Starting phenix.real_space_refine on Sat Mar 16 23:31:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/03_2024/8io9_35612_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/03_2024/8io9_35612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/03_2024/8io9_35612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/03_2024/8io9_35612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/03_2024/8io9_35612_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8io9_35612/03_2024/8io9_35612_updated.pdb" } resolution = 2.36 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= 0.005 sd= 0.050 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: 6 Type Number sf(0) Gaussians P 60 5.49 5 Mg 12 5.21 5 S 192 5.16 5 C 47904 2.51 5 N 13572 2.21 5 O 14004 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 542": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 585": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G PHE 660": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.18s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 75744 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "B" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "C" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "D" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "E" Number of atoms: 6254 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "F" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "G" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "H" Number of atoms: 6254 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "C" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "I" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "J" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "K" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "L" Number of atoms: 6254 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} Conformer: "B" Number of residues, atoms: 788, 6240 Classifications: {'peptide': 788} Link IDs: {'PTRANS': 49, 'TRANS': 738} bond proxies already assigned to first conformer: 6399 Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "F" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "I" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "J" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "K" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "L" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 58 Unusual residues: {' MG': 1, 'ANP': 1, 'TPP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Residues with excluded nonbonded symmetry interactions: 12 residue: pdb=" N ATRP A 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP A 703 " occ=0.62 residue: pdb=" N ATRP B 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP B 703 " occ=0.62 residue: pdb=" N ATRP C 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP C 703 " occ=0.62 residue: pdb=" N ATRP D 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP D 703 " occ=0.50 residue: pdb=" N BTRP E 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP E 703 " occ=0.62 residue: pdb=" N ATRP F 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP F 703 " occ=0.50 residue: pdb=" N ATRP G 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP G 703 " occ=0.62 residue: pdb=" N BTRP H 703 " occ=0.38 ... (26 atoms not shown) pdb=" CH2CTRP H 703 " occ=0.62 residue: pdb=" N ATRP I 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP I 703 " occ=0.50 residue: pdb=" N ATRP J 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP J 703 " occ=0.50 residue: pdb=" N ATRP K 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP K 703 " occ=0.50 residue: pdb=" N ATRP L 703 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP L 703 " occ=0.50 Time building chain proxies: 55.85, per 1000 atoms: 0.74 Number of scatterers: 75744 At special positions: 0 Unit cell: (210.74, 217.3, 99.22, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 192 16.00 P 60 15.00 Mg 12 11.99 O 14004 8.00 N 13572 7.00 C 47904 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=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 23.85 Conformation dependent library (CDL) restraints added in 20.1 seconds 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17568 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 444 helices and 48 sheets defined 44.1% alpha, 9.