Starting phenix.real_space_refine on Mon Sep 14 20:41:34 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.cif Found real_map, /net/cci-nas-00/data/ceres_data/6psn_20459/09_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.cif" model { file = "/net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6psn_20459/09_2026/6psn_20459.map" } 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): 0.04s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2.1-6174/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 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: 6.63, per 1000 atoms: 0.20 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: 2.68 Conformation dependent library (CDL) restraints added in 1.2 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: 1.21 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: 7.46 Time building geometry restraints manager: 3.58 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: 2.190 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: 0.040 Extract box with map and model: 0.620 Check model and map are aligned: 0.110 Set scattering table: 0.090 Process input model: 30.080 Find NCS groups from input model: 0.680 Set up NCS constraints: 0.080 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:1.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7962 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/Z covalent geometry : bond 0.00612 / 0.30 (33389) covalent geometry : angle 0.93067 / 0.55 (45297) hydrogen bonds : bond 0.22736 / 15.85 ( 1285) hydrogen bonds : angle 9.73061 / 6.87 ( 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 : 1.293 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: 0.8557 (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: 0.8259 (mt-10) REVERT: B 509 ASN cc_start: 0.8840 (t0) cc_final: 0.8589 (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: 0.8656 (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: 0.8137 (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: 0.8793 (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: 0.7099 (tpp) REVERT: G 636 ARG cc_start: 0.6911 (ppp-140) cc_final: 0.6581 (tpp-160) REVERT: G 726 ILE cc_start: 0.2915 (OUTLIER) cc_final: 0.2373 (pt) REVERT: L 73 MET cc_start: 0.9086 (mtm) cc_final: 0.8753 (ptp) REVERT: L 217 PHE cc_start: 0.9195 (t80) cc_final: 0.8857 (t80) REVERT: L 221 PHE cc_start: 0.9524 (t80) cc_final: 0.8925 (t80) outliers start: 24 outliers final: 0 residues processed: 277 average time/residue: 0.2261 time to fit residues: 98.8029 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 : 1.292 ------------------------------------------------------------------------------- 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: 9.9990 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: 5.0006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 584 ASN C 705 ASN D 198 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 228 GLN L 250 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.086574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3079 r_free = 0.3079 target = 0.059069 restraints weight = 254263.332| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.059885 restraints weight = 157039.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.060100 restraints weight = 115578.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.060280 restraints weight = 101706.378| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.060332 restraints weight = 93667.428| |-----------------------------------------------------------------------------| r_work (final): 0.2959 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7677 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.090 33389 Z= 0.200 Angle : 0.622 10.093 45297 Z= 0.332 Chirality : 0.045 0.166 5178 Planarity : 0.004 0.059 5940 Dihedral : 5.213 23.739 4470 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.03 % Allowed : 1.38 % 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: -0.84 (0.13), residues: 4138 helix: -0.36 (0.20), residues: 690 sheet: 0.16 (0.14), residues: 1364 loop : -1.08 (0.13), residues: 2084 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 470 TYR 0.024 0.002 TYR D 542 PHE 0.018 0.002 PHE A 202 TRP 0.013 0.002 TRP A 206 HIS 0.012 0.002 HIS A 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00419 / 0.20 (33389) covalent geometry : angle 0.62241 / 0.33 (45297) hydrogen bonds : bond 