Starting phenix.real_space_refine (version: dev) on Fri Apr 8 07:05:33 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/04_2022/6psn_20459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/04_2022/6psn_20459.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/04_2022/6psn_20459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/04_2022/6psn_20459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/04_2022/6psn_20459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/04_2022/6psn_20459.pdb" } 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 ------------------------------------------------------------------------------- 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 Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "A ARG 449": "NH1" <-> "NH2" Residue "B ARG 449": "NH1" <-> "NH2" Residue "C ARG 449": "NH1" <-> "NH2" Residue "D ARG 449": "NH1" <-> "NH2" Residue "E ARG 449": "NH1" <-> "NH2" Residue "F ARG 449": "NH1" <-> "NH2" Residue "G ARG 449": "NH1" <-> "NH2" Time to flip residues: 0.09s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 21, 'TRANS': 539, 'PCIS': 1} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'GLU:plan': 1, 'ASP: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: {'PTRANS': 5, 'TRANS': 213, 'PCIS': 1} 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: 17.60, per 1000 atoms: 0.54 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 - 3.50 Amino acid : False - 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: 12.11 Conformation dependent library (CDL) restraints added in 5.0 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: 2.50 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: 15.88 Time building geometry restraints manager: 13.05 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: 98.53 - 105.66: 637 105.66 - 112.78: 18052 112.78 - 119.91: 10964 119.91 - 127.03: 15359 127.03 - 134.16: 285 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 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 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. 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: 1.460 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.040 Extract box with map and model: 9.890 Check model and map are aligned: 0.450 Convert atoms to be neutral: 0.290 Process input model: 84.430 Find NCS groups from input model: 2.660 Set up NCS constraints: 0.280 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:2.830 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 102.390 ------------------------------------------------------------------------------- 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= 0.401 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 : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. 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 *********************** 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 fitting. rotamer outliers: 24 poor density : 253 time to evaluate : 3.751 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 outliers start: 24 outliers final: 0 residues processed: 277 average time/residue: 0.4861 time to fit residues: 212.5503 Evaluate side-chains 103 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 3.831 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.3468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 349 optimal weight: 20.0000 chunk 313 optimal weight: 8.9990 chunk 174 optimal weight: 3.9990 chunk 107 optimal weight: 10.0000 chunk 211 optimal weight: 20.0000 chunk 167 optimal weight: 1.9990 chunk 324 optimal weight: 40.0000 chunk 125 optimal weight: 30.0000 chunk 197 optimal weight: 10.0000 chunk 241 optimal weight: 6.9990 chunk 375 optimal weight: 6.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 209 ASN A 263 HIS A 336 HIS A 389 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 ASN A 584 ASN B 424 GLN B 553 ASN B 564 ASN B 584 ASN C 198 ASN C 424 GLN C 553 ASN C 584 ASN C 705 ASN D 198 ASN D 424 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 564 ASN D 584 ASN E 198 ASN E 304 HIS E 553 ASN E 564 ASN E 584 ASN F 198 ASN F 389 GLN F 564 ASN F 584 ASN F 705 ASN G 198 ASN G 424 GLN ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 584 ASN ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN ** L 228 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 250 GLN Total number of N/Q/H flips: 34 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.104 33389 Z= 0.323 Angle : 0.674 12.202 45297 Z= 0.359 Chirality : 0.045 0.265 5178 Planarity : 0.005 0.060 5940 Dihedral : 5.388 26.732 4470 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 16.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.12), residues: 4138 helix: -0.54 (0.20), residues: 725 sheet: 0.20 (0.14), residues: 1195 loop : -1.42 (0.12), residues: 2218 *********************** 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 121 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 117 time to evaluate : 3.886 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 outliers start: 4 outliers final: 3 residues processed: 121 average time/residue: 0.4626 time to fit residues: 94.8518 Evaluate side-chains 78 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 4.067 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2963 time to fit residues: 7.1665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 208 optimal weight: 8.9990 chunk 116 optimal weight: 8.9990 chunk 312 optimal weight: 0.8980 chunk 256 optimal weight: 20.0000 chunk 103 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 406 optimal weight: 0.9980 chunk 335 optimal weight: 1.9990 chunk 373 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 302 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN B 299 HIS B 403 GLN B 424 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 424 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 ASN D 705 ASN E 304 HIS F 553 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 553 ASN ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 ASN L 186 GLN L 228 GLN L 250 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8054 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.045 33389 Z= 0.137 Angle : 0.492 6.895 45297 Z= 0.261 Chirality : 0.043 0.162 5178 Planarity : 0.003 0.042 5940 Dihedral : 4.701 20.640 4470 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.13), residues: 4138 helix: -0.25 (0.20), residues: 