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 13.35 Creating SS restraints... Processing helix chain 'A' and resid 15 through 37 Processing helix chain 'A' and resid 50 through 52 No H-bonds generated for 'chain 'A' and resid 50 through 52' Processing helix chain 'A' and resid 64 through 81 removed outlier: 3.669A pdb=" N HIS A 73 " --> pdb=" O PHE A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 105 Proline residue: A 96 - end of helix removed outlier: 3.570A pdb=" N GLU A 105 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 107 through 111 Processing helix chain 'A' and resid 119 through 128 Processing helix chain 'A' and resid 156 through 164 Processing helix chain 'A' and resid 178 through 182 Processing helix chain 'A' and resid 184 through 195 removed outlier: 3.631A pdb=" N TRP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) removed outlier: 5.205A pdb=" N HIS A 191 " --> pdb=" O ALA A 187 " (cutoff:3.500A) removed outlier: 4.789A pdb=" N SER A 192 " --> pdb=" O THR A 188 " (cutoff:3.500A) removed outlier: 5.286A pdb=" N ASN A 193 " --> pdb=" O SER A 189 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N LYS A 194 " --> pdb=" O TRP A 190 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N PHE A 195 " --> pdb=" O HIS A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 223 No H-bonds generated for 'chain 'A' and resid 220 through 223' Processing helix chain 'A' and resid 226 through 235 Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.283A pdb=" N GLY A 253 " --> pdb=" O ALA A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 324 through 337 removed outlier: 4.053A pdb=" N TYR A 337 " --> pdb=" O TRP A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 351 through 356 removed outlier: 3.887A pdb=" N ILE A 356 " --> pdb=" O GLU A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 372 through 375 Processing helix chain 'A' and resid 384 through 386 No H-bonds generated for 'chain 'A' and resid 384 through 386' Processing helix chain 'A' and resid 401 through 415 removed outlier: 4.511A pdb=" N LEU A 405 " --> pdb=" O SER A 401 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 438 Processing helix chain 'A' and resid 450 through 455 removed outlier: 3.656A pdb=" N ASP A 454 " --> pdb=" O GLU A 451 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N GLY A 455 " --> pdb=" O ASP A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 470 through 482 Processing helix chain 'A' and resid 496 through 515 removed outlier: 4.675A pdb=" N SER A 501 " --> pdb=" O VAL A 498 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N VAL A 512 " --> pdb=" O TRP A 509 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 556 removed outlier: 4.106A pdb=" N LYS A 556 " --> pdb=" O LEU A 552 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 579 Processing helix chain 'A' and resid 602 through 611 Processing helix chain 'A' and resid 637 through 652 Processing helix chain 'A' and resid 666 through 669 Processing helix chain 'A' and resid 681 through 687 Processing helix chain 'A' and resid 702 through 708 removed outlier: 3.744A pdb=" N HIS A 706 " --> pdb=" O PRO A 702 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 717 No H-bonds generated for 'chain 'A' and resid 715 through 717' Processing helix chain 'A' and resid 732 through 738 Processing helix chain 'A' and resid 743 through 753 Processing helix chain 'A' and resid 755 through 757 No H-bonds generated for 'chain 'A' and resid 755 through 757' Processing helix chain 'A' and resid 762 through 782 Processing helix chain 'A' and resid 787 through 790 No H-bonds generated for 'chain 'A' and resid 787 through 790' Processing helix chain 'B' and resid 15 through 37 Processing helix chain 'B' and resid 50 through 52 No H-bonds generated for 'chain 'B' and resid 50 through 52' Processing helix chain 'B' and resid 64 through 81 removed outlier: 3.672A pdb=" N HIS B 73 " --> pdb=" O PHE B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 92 through 105 Proline residue: B 96 - end of helix removed outlier: 3.552A pdb=" N GLU B 105 " --> pdb=" O ALA B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 111 Processing helix chain 'B' and resid 119 through 128 Processing helix chain 'B' and resid 156 through 164 Processing helix chain 'B' and resid 178 through 182 removed outlier: 3.529A pdb=" N GLU B 182 " --> pdb=" O ASP B 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 178 through 182' Processing helix chain 'B' and resid 184 through 195 removed outlier: 3.620A pdb=" N TRP B 190 " --> pdb=" O LEU B 186 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N HIS B 191 " --> pdb=" O ALA B 187 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N SER B 192 " --> pdb=" O THR B 188 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ASN B 193 " --> pdb=" O SER B 189 " (cutoff:3.500A) removed outlier: 5.844A pdb=" N LYS B 194 " --> pdb=" O TRP B 190 " (cutoff:3.500A) removed outlier: 4.591A pdb=" N PHE B 195 " --> pdb=" O HIS B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 223 No H-bonds generated for 'chain 'B' and resid 220 through 223' Processing helix chain 'B' and resid 226 through 235 Processing helix chain 'B' and resid 248 through 274 removed outlier: 4.265A pdb=" N GLY B 253 " --> pdb=" O ALA B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 310 through 312 No H-bonds generated for 'chain 'B' and resid 310 through 312' Processing helix chain 'B' and resid 324 through 337 removed outlier: 4.067A pdb=" N TYR B 337 " --> pdb=" O TRP B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 341 No H-bonds generated for 'chain 'B' and resid 339 through 341' Processing helix chain 'B' and resid 351 through 356 removed outlier: 3.863A pdb=" N ILE B 356 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing helix chain 'B' and resid 360 through 362 No H-bonds generated for 'chain 'B' and resid 360 through 362' Processing helix chain 'B' and resid 372 through 375 Processing helix chain 'B' and resid 384 through 386 No H-bonds generated for 'chain 'B' and resid 384 through 386' Processing helix chain 'B' and resid 401 through 415 removed outlier: 4.499A pdb=" N LEU B 405 " --> pdb=" O SER B 401 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 438 Processing helix chain 'B' and resid 450 through 455 removed outlier: 3.630A pdb=" N ASP B 454 " --> pdb=" O GLU B 451 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY B 455 " --> pdb=" O ASP B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 470 through 482 Processing helix chain 'B' and resid 496 through 515 removed outlier: 4.671A pdb=" N SER B 501 " --> pdb=" O VAL B 498 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL B 512 " --> pdb=" O TRP B 509 " (cutoff:3.500A) Processing helix chain 'B' and resid 548 through 555 Processing helix chain 'B' and resid 569 through 579 Processing helix chain 'B' and resid 602 through 611 Processing helix chain 'B' and resid 637 through 652 Processing helix chain 'B' and resid 666 through 669 Processing helix chain 'B' and resid 681 through 687 Processing helix chain 'B' and resid 702 through 708 Processing helix chain 'B' and resid 715 through 717 No H-bonds generated for 'chain 'B' and resid 715 through 717' Processing helix chain 'B' and resid 732 through 738 Processing helix chain 'B' and resid 743 through 753 Processing helix chain 'B' and resid 755 through 757 No H-bonds generated for 'chain 'B' and resid 755 through 757' Processing helix chain 'B' and resid 762 through 782 Processing helix chain 'B' and resid 787 through 790 No H-bonds generated for 'chain 'B' and resid 787 through 790' Processing helix chain 'C' and resid 15 through 37 Processing helix chain 'C' and resid 50 through 52 No H-bonds generated for 'chain 'C' and resid 50 through 52' Processing helix chain 'C' and resid 64 through 81 removed outlier: 3.672A pdb=" N HIS C 73 " --> pdb=" O PHE C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 105 Proline residue: C 96 - end of helix removed outlier: 3.575A pdb=" N GLU C 105 " --> pdb=" O ALA C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 111 Processing helix chain 'C' and resid 119 through 128 Processing helix chain 'C' and