Starting phenix.real_space_refine on Tue Nov 21 07:06:57 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/11_2023/6psn_20459.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/11_2023/6psn_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_20459/11_2023/6psn_20459.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/11_2023/6psn_20459.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/11_2023/6psn_20459.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6psn_20459/11_2023/6psn_20459.pdb" } resolution = 4.6 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Ca 14 9.91 5 S 45 5.16 5 C 20537 2.51 5 N 5641 2.21 5 O 6593 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped 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: 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 539} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'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: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 213} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CA': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 16.10, per 1000 atoms: 0.49 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: 12.70 Conformation dependent library (CDL) restraints added in 6.4 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: 3.85 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: 13.32 Time building geometry restraints manager: 13.63 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 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: 1.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 8.860 Check model and map are aligned: 0.430 Set scattering table: 0.260 Process input model: 84.200 Find NCS groups from input model: 2.270 Set up NCS constraints: 0.230 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 100.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.112 33389 Z= 0.401 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 % Allowed : 1.90 % Favored : 97.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : 3.979 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: 0.5139 time to fit residues: 224.2259 Evaluate side-chains 103 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 3.784 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4932 ------------------------------------------------------------------------------- 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: 0.8143 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 12.203 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 % Allowed : 1.84 % Favored : 98.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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 : 3.771 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: 0.4689 time to fit residues: 95.4740 Evaluate side-chains 78 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 4.161 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.3022 time to fit residues: 7.4953 ------------------------------------------------------------------------------- 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: 6.9990 chunk 116 optimal weight: 8.9990 chunk 312 optimal weight: 0.9980 chunk 256 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 376 optimal weight: 3.9990 chunk 406 optimal weight: 1.9990 chunk 335 optimal weight: 0.6980 chunk 373 optimal weight: 10.0000 chunk 128 optimal weight: 50.0000 chunk 302 optimal weight: 4.9990 overall best weight: 2.5386 ------------------------------------------------------------------------------- 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** C 564 ASN D 424 GLN ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 553 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: 0.8127 moved from start: 0.3430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 33389 Z= 0.157 Angle : 0.503 7.059 45297 Z= 0.268 Chirality : 0.043 0.161 5178 Planarity : 0.003 0.043 5940 Dihedral : 4.781 21.769 4470 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.00 % Allowed : 1.76 % Favored : 98.24 % 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: -0.72 (0.13), residues: 4138 helix: -0.28 (0.20), residues: 767 sheet: 0.78 (0.15), residues: 1210 loop : -1.32 (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 101 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.500 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: 101 average time/residue: 0.4802 time to fit residues: 81.2337 Evaluate side-chains 76 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 3.836 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 4.7991 ------------------------------------------------------------------------------- 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: 0.5980 chunk 283 optimal weight: 20.0000 chunk 195 optimal weight: 9.9990 chunk 41 optimal weight: 0.0370 chunk 179 optimal weight: 9.9990 chunk 252 optimal weight: 20.0000 chunk 377 optimal weight: 10.0000 chunk 400 optimal weight: 20.0000 chunk 197 optimal weight: 0.9980 chunk 358 optimal weight: 0.9980 chunk 107 optimal weight: 5.9990 overall best weight: 1.7260 ------------------------------------------------------------------------------- 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 705 ASN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.3767 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= 0.123 Angle : 0.464 6.329 45297 Z= 0.246 Chirality : 0.043 0.153 5178 Planarity : 0.003 0.033 5940 Dihedral : 4.414 17.269 4470 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 9.