0.03905 / 2.66 ( 1285) hydrogen bonds : angle 6.44305 / 4.59 ( 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 131 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 130 time to evaluate : 1.162 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: 0.9334 (m-80) cc_final: 0.9004 (m-10) REVERT: A 434 MET cc_start: 0.9039 (ttm) cc_final: 0.8624 (mmt) REVERT: B 405 LEU cc_start: 0.8632 (tp) cc_final: 0.8106 (tp) REVERT: B 434 MET cc_start: 0.9399 (ttp) cc_final: 0.9115 (ttp) REVERT: B 509 ASN cc_start: 0.8981 (t0) cc_final: 0.8703 (t0) REVERT: B 520 ASP cc_start: 0.8677 (p0) cc_final: 0.8460 (t70) REVERT: C 299 HIS cc_start: 0.8718 (m90) cc_final: 0.7822 (t70) REVERT: C 434 MET cc_start: 0.9037 (ttm) cc_final: 0.8780 (ttm) REVERT: C 587 MET cc_start: 0.8039 (mmp) cc_final: 0.7804 (mmm) REVERT: D 434 MET cc_start: 0.8919 (ttm) cc_final: 0.8683 (ttm) REVERT: D 515 GLU cc_start: 0.8674 (tp30) cc_final: 0.8118 (tp30) REVERT: E 543 GLN cc_start: 0.9301 (OUTLIER) cc_final: 0.9059 (mp10) REVERT: F 256 VAL cc_start: 0.9199 (t) cc_final: 0.8795 (p) REVERT: F 426 ASP cc_start: 0.9025 (m-30) cc_final: 0.8399 (t70) REVERT: F 587 MET cc_start: 0.9199 (mmp) cc_final: 0.8978 (mmm) REVERT: G 515 GLU cc_start: 0.9270 (tp30) cc_final: 0.8584 (tp30) REVERT: L 40 MET cc_start: 0.8096 (ppp) cc_final: 0.7862 (ppp) REVERT: L 73 MET cc_start: 0.9120 (mtm) cc_final: 0.8706 (mmp) REVERT: L 217 PHE cc_start: 0.9226 (t80) cc_final: 0.8931 (t80) REVERT: L 221 PHE cc_start: 0.9401 (t80) cc_final: 0.8930 (t80) REVERT: L 244 MET cc_start: 0.9327 (mmm) cc_final: 0.8842 (mmm) outliers start: 1 outliers final: 0 residues processed: 131 average time/residue: 0.2152 time to fit residues: 46.7434 Evaluate side-chains 87 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 86 time to evaluate : 1.308 ------------------------------------------------------------------------------- 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: 3.9990 chunk 18 optimal weight: 5.9990 chunk 268 optimal weight: 20.0000 chunk 113 optimal weight: 6.9990 chunk 47 optimal weight: 0.1980 chunk 251 optimal weight: 7.9990 chunk 163 optimal weight: 7.9990 chunk 301 optimal weight: 5.9990 chunk 77 optimal weight: 0.8980 chunk 176 optimal weight: 6.9990 chunk 142 optimal weight: 0.6980 overall best weight: 2.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 553 ASN A 616 HIS B 424 GLN ** 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 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 = 0.3784 r_free = 0.3784 target = 0.086352 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.060598 restraints weight = 293082.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.061520 restraints weight = 166474.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.062180 restraints weight = 115893.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.062694 restraints weight = 91101.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3155 r_free = 0.3155 target = 0.062831 restraints weight = 79116.659| |-----------------------------------------------------------------------------| r_work (final): 0.2982 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.3169 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 33389 Z= 0.107 Angle : 0.496 8.012 45297 Z= 0.265 Chirality : 0.043 0.155 5178 Planarity : 0.003 0.053 5940 Dihedral : 4.591 18.992 4470 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % 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: -0.40 (0.13), residues: 4138 helix: 0.34 (0.21), residues: 683 sheet: 0.44 (0.14), residues: 1315 loop : -0.89 (0.13), residues: 2140 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG D 470 TYR 0.015 0.001 TYR L 148 PHE 0.016 0.001 PHE A 727 TRP 0.010 0.001 TRP E 206 HIS 0.004 0.001 HIS A 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00223 / 0.11 (33389) covalent geometry : angle 0.49581 / 0.26 (45297) hydrogen bonds : bond 0.02931 / 2.01 ( 1285) hydrogen bonds : angle 5.55384 / 3.95 ( 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 : 1.248 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 233 TYR cc_start: 0.9353 (m-80) cc_final: 0.8832 (m-10) REVERT: A 350 MET cc_start: 0.9220 (ppp) cc_final: 0.8980 (ppp) REVERT: A 434 MET cc_start: 0.9114 (ttm) cc_final: 0.8648 (mmt) REVERT: B 405 LEU cc_start: 0.8767 (tp) cc_final: 0.8312 (tp) REVERT: B 434 MET cc_start: 0.9365 (ttp) cc_final: 0.9007 (ttp) REVERT: B 465 GLU