resid 156 through 164 Processing helix chain 'C' and resid 178 through 182 removed outlier: 3.524A pdb=" N GLU C 182 " --> pdb=" O ASP C 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 178 through 182' Processing helix chain 'C' and resid 184 through 195 removed outlier: 3.612A pdb=" N TRP C 190 " --> pdb=" O LEU C 186 " (cutoff:3.500A) removed outlier: 5.174A pdb=" N HIS C 191 " --> pdb=" O ALA C 187 " (cutoff:3.500A) removed outlier: 4.800A pdb=" N SER C 192 " --> pdb=" O THR C 188 " (cutoff:3.500A) removed outlier: 5.295A pdb=" N ASN C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LYS C 194 " --> pdb=" O TRP C 190 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N PHE C 195 " --> pdb=" O HIS C 191 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 223 No H-bonds generated for 'chain 'C' and resid 220 through 223' Processing helix chain 'C' and resid 226 through 235 Processing helix chain 'C' and resid 248 through 274 removed outlier: 4.291A pdb=" N GLY C 253 " --> pdb=" O ALA C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 310 through 312 No H-bonds generated for 'chain 'C' and resid 310 through 312' Processing helix chain 'C' and resid 324 through 337 removed outlier: 4.053A pdb=" N TYR C 337 " --> pdb=" O TRP C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 339 through 341 No H-bonds generated for 'chain 'C' and resid 339 through 341' Processing helix chain 'C' and resid 351 through 356 removed outlier: 3.864A pdb=" N ILE C 356 " --> pdb=" O GLU C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 360 through 362 No H-bonds generated for 'chain 'C' and resid 360 through 362' Processing helix chain 'C' and resid 372 through 375 Processing helix chain 'C' and resid 384 through 386 No H-bonds generated for 'chain 'C' and resid 384 through 386' Processing helix chain 'C' and resid 401 through 415 removed outlier: 4.517A pdb=" N LEU C 405 " --> pdb=" O SER C 401 " (cutoff:3.500A) Processing helix chain 'C' and resid 434 through 438 Processing helix chain 'C' and resid 450 through 455 removed outlier: 3.666A pdb=" N ASP C 454 " --> pdb=" O GLU C 451 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY C 455 " --> pdb=" O ASP C 452 " (cutoff:3.500A) Processing helix chain 'C' and resid 470 through 482 Processing helix chain 'C' and resid 496 through 515 removed outlier: 4.694A pdb=" N SER C 501 " --> pdb=" O VAL C 498 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N VAL C 512 " --> pdb=" O TRP C 509 " (cutoff:3.500A) Processing helix chain 'C' and resid 548 through 556 removed outlier: 3.842A pdb=" N LYS C 556 " --> pdb=" O LEU C 552 " (cutoff:3.500A) Processing helix chain 'C' and resid 569 through 579 Processing helix chain 'C' and resid 602 through 611 Processing helix chain 'C' and resid 637 through 652 Processing helix chain 'C' and resid 666 through 669 Processing helix chain 'C' and resid 681 through 687 Processing helix chain 'C' and resid 702 through 708 Processing helix chain 'C' and resid 715 through 717 No H-bonds generated for 'chain 'C' and resid 715 through 717' Processing helix chain 'C' and resid 732 through 738 Processing helix chain 'C' and resid 743 through 753 Processing helix chain 'C' and resid 755 through 757 No H-bonds generated for 'chain 'C' and resid 755 through 757' Processing helix chain 'C' and resid 762 through 782 Processing helix chain 'C' and resid 787 through 790 No H-bonds generated for 'chain 'C' and resid 787 through 790' Processing helix chain 'D' and resid 15 through 37 Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 64 through 81 removed outlier: 3.667A pdb=" N HIS D 73 " --> pdb=" O PHE D 69 " (cutoff:3.500A) Processing helix chain 'D' and resid 92 through 105 Proline residue: D 96 - end of helix removed outlier: 3.579A pdb=" N GLU D 105 " --> pdb=" O ALA D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 111 Processing helix chain 'D' and resid 119 through 128 Processing helix chain 'D' and resid 156 through 164 Processing helix chain 'D' and resid 178 through 182 removed outlier: 3.536A pdb=" N GLU D 182 " --> pdb=" O ASP D 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 178 through 182' Processing