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % 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: -0.33 (0.13), residues: 4138 helix: -0.06 (0.20), residues: 768 sheet: 1.05 (0.15), residues: 1238 loop : -1.07 (0.13), residues: 2132 *********************** 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 101 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 3.905 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: 101 average time/residue: 0.5335 time to fit residues: 88.3700 Evaluate side-chains 76 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 76 time to evaluate : 4.050 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.1796 ------------------------------------------------------------------------------- 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: 0.1980 chunk 227 optimal weight: 20.0000 chunk 5 optimal weight: 0.0030 chunk 297 optimal weight: 20.0000 chunk 165 optimal weight: 0.0980 chunk 341 optimal weight: 6.9990 chunk 276 optimal weight: 40.0000 chunk 0 optimal weight: 20.0000 chunk 204 optimal weight: 8.9990 chunk 359 optimal weight: 10.0000 chunk 100 optimal weight: 40.0000 overall best weight: 3.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 389 GLN F 553 ASN ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.4240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 33389 Z= 0.186 Angle : 0.506 8.458 45297 Z= 0.267 Chirality : 0.042 0.157 5178 Planarity : 0.003 0.034 5940 Dihedral : 4.484 17.569 4470 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % 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: -0.18 (0.13), residues: 4138 helix: -0.10 (0.20), residues: 768 sheet: 1.48 (0.15), residues: 1154 loop : -1.03 (0.13), 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 : 3.745 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: 0.5054 time to fit residues: 82.7102 Evaluate side-chains 75 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 4.079 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.4928 ------------------------------------------------------------------------------- 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: 1.9990 chunk 360 optimal weight: 40.0000 chunk 79 optimal weight: 9.9990 chunk 234 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 400 optimal weight: 1.9990 chunk 332 optimal weight: 10.0000 chunk 185 optimal weight: 7.9990 chunk 33 optimal weight: 0.0000 chunk 132 optimal weight: 9.9990 chunk 210 optimal weight: 0.8980 overall best weight: 1.7790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 HIS ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** 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: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 33389 Z= 0.119 Angle : 0.463 6.026 45297 Z= 0.243 Chirality : 0.043 0.159 5178 Planarity : 0.003 0.034 5940 Dihedral : 4.278 18.537 4470 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % 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: -0.23 (0.13), residues: 4138 helix: 0.04 (0.20), residues: 768 sheet: 1.39 (0.16), residues: 1063 loop : -1.00 (0.13), residues: 2307 *********************** 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 94 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 3.714 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: 94 average time/residue: 0.4769 time to fit residues: 76.6198 Evaluate side-chains 75 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 3.749 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2964 ------------------------------------------------------------------------------- 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: 7.9990 chunk 45 optimal weight: 50.0000 chunk 228 optimal weight: 2.9990 chunk 292 optimal weight: 30.0000 chunk 226 optimal weight: 7.9990 chunk 337 optimal weight: 9.9990 chunk 223 optimal weight: 40.0000 chunk 399 optimal weight: 7.9990 chunk 249 optimal weight: 0.9990 chunk 243 optimal weight: 9.9990 chunk 184 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS ** A 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN B 299 HIS B 541 GLN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 363 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 693 ASN D 280 GLN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN D 693 ASN E 280 GLN E 304 HIS E 389 GLN E 403 GLN ** F 403 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** 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 186 GLN L 228 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8194 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 33389 Z= 0.300 Angle : 0.600 9.759 45297 Z= 0.316 Chirality : 0.043 0.153 5178 Planarity : 0.003 0.035 5940 Dihedral : 4.872 20.595 4470 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 16.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.54 % Favored : 95.46 % Rotamer: Outliers : 0.00 % Allowed : 1.19 % Favored : 98.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.36 (0.19), residues: 809 sheet: 1.32 (0.15), residues: 1189 loop : -1.18 (0.13), residues: 2140 *********************** 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 86 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 86 time to evaluate : 3.734 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: 86 average time/residue: 0.5008 time to fit residues: 72.7122 Evaluate side-chains 71 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 3.451 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.2739 ------------------------------------------------------------------------------- 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: 1.9990 chunk 159 optimal weight: 9.9990 chunk 238 optimal weight: 5.9990 chunk 120 optimal weight: 7.9990 chunk 78 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 253 optimal weight: 7.9990 chunk 271 optimal weight: 0.9980 chunk 197 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 313 optimal weight: 6.9990 overall best weight: 3.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 553 ASN ** B 565 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 363 ASN ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 280 GLN 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 186 GLN L 228 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.5366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 33389 Z= 0.199 Angle : 0.518 6.973 45297 Z= 0.273 Chirality : 0.043 0.153 5178 Planarity : 0.003 0.037 5940 Dihedral : 4.684 20.521 4470 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 14.