767 sheet: 0.80 (0.15), residues: 1210 loop : -1.30 (0.13), residues: 2161 *********************** 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 102 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 102 time to evaluate : 3.881 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 outliers start: 0 outliers final: 0 residues processed: 102 average time/residue: 0.4752 time to fit residues: 81.2925 Evaluate side-chains 78 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 78 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 372 optimal weight: 0.9990 chunk 283 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 41 optimal weight: 0.1980 chunk 179 optimal weight: 20.0000 chunk 252 optimal weight: 9.9990 chunk 377 optimal weight: 10.0000 chunk 400 optimal weight: 1.9990 chunk 197 optimal weight: 5.9990 chunk 358 optimal weight: 6.9990 chunk 107 optimal weight: 9.9990 overall best weight: 3.2388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN C 564 ASN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 553 ASN G 424 GLN ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 564 ASN ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN L 250 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.4077 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= 0.193 Angle : 0.516 7.794 45297 Z= 0.274 Chirality : 0.043 0.150 5178 Planarity : 0.003 0.032 5940 Dihedral : 4.667 19.310 4470 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.13), residues: 4138 helix: -0.15 (0.20), residues: 768 sheet: 1.13 (0.15), residues: 1175 loop : -1.11 (0.13), residues: 2195 *********************** 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 93 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 4.082 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 outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 0.4866 time to fit residues: 76.1954 Evaluate side-chains 74 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 3.897 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 333 optimal weight: 40.0000 chunk 227 optimal weight: 10.0000 chunk 5 optimal weight: 0.0970 chunk 297 optimal weight: 20.0000 chunk 165 optimal weight: 5.9990 chunk 341 optimal weight: 6.9990 chunk 276 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 204 optimal weight: 0.4980 chunk 359 optimal weight: 9.9990 chunk 100 optimal weight: 40.0000 overall best weight: 4.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 299 HIS B 389 GLN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN D 280 GLN D 693 ASN E 304 HIS E 403 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN L 250 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.4735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.087 33389 Z= 0.230 Angle : 0.545 8.428 45297 Z= 0.290 Chirality : 0.043 0.155 5178 Planarity : 0.003 0.037 5940 Dihedral : 4.834 18.883 4470 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.48 (0.13), residues: 4138 helix: -0.34 (0.19), residues: 810 sheet: 1.37 (0.15), residues: 1112 loop : -1.24 (0.12), residues: 2216 *********************** 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 98 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 4.066 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 outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.5002 time to fit residues: 83.1750 Evaluate side-chains 70 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 4.091 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.8612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 134 optimal weight: 4.9990 chunk 360 optimal weight: 10.0000 chunk 79 optimal weight: 10.0000 chunk 234 optimal weight: 9.9990 chunk 98 optimal weight: 2.9990 chunk 400 optimal weight: 20.0000 chunk 332 optimal weight: 10.0000 chunk 185 optimal weight: 5.9990 chunk 33 optimal weight: 2.9990 chunk 132 optimal weight: 8.9990 chunk 210 optimal weight: 0.5980 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 304 HIS ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 541 GLN B 565 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN D 561 ASN D 584 ASN ** E 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.079 33389 Z= 0.187 Angle : 0.509 6.897 45297 Z= 0.269 Chirality : 0.043 0.166 5178 Planarity : 0.003 0.036 5940 Dihedral : 4.669 18.498 4470 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 13.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.39 (0.13), residues: 4138 helix: -0.24 (0.19), residues: 817 sheet: 1.29 (0.15), residues: 1189 loop : -1.20 (0.13), residues: 2132 *********************** 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 91 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 91 time to evaluate : 3.992 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 outliers start: 0 outliers final: 0 residues processed: 91 average time/residue: 0.4608 time to fit residues: 72.3671 Evaluate side-chains 71 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.765 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 386 optimal weight: 50.0000 chunk 45 optimal weight: 50.0000 chunk 228 optimal weight: 7.9990 chunk 292 optimal weight: 30.0000 chunk 226 optimal weight: 9.9990 chunk 337 optimal weight: 7.9990 chunk 223 optimal weight: 20.0000 chunk 399 optimal weight: 7.9990 chunk 249 optimal weight: 5.9990 chunk 243 optimal weight: 0.5980 chunk 184 optimal weight: 40.0000 overall best weight: 6.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 424 GLN A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN B 292 ASN B 299 HIS B 389 GLN ** B 458 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 280 GLN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 304 HIS ** E 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 454 GLN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 424 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN L 248 ASN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8167 moved from start: 0.5871 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.114 33389 Z= 0.311 Angle : 0.642 9.303 45297 Z= 0.340 Chirality : 0.044 0.163 5178 Planarity : 0.004 0.038 5940 Dihedral : 5.373 20.772 4470 Min Nonbonded Distance : 2.063 Molprobity Statistics. All-atom Clashscore : 20.