helix chain 'D' and resid 184 through 195 removed outlier: 3.613A pdb=" N TRP D 190 " --> pdb=" O LEU D 186 " (cutoff:3.500A) removed outlier: 5.165A pdb=" N HIS D 191 " --> pdb=" O ALA D 187 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N SER D 192 " --> pdb=" O THR D 188 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN D 193 " --> pdb=" O SER D 189 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N LYS D 194 " --> pdb=" O TRP D 190 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N PHE D 195 " --> pdb=" O HIS D 191 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 223 No H-bonds generated for 'chain 'D' and resid 220 through 223' Processing helix chain 'D' and resid 226 through 235 Processing helix chain 'D' and resid 248 through 274 removed outlier: 4.288A pdb=" N GLY D 253 " --> pdb=" O ALA D 249 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 312 No H-bonds generated for 'chain 'D' and resid 310 through 312' Processing helix chain 'D' and resid 324 through 337 removed outlier: 4.079A pdb=" N TYR D 337 " --> pdb=" O TRP D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 341 No H-bonds generated for 'chain 'D' and resid 339 through 341' Processing helix chain 'D' and resid 351 through 356 removed outlier: 3.853A pdb=" N ILE D 356 " --> pdb=" O GLU D 352 " (cutoff:3.500A) Processing helix chain 'D' and resid 360 through 362 No H-bonds generated for 'chain 'D' and resid 360 through 362' Processing helix chain 'D' and resid 372 through 375 Processing helix chain 'D' and resid 384 through 386 No H-bonds generated for 'chain 'D' and resid 384 through 386' Processing helix chain 'D' and resid 401 through 415 removed outlier: 4.499A pdb=" N LEU D 405 " --> pdb=" O SER D 401 " (cutoff:3.500A) Processing helix chain 'D' and resid 434 through 438 Processing helix chain 'D' and resid 450 through 455 removed outlier: 3.626A pdb=" N ASP D 454 " --> pdb=" O GLU D 451 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLY D 455 " --> pdb=" O ASP D 452 " (cutoff:3.500A) Processing helix chain 'D' and resid 470 through 482 Processing helix chain 'D' and resid 496 through 515 removed outlier: 4.710A pdb=" N SER D 501 " --> pdb=" O VAL D 498 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N VAL D 512 " --> pdb=" O TRP D 509 " (cutoff:3.500A) Processing helix chain 'D' and resid 548 through 556 removed outlier: 3.878A pdb=" N LYS D 556 " --> pdb=" O LEU D 552 " (cutoff:3.500A) Processing helix chain 'D' and resid 569 through 579 Processing helix chain 'D' and resid 602 through 611 Processing helix chain 'D' and resid 637 through 652 Processing helix chain 'D' and resid 666 through 669 Processing helix chain 'D' and resid 681 through 687 Processing helix chain 'D' and resid 702 through 708 Processing helix chain 'D' and resid 715 through 717 No H-bonds generated for 'chain 'D' and resid 715 through 717' Processing helix chain 'D' and resid 732 through 738 Processing helix chain 'D' and resid 743 through 753 Processing helix chain 'D' and resid 755 through 757 No H-bonds generated for 'chain 'D' and resid 755 through 757' Processing helix chain 'D' and resid 762 through 782 Processing helix chain 'D' and resid 787 through 790 No H-bonds generated for 'chain 'D' and resid 787 through 790' Processing helix chain 'E' and resid 15 through 37 Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 64 through 81 removed outlier: 3.679A pdb=" N HIS E 73 " --> pdb=" O PHE E 69 " (cutoff:3.500A) Processing helix chain 'E' and resid 92 through 105 Proline residue: E 96 - end of helix removed outlier: 3.551A pdb=" N GLU E 105 " --> pdb=" O ALA E 102 " (cutoff:3.500A) Processing helix chain 'E' and resid 107 through 111 Processing helix chain 'E' and resid 119 through 128 Processing helix chain 'E' and resid 156 through 164 Processing helix chain 'E' and resid 178 through 182 removed outlier: 3.509A pdb=" N GLU E 182 " --> pdb=" O ASP E 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 178 through 182' Processing helix chain 'E' and resid 184 through 195 removed outlier: 3.592A pdb=" N TRP E 190 " --> pdb=" O LEU E 186 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N