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % 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: -0.27 (0.13), residues: 4138 helix: -0.25 (0.19), residues: 810 sheet: 1.59 (0.15), residues: 1119 loop : -1.14 (0.13), residues: 2209 *********************** 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 89 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 89 time to evaluate : 4.038 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 outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.4821 time to fit residues: 73.7526 Evaluate side-chains 70 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 3.882 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.7564 ------------------------------------------------------------------------------- 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: 9.9990 chunk 382 optimal weight: 5.9990 chunk 348 optimal weight: 10.0000 chunk 371 optimal weight: 3.9990 chunk 223 optimal weight: 2.9990 chunk 161 optimal weight: 0.7980 chunk 291 optimal weight: 8.9990 chunk 114 optimal weight: 3.9990 chunk 336 optimal weight: 1.9990 chunk 351 optimal weight: 7.9990 chunk 370 optimal weight: 6.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 HIS A 424 GLN A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 389 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 186 GLN L 228 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8176 moved from start: 0.5563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.053 33389 Z= 0.157 Angle : 0.491 8.665 45297 Z= 0.258 Chirality : 0.043 0.161 5178 Planarity : 0.003 0.038 5940 Dihedral : 4.474 20.604 4470 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 12.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: -0.11 (0.13), residues: 4138 helix: -0.07 (0.20), residues: 810 sheet: 1.58 (0.15), residues: 1189 loop : -1.07 (0.13), residues: 2139 *********************** 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 : 4.068 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: 0.5244 time to fit residues: 79.1144 Evaluate side-chains 73 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 4.038 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5523 ------------------------------------------------------------------------------- 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: 6.9990 chunk 393 optimal weight: 0.9990 chunk 239 optimal weight: 9.9990 chunk 186 optimal weight: 9.9990 chunk 273 optimal weight: 40.0000 chunk 412 optimal weight: 0.0570 chunk 379 optimal weight: 30.0000 chunk 328 optimal weight: 40.0000 chunk 34 optimal weight: 0.7980 chunk 253 optimal weight: 7.9990 chunk 201 optimal weight: 10.0000 overall best weight: 3.3704 ------------------------------------------------------------------------------- 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** B 389 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 541 GLN E 280 GLN ** E 454 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 186 GLN L 228 GLN L 248 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.5843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 33389 Z= 0.184 Angle : 0.513 7.390 45297 Z= 0.269 Chirality : 0.043 0.178 5178 Planarity : 0.003 0.037 5940 Dihedral : 4.582 20.456 4470 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.15 (0.13), residues: 4138 helix: -0.09 (0.20), residues: 810 sheet: 1.54 (0.15), residues: 1189 loop : -1.09 (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 85 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 3.812 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 outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.4838 time to fit residues: 70.0441 Evaluate side-chains 73 residues out of total 3705 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 73 time to evaluate : 4.087 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 5.5830 ------------------------------------------------------------------------------- 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: 0.6980 chunk 349 optimal weight: 30.0000 chunk 100 optimal weight: 4.9990 chunk 302 optimal weight: 8.9990 chunk 48 optimal weight: 30.0000 chunk 91 optimal weight: 0.9980 chunk 328 optimal weight: 30.0000 chunk 137 optimal weight: 0.0570 chunk 337 optimal weight: 0.6980 chunk 41 optimal weight: 10.0000 chunk 60 optimal weight: 8.9990 overall best weight: 1.4900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 454 GLN ** A 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 299 HIS B 389 GLN ** B 705 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 454 GLN D 541 GLN E 280 GLN E 454 GLN ** E 483 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 389 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 424 GLN ** 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 146 ASN L 186 GLN L 228 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.085612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3055 r_free = 0.3055 target = 0.059271 restraints weight = 269830.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.060128 restraints weight = 166073.727| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.060589 restraints weight = 122030.903| |-----------------------------------------------------------------------------| r_work (final): 0.2950 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.5847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 33389 Z= 0.113 Angle : 0.467 7.552 45297 Z= 0.244 Chirality : 0.043 0.156 5178 Planarity : 0.003 0.037 5940 Dihedral : 4.284 20.485 4470 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -0.13 (0.13), residues: 4138 helix: 0.04 (0.20), residues: 810 sheet: 1.70 (0.16), residues: 1091 loop : -1.10 (0.13), residues: 2237 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4445.88 seconds wall clock time: 85 minutes 8.09 seconds (5108.09 seconds total)