cc_start: 0.9702 (tt0) cc_final: 0.9491 (tm-30) REVERT: B 509 ASN cc_start: 0.8994 (t0) cc_final: 0.8735 (t0) REVERT: C 299 HIS cc_start: 0.8699 (m90) cc_final: 0.7798 (t-90) REVERT: C 587 MET cc_start: 0.7886 (mmp) cc_final: 0.7684 (mmm) REVERT: D 233 TYR cc_start: 0.9034 (m-80) cc_final: 0.8738 (m-80) REVERT: D 515 GLU cc_start: 0.8752 (tp30) cc_final: 0.8065 (tp30) REVERT: F 426 ASP cc_start: 0.9028 (m-30) cc_final: 0.8470 (t70) REVERT: G 434 MET cc_start: 0.9053 (ttm) cc_final: 0.8714 (tmm) REVERT: G 442 LEU cc_start: 0.9193 (tp) cc_final: 0.8858 (pp) REVERT: G 515 GLU cc_start: 0.9247 (tp30) cc_final: 0.8544 (tp30) REVERT: L 40 MET cc_start: 0.8215 (ppp) cc_final: 0.7968 (ppp) REVERT: L 73 MET cc_start: 0.9105 (mtm) cc_final: 0.8696 (mmp) REVERT: L 217 PHE cc_start: 0.9371 (t80) cc_final: 0.9075 (t80) REVERT: L 221 PHE cc_start: 0.9455 (t80) cc_final: 0.9006 (t80) REVERT: L 244 MET cc_start: 0.9388 (mmm) cc_final: 0.8892 (mmm) outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.2288 time to fit residues: 40.9534 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 : 1.317 ------------------------------------------------------------------------------- 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: 2.9990 chunk 352 optimal weight: 50.0000 chunk 10 optimal weight: 8.9990 chunk 232 optimal weight: 0.8980 chunk 195 optimal weight: 7.9990 chunk 287 optimal weight: 0.2980 chunk 14 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 310 optimal weight: 10.0000 chunk 215 optimal weight: 6.9990 chunk 222 optimal weight: 0.3980 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 705 ASN B 299 HIS ** C 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 483 GLN E 304 HIS ** 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 L 250 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.086694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058794 restraints weight = 282932.665| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.059704 restraints weight = 164264.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.060298 restraints weight = 117129.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.060581 restraints weight = 95539.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.060948 restraints weight = 84915.253| |-----------------------------------------------------------------------------| r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3643 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= 0.108 Angle : 0.482 6.766 45297 Z= 0.256 Chirality : 0.043 0.156 5178 Planarity : 0.003 0.036 5940 Dihedral : 4.403 16.285 4470 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.00 % Allowed : 1.14 % Favored : 98.86 % 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: -0.09 (0.13), residues: 4138 helix: 0.18 (0.21), residues: 726 sheet: 1.20 (0.15), residues: 1203 loop : -0.87 (0.13), residues: 2209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG F 359 TYR 0.014 0.001 TYR G 233 PHE 0.013 0.001 PHE A 202 TRP 0.008 0.001 TRP E 206 HIS 0.004 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00231 / 0.11 (33389) covalent geometry : angle 0.48240 / 0.26 (45297) hydrogen bonds : bond 0.02655 / 1.82 ( 1285) hydrogen bonds : angle 5.22019 / 3.72 ( 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 105 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 105 time to evaluate : 1.145 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: 0.9477 (m-80) cc_final: 0.9018 (m-80) REVERT: A 350 MET cc_start: 0.9347 (ppp) cc_final: 0.9113 (ppp) REVERT: A 434 MET cc_start: 0.9125 (ttm) cc_final: 0.8614 (mmt) REVERT: B 405 LEU cc_start: 0.8628 (tp) cc_final: 0.8136 (tp) REVERT: B 434 MET cc_start: 0.9362 (ttp) cc_final: 0.9085 (ttp) REVERT: B 447 GLN cc_start: 0.9216 (mt0) cc_final: 0.8879 (tm-30) REVERT: B 509 ASN cc_start: 0.9018 (t0) cc_final: 0.8749 (t0) REVERT: C 299 HIS cc_start: 0.8734 (m90) cc_final: 0.7898 (t-170) REVERT: C 587 MET cc_start: 0.7956 (mmp) cc_final: 0.7752 (mmm) REVERT: D 233 TYR cc_start: 0.9158 (m-80) cc_final: 0.8571 (m-80) REVERT: D 515 GLU cc_start: 0.8775 (tp30) cc_final: 0.8052 (tp30) REVERT: D 587 MET cc_start: 0.8899 (mtt) cc_final: 0.8599 (mtm) REVERT: F 426 ASP cc_start: 0.8995 (m-30) cc_final: 0.8378 (t70) REVERT: G 515 GLU cc_start: 0.9222 (tp30) cc_final: 0.8481 (tp30) REVERT: L 217 PHE cc_start: 0.9352 (t80) cc_final: 0.9071 (t80) REVERT: L 221 PHE cc_start: 0.9475 (t80) cc_final: 0.9048 (t80) REVERT: L 244 MET cc_start: 0.9389 (mmm) cc_final: 0.8862 (mmm) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.2251 time to fit residues: 38.7056 Evaluate side-chains 80 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 80 time to evaluate : 1.312 ------------------------------------------------------------------------------- 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: 10.0000 chunk 297 optimal weight: 20.0000 chunk 257 optimal weight: 0.0770 chunk 6 optimal weight: 1.9990 chunk 330 optimal weight: 40.0000 chunk 114 optimal weight: 6.9990 chunk 191 optimal weight: 7.9990 chunk 405 optimal weight: 20.0000 chunk 406 optimal weight: 3.9990 chunk 199 optimal weight: 10.0000 overall best weight: 4.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 499 ASN B 403 GLN B 499 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN C 693 ASN D 280 GLN D 705 ASN E 299 HIS E 304 HIS ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 705 ASN G 424 GLN ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 250 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- 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 = 36)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.057878 restraints weight = 263930.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3061 r_free = 0.3061 target = 0.058587 restraints weight = 164300.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.058955 restraints weight = 121797.357| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 19)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.059246 restraints weight = 99464.941| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.059520 restraints weight = 88529.115| |-----------------------------------------------------------------------------| r_work (final): 0.2921 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.4372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 33389 Z= 0.154 Angle : 0.538 8.900 45297 Z= 0.285 Chirality : 0.043 0.157 5178 Planarity : 0.003 0.047 5940 Dihedral : 4.661 17.445 4470 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % 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: -0.24 (0.13), residues: 4138 helix: 0.01 (0.20), residues: 775 sheet: 1.26 (0.15), residues: 1161 loop : -1.04 (0.13), residues: 2202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.000 ARG A 200 TYR 0.015 0.002 TYR B 542 PHE 0.022 0.001 PHE A 202 TRP 0.012 0.002 TRP E 206 HIS 0.005 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00330 / 0.15 (33389) covalent geometry : angle 0.53772 / 0.29 (45297) hydrogen bonds : bond 0.02897 / 1.97 ( 1285) hydrogen bonds : angle 5.23718 / 3.74 ( 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 96 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.346 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: 0.9447 (ppp) cc_final: 0.9201 (ppp) REVERT: A 434 MET cc_start: 0.9044 (ttm) cc_final: 0.8602 (mmt) REVERT: B 405 LEU cc_start: 0.8773 (tp) cc_final: 0.8197 (tp) REVERT: B 434 MET cc_start: 0.9412 (ttp) cc_final: 0.9147 (ttp) REVERT: B 509 ASN cc_start: 0.9105 (t0) cc_final: 0.8845 (t0) REVERT: C 434 MET cc_start: 0.9078 (ttm) cc_final: 0.8803 (ttm) REVERT: D 515 GLU cc_start: 0.8750 (tp30) cc_final: 0.8133 (tp30) REVERT: D 587 MET cc_start: 0.9081 (mtt) cc_final: 0.8797 (mtm) REVERT: F 426 ASP cc_start: 0.9024 (m-30) cc_final: 0.8759 (p0) REVERT: G 434 MET cc_start: 0.9054 (ttm) cc_final: 0.8742 (tmm) REVERT: G 442 LEU cc_start: 0.9318 (tp) cc_final: 0.8851 (pp) REVERT: G 515 GLU cc_start: 0.9232 (tp30) cc_final: 0.8338 (tp30) REVERT: L 221 PHE cc_start: 0.9407 (t80) cc_final: 0.9052 (t80) REVERT: L 244 MET cc_start: 0.9423 (mmm) cc_final: 0.9143 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2205 time to fit residues: 35.1102 Evaluate side-chains 76 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.211 ------------------------------------------------------------------------------- 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: 0.9990 chunk 300 optimal weight: 9.9990 chunk 263 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 157 optimal weight: 50.0000 chunk 219 optimal weight: 30.0000 chunk 89 optimal weight: 6.9990 chunk 49 optimal weight: 6.9990 chunk 359 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 153 optimal weight: 7.9990 overall best weight: 4.