HIS E 191 " --> pdb=" O ALA E 187 " (cutoff:3.500A) removed outlier: 4.831A pdb=" N SER E 192 " --> pdb=" O THR E 188 " (cutoff:3.500A) removed outlier: 5.302A pdb=" N ASN E 193 " --> pdb=" O SER E 189 " (cutoff:3.500A) removed outlier: 5.893A pdb=" N LYS E 194 " --> pdb=" O TRP E 190 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N PHE E 195 " --> pdb=" O HIS E 191 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 223 No H-bonds generated for 'chain 'E' and resid 220 through 223' Processing helix chain 'E' and resid 226 through 235 Processing helix chain 'E' and resid 248 through 274 removed outlier: 4.311A pdb=" N GLY E 253 " --> pdb=" O ALA E 249 " (cutoff:3.500A) Processing helix chain 'E' and resid 310 through 312 No H-bonds generated for 'chain 'E' and resid 310 through 312' Processing helix chain 'E' and resid 324 through 337 removed outlier: 4.050A pdb=" N TYR E 337 " --> pdb=" O TRP E 333 " (cutoff:3.500A) Processing helix chain 'E' and resid 339 through 341 No H-bonds generated for 'chain 'E' and resid 339 through 341' Processing helix chain 'E' and resid 351 through 356 removed outlier: 3.878A pdb=" N ILE E 356 " --> pdb=" O GLU E 352 " (cutoff:3.500A) Processing helix chain 'E' and resid 360 through 362 No H-bonds generated for 'chain 'E' and resid 360 through 362' Processing helix chain 'E' and resid 372 through 375 Processing helix chain 'E' and resid 384 through 386 No H-bonds generated for 'chain 'E' and resid 384 through 386' Processing helix chain 'E' and resid 401 through 415 removed outlier: 4.486A pdb=" N LEU E 405 " --> pdb=" O SER E 401 " (cutoff:3.500A) Processing helix chain 'E' and resid 434 through 438 Processing helix chain 'E' and resid 450 through 455 removed outlier: 3.663A pdb=" N ASP E 454 " --> pdb=" O GLU E 451 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N GLY E 455 " --> pdb=" O ASP E 452 " (cutoff:3.500A) Processing helix chain 'E' and resid 470 through 482 Processing helix chain 'E' and resid 496 through 515 removed outlier: 4.665A pdb=" N SER E 501 " --> pdb=" O VAL E 498 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL E 512 " --> pdb=" O TRP E 509 " (cutoff:3.500A) Processing helix chain 'E' and resid 548 through 556 removed outlier: 4.096A pdb=" N LYS E 556 " --> pdb=" O LEU E 552 " (cutoff:3.500A) Processing helix chain 'E' and resid 569 through 579 Processing helix chain 'E' and resid 602 through 611 Processing helix chain 'E' and resid 637 through 652 Processing helix chain 'E' and resid 666 through 669 Processing helix chain 'E' and resid 681 through 687 Processing helix chain 'E' and resid 702 through 708 removed outlier: 3.733A pdb=" N HIS E 706 " --> pdb=" O PRO E 702 " (cutoff:3.500A) Processing helix chain 'E' and resid 715 through 717 No H-bonds generated for 'chain 'E' and resid 715 through 717' Processing helix chain 'E' and resid 732 through 738 Processing helix chain 'E' and resid 743 through 753 Processing helix chain 'E' and resid 755 through 757 No H-bonds generated for 'chain 'E' and resid 755 through 757' Processing helix chain 'E' and resid 762 through 782 Processing helix chain 'E' and resid 787 through 790 No H-bonds generated for 'chain 'E' and resid 787 through 790' Processing helix chain 'F' and resid 15 through 37 Processing helix chain 'F' and resid 50 through 52 No H-bonds generated for 'chain 'F' and resid 50 through 52' Processing helix chain 'F' and resid 64 through 81 removed outlier: 3.660A pdb=" N HIS F 73 " --> pdb=" O PHE F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 92 through 105 Proline residue: F 96 - end of helix removed outlier: 3.567A pdb=" N GLU F 105 " --> pdb=" O ALA F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 111 Processing helix chain 'F' and resid 119 through 128 Processing helix chain 'F' and resid 156 through 164 Processing helix chain 'F' and resid 178 through 182 Processing helix chain 'F' and resid 184 through 195 removed outlier: 3.641A pdb=" N TRP F 190 " --> pdb=" O LEU F 186 " (cutoff:3.500A) removed outlier: 5.194A pdb=" N HIS F 191 " --> pdb=" O ALA F 187 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N SER F 192 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 