Evaluate side-chains 78 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 77 time to evaluate : 1.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 317 optimal weight: 6.9990 chunk 278 optimal weight: 40.0000 chunk 222 optimal weight: 2.9990 chunk 266 optimal weight: 8.9990 chunk 145 optimal weight: 9.9990 chunk 85 optimal weight: 9.9990 chunk 197 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 241 optimal weight: 5.9990 chunk 320 optimal weight: 30.0000 chunk 277 optimal weight: 0.6980 overall best weight: 5.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN B 458 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.083932 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2997 r_free = 0.2997 target = 0.057089 restraints weight = 262068.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3026 r_free = 0.3026 target = 0.057805 restraints weight = 160580.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058042 restraints weight = 114794.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058089 restraints weight = 101300.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.058174 restraints weight = 97215.228| |-----------------------------------------------------------------------------| r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.5969 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.097 33389 Z= 0.189 Angle : 0.592 9.244 45297 Z= 0.311 Chirality : 0.044 0.156 5178 Planarity : 0.003 0.035 5940 Dihedral : 4.948 24.073 4470 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 12.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.47 (0.13), residues: 4138 helix: -0.31 (0.19), residues: 809 sheet: 1.32 (0.17), residues: 1007 loop : -1.09 (0.12), residues: 2322 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 592 TYR 0.032 0.002 TYR E 233 PHE 0.014 0.002 PHE A 550 TRP 0.013 0.002 TRP E 206 HIS 0.005 0.001 HIS G 211 Details of bonding type rmsd covalent geometry : bond 0.00403 (33389) covalent geometry : angle 0.59193 (45297) hydrogen bonds : bond 0.03013 ( 1285) hydrogen bonds : angle 5.34712 ( 3528) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8276 Ramachandran restraints generated. 4138 Oldfield, 0 Emsley, 4138 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.917 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 350 MET cc_start: 0.9433 (ppp) cc_final: 0.9180 (ppp) REVERT: B 233 TYR cc_start: 0.9380 (m-10) cc_final: 0.9147 (m-80) REVERT: B 405 LEU cc_start: 0.8875 (tp) cc_final: 0.8624 (tp) REVERT: B 434 MET cc_start: 0.9487 (ttt) cc_final: 0.9218 (tmm) REVERT: B 465 GLU cc_start: 0.9666 (tt0) cc_final: 0.9307 (tm-30) REVERT: C 434 MET cc_start: 0.9177 (ttm) cc_final: 0.8895 (ttm) REVERT: C 587 MET cc_start: 0.8577 (mmp) cc_final: 0.8274 (mmm) REVERT: D 515 GLU cc_start: 0.8815 (tp30) cc_final: 0.8250 (tp30) REVERT: D 587 MET cc_start: 0.9292 (mtt) cc_final: 0.9044 (mtm) REVERT: F 587 MET cc_start: 0.8897 (mmp) cc_final: 0.8689 (mmm) REVERT: F 600 ARG cc_start: 0.5689 (tpm170) cc_final: 0.5403 (tpm170) REVERT: L 244 MET cc_start: 0.9428 (mmm) cc_final: 0.9208 (mmm) outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.2186 time to fit residues: 30.9345 Evaluate side-chains 70 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 70 time to evaluate : 1.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 14 optimal weight: 7.9990 chunk 346 optimal weight: 5.9990 chunk 98 optimal weight: 8.9990 chunk 112 optimal weight: 20.0000 chunk 166 optimal weight: 30.0000 chunk 25 optimal weight: 0.0270 chunk 156 optimal weight: 10.0000 chunk 270 optimal weight: 6.9990 chunk 260 optimal weight: 4.9990 chunk 140 optimal weight: 9.9990 chunk 198 optimal weight: 8.9990 overall best weight: 5.2046 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 389 GLN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.083790 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.056872 restraints weight = 260990.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.057657 restraints weight = 161986.198| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.058091 restraints weight = 118075.481| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.058320 restraints weight = 97354.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.058190 restraints weight = 85798.946| |-----------------------------------------------------------------------------| r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.6347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.089 33389 Z= 0.184 Angle : 0.576 8.211 45297 Z= 0.304 Chirality : 0.044 0.210 5178 Planarity : 0.003 0.050 5940 Dihedral : 4.977 28.514 4470 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 0.11 % Favored : 99.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.31 (0.13), residues: 4138 helix: -0.23 (0.20), residues: 767 sheet: 1.21 (0.16), residues: 1105 loop : -0.94 (0.13), residues: 2266 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG E 297 TYR 0.027 0.002 TYR E 233 PHE 0.013 0.002 PHE A 727 TRP 0.017 0.002 TRP D 346 HIS 0.005 0.001 HIS D 253 Details of bonding type rmsd covalent geometry : bond 0.00389 (33389) covalent geometry : angle 0.57620 (45297) hydrogen bonds : bond 0.03011 ( 1285) hydrogen bonds : angle 5.41297 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4992.30 seconds wall clock time: 87 minutes 37.68 seconds (5257.68 seconds total)