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 304 HIS A 458 ASN B 299 HIS B 389 GLN B 541 GLN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN D 693 ASN E 304 HIS F 403 GLN G 336 HIS ** 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 = 0.3712 r_free = 0.3712 target = 0.085039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.057038 restraints weight = 263036.705| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.057802 restraints weight = 157828.037| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.058423 restraints weight = 115724.305| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.058696 restraints weight = 94191.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.058945 restraints weight = 84431.636| |-----------------------------------------------------------------------------| r_work (final): 0.2903 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7810 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 33389 Z= 0.158 Angle : 0.538 8.785 45297 Z= 0.285 Chirality : 0.043 0.149 5178 Planarity : 0.003 0.035 5940 Dihedral : 4.721 18.179 4470 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.00 % Allowed : 1.27 % Favored : 98.73 % 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: -0.22 (0.13), residues: 4138 helix: -0.06 (0.20), residues: 775 sheet: 1.31 (0.15), residues: 1133 loop : -0.98 (0.13), residues: 2230 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 200 TYR 0.018 0.001 TYR E 233 PHE 0.014 0.001 PHE A 202 TRP 0.011 0.002 TRP E 206 HIS 0.011 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.16 (33389) covalent geometry : angle 0.53781 / 0.28 (45297) hydrogen bonds : bond 0.02845 / 1.95 ( 1285) hydrogen bonds : angle 5.27660 / 3.77 ( 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 95 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 1.201 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: A 350 MET cc_start: 0.9464 (ppp) cc_final: 0.9241 (ppp) REVERT: A 434 MET cc_start: 0.9089 (ttm) cc_final: 0.8579 (mmt) REVERT: B 405 LEU cc_start: 0.8753 (tp) cc_final: 0.8165 (tp) REVERT: B 434 MET cc_start: 0.9487 (ttp) cc_final: 0.9121 (ttp) REVERT: C 434 MET cc_start: 0.9097 (ttm) cc_final: 0.8810 (ttm) REVERT: D 515 GLU cc_start: 0.8735 (tp30) cc_final: 0.8144 (tp30) REVERT: D 587 MET cc_start: 0.9128 (mtt) cc_final: 0.8900 (mtm) REVERT: G 434 MET cc_start: 0.9085 (ttm) cc_final: 0.8734 (tmm) REVERT: G 442 LEU cc_start: 0.9272 (tp) cc_final: 0.8671 (pp) REVERT: G 515 GLU cc_start: 0.9241 (tp30) cc_final: 0.8314 (tp30) REVERT: L 217 PHE cc_start: 0.9353 (t80) cc_final: 0.9126 (t80) REVERT: L 221 PHE cc_start: 0.9370 (t80) cc_final: 0.9075 (t80) REVERT: L 244 MET cc_start: 0.9425 (mmm) cc_final: 0.9171 (mmm) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.2286 time to fit residues: 35.9738 Evaluate side-chains 76 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.289 ------------------------------------------------------------------------------- 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: 40.0000 chunk 125 optimal weight: 7.9990 chunk 172 optimal weight: 7.9990 chunk 241 optimal weight: 5.9990 chunk 395 optimal weight: 8.9990 chunk 49 optimal weight: 3.9990 chunk 101 optimal weight: 8.9990 chunk 62 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 overall best weight: 2.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN C 553 ASN D 541 GLN D 553 ASN E 304 HIS ** 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 = 0.3729 r_free = 0.3729 target = 0.085545 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.059073 restraints weight = 266318.585| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.059941 restraints weight = 157675.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.060145 restraints weight = 109765.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.060184 restraints weight = 96856.