5.261A pdb=" N ASN F 193 " --> pdb=" O SER F 189 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS F 194 " --> pdb=" O TRP F 190 " (cutoff:3.500A) removed outlier: 4.609A pdb=" N PHE F 195 " --> pdb=" O HIS F 191 " (cutoff:3.500A) Processing helix chain 'F' and resid 220 through 223 No H-bonds generated for 'chain 'F' and resid 220 through 223' Processing helix chain 'F' and resid 226 through 235 Processing helix chain 'F' and resid 248 through 274 removed outlier: 4.315A pdb=" N GLY F 253 " --> pdb=" O ALA F 249 " (cutoff:3.500A) Processing helix chain 'F' and resid 310 through 312 No H-bonds generated for 'chain 'F' and resid 310 through 312' Processing helix chain 'F' and resid 324 through 337 removed outlier: 4.064A pdb=" N TYR F 337 " --> pdb=" O TRP F 333 " (cutoff:3.500A) Processing helix chain 'F' and resid 339 through 341 No H-bonds generated for 'chain 'F' and resid 339 through 341' Processing helix chain 'F' and resid 351 through 356 removed outlier: 3.884A pdb=" N ILE F 356 " --> pdb=" O GLU F 352 " (cutoff:3.500A) Processing helix chain 'F' and resid 360 through 362 No H-bonds generated for 'chain 'F' and resid 360 through 362' Processing helix chain 'F' and resid 372 through 375 Processing helix chain 'F' and resid 384 through 386 No H-bonds generated for 'chain 'F' and resid 384 through 386' Processing helix chain 'F' and resid 401 through 415 removed outlier: 4.513A pdb=" N LEU F 405 " --> pdb=" O SER F 401 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'F' and resid 450 through 455 removed outlier: 3.635A pdb=" N ASP F 454 " --> pdb=" O GLU F 451 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY F 455 " --> pdb=" O ASP F 452 " (cutoff:3.500A) Processing helix chain 'F' and resid 470 through 482 Processing helix chain 'F' and resid 496 through 515 removed outlier: 4.691A pdb=" N SER F 501 " --> pdb=" O VAL F 498 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL F 512 " --> pdb=" O TRP F 509 " (cutoff:3.500A) Processing helix chain 'F' and resid 548 through 555 Processing helix chain 'F' and resid 569 through 579 Processing helix chain 'F' and resid 602 through 611 Processing helix chain 'F' and resid 637 through 652 Processing helix chain 'F' and resid 666 through 669 Processing helix chain 'F' and resid 681 through 687 Processing helix chain 'F' and resid 702 through 708 removed outlier: 3.755A pdb=" N HIS F 706 " --> pdb=" O PRO F 702 " (cutoff:3.500A) Processing helix chain 'F' and resid 715 through 717 No H-bonds generated for 'chain 'F' and resid 715 through 717' Processing helix chain 'F' and resid 732 through 738 Processing helix chain 'F' and resid 743 through 753 Processing helix chain 'F' and resid 755 through 757 No H-bonds generated for 'chain 'F' and resid 755 through 757' Processing helix chain 'F' and resid 762 through 782 Processing helix chain 'F' and resid 787 through 790 No H-bonds generated for 'chain 'F' and resid 787 through 790' Processing helix chain 'G' and resid 15 through 37 Processing helix chain 'G' and resid 50 through 52 No H-bonds generated for 'chain 'G' and resid 50 through 52' Processing helix chain 'G' and resid 64 through 81 removed outlier: 3.670A pdb=" N HIS G 73 " --> pdb=" O PHE G 69 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 105 Proline residue: G 96 - end of helix removed outlier: 3.574A pdb=" N GLU G 105 " --> pdb=" O ALA G 102 " (cutoff:3.500A) Processing helix chain 'G' and resid 107 through 111 Processing helix chain 'G' and resid 119 through 128 Processing helix chain 'G' and resid 156 through 164 Processing helix chain 'G' and resid 178 through 182 Processing helix chain 'G' and resid 184 through 195 removed outlier: 3.646A pdb=" N TRP G 190 " --> pdb=" O LEU G 186 " (cutoff:3.500A) removed outlier: 5.215A pdb=" N HIS G 191 " --> pdb=" O ALA G 187 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N SER G 192 " --> pdb=" O THR G 188 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN G 193 " --> pdb=" O SER G 189 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N LYS G 194 " --> pdb=" O TRP G 190 " (cutoff:3.500A) removed outlier: 4.618A pdb=" N PHE G 195 " --> pdb=" O