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.64 (0.13), residues: 4138 helix: -0.73 (0.18), residues: 809 sheet: 1.06 (0.14), residues: 1258 loop : -1.25 (0.13), residues: 2071 *********************** 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 87 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 87 time to evaluate : 4.891 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 outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.5193 time to fit residues: 75.9707 Evaluate side-chains 68 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 3.791 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 246 optimal weight: 5.9990 chunk 159 optimal weight: 2.9990 chunk 238 optimal weight: 7.9990 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 0.0770 chunk 253 optimal weight: 10.0000 chunk 271 optimal weight: 6.9990 chunk 197 optimal weight: 20.0000 chunk 37 optimal weight: 9.9990 chunk 313 optimal weight: 10.0000 overall best weight: 4.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 403 GLN E 454 GLN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 146 ASN L 186 GLN L 228 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.5997 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= 0.214 Angle : 0.538 7.407 45297 Z= 0.286 Chirality : 0.043 0.171 5178 Planarity : 0.003 0.037 5940 Dihedral : 4.969 24.463 4470 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 15.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.41 (0.13), residues: 4138 helix: -0.45 (0.19), residues: 810 sheet: 1.33 (0.15), residues: 1153 loop : -1.13 (0.13), residues: 2175 *********************** 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 84 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 3.961 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 outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.4891 time to fit residues: 70.3417 Evaluate side-chains 68 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 68 time to evaluate : 3.890 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 362 optimal weight: 3.9990 chunk 382 optimal weight: 0.9980 chunk 348 optimal weight: 10.0000 chunk 371 optimal weight: 0.6980 chunk 223 optimal weight: 2.9990 chunk 161 optimal weight: 30.0000 chunk 291 optimal weight: 6.9990 chunk 114 optimal weight: 10.0000 chunk 336 optimal weight: 0.7980 chunk 351 optimal weight: 20.0000 chunk 370 optimal weight: 20.0000 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 705 ASN B 565 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN D 584 ASN E 280 GLN E 454 GLN F 424 GLN F 454 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.5994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 33389 Z= 0.129 Angle : 0.482 7.691 45297 Z= 0.254 Chirality : 0.043 0.155 5178 Planarity : 0.003 0.038 5940 Dihedral : 4.508 23.055 4470 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 11.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4138 helix: -0.11 (0.20), residues: 810 sheet: 1.61 (0.15), residues: 1119 loop : -1.07 (0.13), residues: 2209 *********************** 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 fitting. rotamer outliers: 0 poor density : 88 time to evaluate : 3.939 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 outliers start: 0 outliers final: 0 residues processed: 88 average time/residue: 0.4956 time to fit residues: 74.7416 Evaluate side-chains 71 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.855 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 244 optimal weight: 7.9990 chunk 393 optimal weight: 6.9990 chunk 239 optimal weight: 20.0000 chunk 186 optimal weight: 9.9990 chunk 273 optimal weight: 0.8980 chunk 412 optimal weight: 6.9990 chunk 379 optimal weight: 20.0000 chunk 328 optimal weight: 0.0010 chunk 34 optimal weight: 6.9990 chunk 253 optimal weight: 3.9990 chunk 201 optimal weight: 8.9990 overall best weight: 3.7792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 328 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 198 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 454 GLN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.6215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.072 33389 Z= 0.200 Angle : 0.526 7.562 45297 Z= 0.277 Chirality : 0.043 0.155 5178 Planarity : 0.003 0.039 5940 Dihedral : 4.678 22.229 4470 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.13), residues: 4138 helix: -0.15 (0.19), residues: 810 sheet: 1.50 (0.15), residues: 1189 loop : -1.07 (0.13), residues: 2139 ********************** 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 84 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 84 time to evaluate : 3.833 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.4852 time to fit residues: 69.6048 Evaluate side-chains 69 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 3.822 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.6789 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 414 random chunks: chunk 260 optimal weight: 7.9990 chunk 349 optimal weight: 0.9990 chunk 100 optimal weight: 0.0570 chunk 302 optimal weight: 9.9990 chunk 48 optimal weight: 7.9990 chunk 91 optimal weight: 0.9980 chunk 328 optimal weight: 0.0010 chunk 137 optimal weight: 9.9990 chunk 337 optimal weight: 4.9990 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 overall best weight: 1.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN E 454 GLN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 186 GLN L 228 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.085525 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.060017 restraints weight = 266500.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.060712 restraints weight = 165849.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.061117 restraints weight = 124249.372| |-----------------------------------------------------------------------------| r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.6193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.036 33389 Z= 0.111 Angle : 0.473 7.597 45297 Z= 0.248 Chirality : 0.043 0.171 5178 Planarity : 0.003 0.040 5940 Dihedral : 4.336 21.028 4470 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 11.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.20 (0.13), residues: 4138 helix: 0.04 (0.20), residues: 812 sheet: 1.61 (0.16), residues: 1091 loop : -1.15 (0.13), residues: 2235 =============================================================================== Job complete usr+sys time: 4130.72 seconds wall clock time: 79 minutes 15.54 seconds (4755.54 seconds total)