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.060184 restraints weight = 90916.212| |-----------------------------------------------------------------------------| r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.4987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.054 33389 Z= 0.105 Angle : 0.484 6.462 45297 Z= 0.256 Chirality : 0.043 0.152 5178 Planarity : 0.003 0.033 5940 Dihedral : 4.447 19.196 4470 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 0.00 % Allowed : 0.62 % Favored : 99.38 % 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: -0.13 (0.13), residues: 4138 helix: 0.14 (0.20), residues: 768 sheet: 1.39 (0.15), residues: 1112 loop : -0.95 (0.13), residues: 2258 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.026 0.001 TYR E 233 PHE 0.012 0.001 PHE C 493 TRP 0.010 0.002 TRP E 206 HIS 0.004 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00227 / 0.11 (33389) covalent geometry : angle 0.48352 / 0.26 (45297) hydrogen bonds : bond 0.02562 / 1.76 ( 1285) hydrogen bonds : angle 5.09075 / 3.64 ( 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 96 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 96 time to evaluate : 1.211 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 237 GLU cc_start: 0.9436 (pt0) cc_final: 0.9089 (pp20) REVERT: A 350 MET cc_start: 0.9434 (ppp) cc_final: 0.9164 (ppp) REVERT: A 434 MET cc_start: 0.8983 (ttm) cc_final: 0.8635 (mmt) REVERT: B 405 LEU cc_start: 0.8712 (tp) cc_final: 0.8194 (tp) REVERT: B 434 MET cc_start: 0.9506 (ttp) cc_final: 0.9114 (ttp) REVERT: B 509 ASN cc_start: 0.9222 (t0) cc_final: 0.8968 (t0) REVERT: C 434 MET cc_start: 0.9132 (ttm) cc_final: 0.8868 (ttm) REVERT: C 587 MET cc_start: 0.8110 (mmp) cc_final: 0.7907 (mmm) REVERT: D 515 GLU cc_start: 0.8752 (tp30) cc_final: 0.8099 (tp30) REVERT: D 587 MET cc_start: 0.9262 (mtt) cc_final: 0.9023 (mtm) REVERT: G 434 MET cc_start: 0.9098 (ttm) cc_final: 0.8854 (tmm) REVERT: G 515 GLU cc_start: 0.9271 (tp30) cc_final: 0.8306 (tp30) REVERT: L 73 MET cc_start: 0.9044 (mtm) cc_final: 0.8770 (ptp) REVERT: L 217 PHE cc_start: 0.9368 (t80) cc_final: 0.9157 (t80) REVERT: L 221 PHE cc_start: 0.9404 (t80) cc_final: 0.9090 (t80) REVERT: L 244 MET cc_start: 0.9430 (mmm) cc_final: 0.9166 (mmm) outliers start: 0 outliers final: 0 residues processed: 96 average time/residue: 0.2058 time to fit residues: 33.1669 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 : 1.509 ------------------------------------------------------------------------------- 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: 20.0000 chunk 390 optimal weight: 7.9990 chunk 122 optimal weight: 10.0000 chunk 146 optimal weight: 9.9990 chunk 242 optimal weight: 10.0000 chunk 333 optimal weight: 6.9990 chunk 201 optimal weight: 0.5980 chunk 65 optimal weight: 10.0000 chunk 136 optimal weight: 7.9990 chunk 384 optimal weight: 7.9990 chunk 323 optimal weight: 5.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 328 ASN A 424 GLN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 ASN A 564 ASN B 458 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN ** E 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: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.083763 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.056851 restraints weight = 266924.871| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057462 restraints weight = 162090.633| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057462 restraints weight = 123297.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057462 restraints weight = 123297.601| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.057462 restraints weight = 123297.601| |-----------------------------------------------------------------------------| r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.5645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.111 33389 Z= 0.217 Angle : 0.621 10.517 45297 Z= 0.327 Chirality : 0.044 0.176 5178 Planarity : 0.004 0.038 5940 Dihedral : 5.087 19.945 4470 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 13.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % 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: -0.48 (0.13), residues: 4138 helix: -0.37 (0.19), residues: 809 sheet: 1.15 (0.16), residues: 1105 loop : -1.09 (0.13), residues: 2224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 659 TYR 0.031 0.002 TYR E 233 PHE 0.020 0.002 PHE A 202 TRP 0.014 0.002 TRP E 206 HIS 0.006 0.001 HIS G 211 Details of bonding type rmsd/Z covalent geometry : bond 0.00461 / 0.22 (33389) covalent geometry : angle 0.62058 / 0.33 (45297) hydrogen bonds : bond 0.03187 / 2.17 ( 1285) hydrogen bonds : angle 5.47648 / 3.91 ( 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 85 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 1.201 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: A 350 MET cc_start: 0.9474 (ppp) cc_final: 0.9179 (ppp) REVERT: A 434 MET cc_start: 0.9163 (ttm) cc_final: 0.8559 (mmt) REVERT: B 405 LEU cc_start: 0.8883 (tp) cc_final: 0.8680 (tp) REVERT: B 434 MET cc_start: 0.9562 (ttp) cc_final: 0.9298 (ttt) REVERT: C 434 MET cc_start: 0.9178 (ttm) cc_final: 0.8907 (ttm) REVERT: C 587 MET cc_start: 0.8415 (mmp) cc_final: 0.8120 (mmm) REVERT: D 515 GLU cc_start: 0.8919 (tp30) cc_final: 0.8343 (tp30) REVERT: L 244 MET cc_start: 0.9455 (mmm) cc_final: 0.9227 (mmm) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2318 time to fit residues: 32.6798 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 : 1.330 ------------------------------------------------------------------------------- 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: 7.9990 chunk 154 optimal weight: 0.6980 chunk 135 optimal weight: 5.9990 chunk 193 optimal weight: 5.9990 chunk 215 optimal weight: 3.9990 chunk 275 optimal weight: 0.6980 chunk 334 optimal weight: 0.1980 chunk 246 optimal weight: 10.0000 chunk 136 optimal weight: 40.0000 chunk 190 optimal weight: 1.9990 chunk 138 optimal weight: 3.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN B 299 HIS 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.085377 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.059687 restraints weight = 269829.676| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.060466 restraints weight = 162282.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.060850 restraints weight = 120161.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061049 restraints weight = 97985.180| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.061015 restraints weight = 87466.704| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.5587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.047 33389 Z= 0.090 Angle : 0.485 7.246 45297 Z= 0.257 Chirality : 0.044 0.175 5178 Planarity : 0.003 0.034 5940 Dihedral : 4.487 22.757 4470 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.00 % Allowed : 0.24 % Favored : 99.76 % 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: -0.10 (0.13), residues: 4138 helix: 0.10 (0.20), residues: 768 sheet: 1.45 (0.16), residues: 1035 loop : -0.85 (0.13), residues: 2335 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 297 TYR 0.024 0.001 TYR E 233 PHE 0.011 0.001 PHE E 493 TRP 0.014 0.002 TRP E 226 HIS 0.005 0.001 HIS A 304 Details of bonding type rmsd/Z covalent geometry : bond 0.00195 / 0.09 (33389) covalent geometry : angle 0.48500 / 0.26 (45297) hydrogen bonds : bond 0.02539 / 1.74 ( 1285) hydrogen bonds : angle 5.10252 / 3.64 ( 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 88 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 88 time to evaluate : 1.271 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 350 MET cc_start: 0.9366 (ppp) cc_final: 0.9150 (ppp) REVERT: A 434 MET cc_start: 0.8988 (ttm) cc_final: 0.8644 (mmt) REVERT: B 405 LEU cc_start: 0.8754 (tp) cc_final: 0.8167 (tp) REVERT: B 434 MET cc_start: 0.9521 (ttp) cc_final: 0.9102 (ttp) REVERT: B 509 ASN cc_start: 0.9209 (t0) cc_final: 0.8924 (t0) REVERT: C 434 MET cc_start: 0.9162 (ttm) cc_final: 0.8900 (ttm) REVERT: C 587 MET cc_start: 0.8253 (mmp) cc_final: 0.8052 (mmm) REVERT: D 515 GLU cc_start: 0.8754 (tp30) cc_final: 0.8099 (tp30) REVERT: D 587 MET cc_start: 0.9317 (mtt) cc_final: 0.9091 (mtm) REVERT: L 73 MET cc_start: 0.9037 (mtm) cc_final: 0.8619 (mmp) REVERT: L 221 PHE cc_start: 0.9433 (t80) cc_final: 0.9109 (t80) REVERT: L 244 MET cc_start: 0.9423 (mmm) cc_final: 0.9189 (mmm) outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.2371 time to fit residues: 34.3852 Evaluate side-chains 76 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 1.264 ------------------------------------------------------------------------------- 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: 7.9990 chunk 278 optimal weight: 20.0000 chunk 222 optimal weight: 20.0000 chunk 266 optimal weight: 7.9990 chunk 145 optimal weight: 10.0000 chunk 85 optimal weight: 7.9990 chunk 197 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 241 optimal weight: 2.9990 chunk 320 optimal weight: 6.9990 chunk 277 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 458 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN ** 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 = 0.3691 r_free = 0.3691 target = 0.084376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3013 r_free = 0.3013 target = 0.057551 restraints weight = 258897.129| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3038 r_free = 0.3038 target = 0.058210 restraints weight = 160051.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.058705 restraints weight = 120575.177| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3063 r_free = 0.3063 target = 0.059002 restraints weight = 96982.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 15)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.059177 restraints weight = 86083.838| |-----------------------------------------------------------------------------| r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.081 33389 Z= 0.160 Angle : 0.544 7.719 45297 Z= 0.287 Chirality : 0.043 0.155 5178 Planarity : 0.003 0.035 5940 Dihedral : 4.712 22.843 4470 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 10.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: -0.17 (0.13), residues: 4138 helix: 0.00 (0.20), residues: 767 sheet: 1.40 (0.16), residues: 1035 loop : -0.88 (0.13), residues: 2336 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 200 TYR 0.029 0.002 TYR E 233 PHE 0.014 0.001 PHE A 202 TRP 0.012 0.001 TRP D 346 HIS 0.006 0.001 HIS G 336 Details of bonding type rmsd/Z covalent geometry : bond 0.00342 / 0.16 (33389) covalent geometry : angle 0.54382 / 0.29 (45297) hydrogen bonds : bond 0.02808 / 1.91 ( 1285) hydrogen bonds : angle 5.24894 / 3.76 ( 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 82 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 82 time to evaluate : 1.359 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: 0.9477 (ppp) cc_final: 0.9204 (ppp) REVERT: B 405 LEU cc_start: 0.8762 (tp) cc_final: 0.8162 (tp) REVERT: B 434 MET cc_start: 0.9544 (ttp) cc_final: 0.9249 (ttt) REVERT: C 434 MET cc_start: 0.9109 (ttm) cc_final: 0.8841 (ttm) REVERT: D 515 GLU cc_start: 0.8761 (tp30) cc_final: 0.8158 (tp30) REVERT: D 587 MET cc_start: 0.9307 (mtt) cc_final: 0.9030 (mtm) REVERT: L 221 PHE cc_start: 0.9382 (t80) cc_final: 0.9126 (t80) REVERT: L 244 MET cc_start: 0.9411 (mmm) cc_final: 0.9160 (mmm) outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 0.2317 time to fit residues: 31.6485 Evaluate side-chains 71 residues out of total 3705 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 1.464 ------------------------------------------------------------------------------- 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: 30.0000 chunk 346 optimal weight: 9.9990 chunk 98 optimal weight: 4.9990 chunk 112 optimal weight: 20.0000 chunk 166 optimal weight: 40.0000 chunk 25 optimal weight: 0.3980 chunk 156 optimal weight: 30.0000 chunk 270 optimal weight: 0.5980 chunk 260 optimal weight: 4.9990 chunk 140 optimal weight: 10.0000 chunk 198 optimal weight: 10.0000 overall best weight: 4.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 277 GLN ** 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 = 0.3685 r_free = 0.3685 target = 0.084069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.057329 restraints weight = 262989.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3034 r_free = 0.3034 target = 0.058111 restraints weight = 157666.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058496 restraints weight = 113497.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058496 restraints weight = 94511.115| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.058496 restraints weight = 94511.116| |-----------------------------------------------------------------------------| r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7809 moved from start: 0.6251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.077 33389 Z= 0.154 Angle : 0.541 8.148 45297 Z= 0.286 Chirality : 0.044 0.190 5178 Planarity : 0.003 0.035 5940 Dihedral : 4.800 26.690 4470 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: -0.32 (0.13), residues: 4138 helix: -0.08 (0.20), residues: 767 sheet: 1.12 (0.17), residues: 1042 loop : -0.89 (0.13), residues: 2329 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 297 TYR 0.027 0.002 TYR E 233 PHE 0.012 0.001 PHE A 727 TRP 0.015 0.002 TRP D 346 HIS 0.004 0.001 HIS D 253 Details of bonding type rmsd/Z covalent geometry : bond 0.00328 / 0.15 (33389) covalent geometry : angle 0.54094 / 0.29 (45297) hydrogen bonds : bond 0.02827 / 1.92 ( 1285) hydrogen bonds : angle 5.29132 / 3.78 ( 3528) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4933.08 seconds wall clock time: 87 minutes 0.27 seconds (5220.27 seconds total)