HIS G 191 " (cutoff:3.500A) Processing helix chain 'G' and resid 220 through 223 No H-bonds generated for 'chain 'G' and resid 220 through 223' Processing helix chain 'G' and resid 226 through 235 Processing helix chain 'G' and resid 248 through 274 removed outlier: 4.289A pdb=" N GLY G 253 " --> pdb=" O ALA G 249 " (cutoff:3.500A) Processing helix chain 'G' and resid 310 through 312 No H-bonds generated for 'chain 'G' and resid 310 through 312' Processing helix chain 'G' and resid 324 through 337 removed outlier: 4.049A pdb=" N TYR G 337 " --> pdb=" O TRP G 333 " (cutoff:3.500A) Processing helix chain 'G' and resid 339 through 341 No H-bonds generated for 'chain 'G' and resid 339 through 341' Processing helix chain 'G' and resid 351 through 356 removed outlier: 3.886A pdb=" N ILE G 356 " --> pdb=" O GLU G 352 " (cutoff:3.500A) Processing helix chain 'G' and resid 360 through 362 No H-bonds generated for 'chain 'G' and resid 360 through 362' Processing helix chain 'G' and resid 372 through 375 Processing helix chain 'G' and resid 384 through 386 No H-bonds generated for 'chain 'G' and resid 384 through 386' Processing helix chain 'G' and resid 401 through 415 removed outlier: 4.511A pdb=" N LEU G 405 " --> pdb=" O SER G 401 " (cutoff:3.500A) Processing helix chain 'G' and resid 434 through 438 Processing helix chain 'G' and resid 450 through 455 removed outlier: 3.656A pdb=" N ASP G 454 " --> pdb=" O GLU G 451 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N GLY G 455 " --> pdb=" O ASP G 452 " (cutoff:3.500A) Processing helix chain 'G' and resid 470 through 482 Processing helix chain 'G' and resid 496 through 515 removed outlier: 4.694A pdb=" N SER G 501 " --> pdb=" O VAL G 498 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N VAL G 512 " --> pdb=" O TRP G 509 " (cutoff:3.500A) Processing helix chain 'G' and resid 548 through 555 Processing helix chain 'G' and resid 569 through 579 Processing helix chain 'G' and resid 602 through 611 Processing helix chain 'G' and resid 637 through 652 Processing helix chain 'G' and resid 666 through 669 Processing helix chain 'G' and resid 681 through 687 Processing helix chain 'G' and resid 702 through 708 removed outlier: 3.753A pdb=" N HIS G 706 " --> pdb=" O PRO G 702 " (cutoff:3.500A) Processing helix chain 'G' and resid 715 through 717 No H-bonds generated for 'chain 'G' and resid 715 through 717' Processing helix chain 'G' and resid 732 through 738 Processing helix chain 'G' and resid 743 through 753 Processing helix chain 'G' and resid 755 through 757 No H-bonds generated for 'chain 'G' and resid 755 through 757' Processing helix chain 'G' and resid 762 through 782 Processing helix chain 'G' and resid 787 through 790 No H-bonds generated for 'chain 'G' and resid 787 through 790' Processing helix chain 'H' and resid 15 through 37 Processing helix chain 'H' and resid 50 through 52 No H-bonds generated for 'chain 'H' and resid 50 through 52' Processing helix chain 'H' and resid 64 through 81 removed outlier: 3.677A pdb=" N HIS H 73 " --> pdb=" O PHE H 69 " (cutoff:3.500A) Processing helix chain 'H' and resid 92 through 105 Proline residue: H 96 - end of helix removed outlier: 3.555A pdb=" N GLU H 105 " --> pdb=" O ALA H 102 " (cutoff:3.500A) Processing helix chain 'H' and resid 107 through 111 Processing helix chain 'H' and resid 119 through 128 Processing helix chain 'H' and resid 156 through 164 Processing helix chain 'H' and resid 178 through 182 removed outlier: 3.531A pdb=" N GLU H 182 " --> pdb=" O ASP H 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 178 through 182' Processing helix chain 'H' and resid 184 through 195 removed outlier: 3.616A pdb=" N TRP H 190 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS H 191 " --> pdb=" O ALA H 187 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N SER H 192 " --> pdb=" O THR H 188 " (cutoff:3.500A) removed outlier: 5.277A pdb=" N ASN H 193 " --> pdb=" O SER H 189 " (cutoff:3.500A) removed outlier: 5.858A pdb=" N LYS H 194 " --> pdb=" O TRP H 190 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N PHE H 195 " --> pdb=" O HIS H 191 " (cutoff:3.500A) Processing helix chain 'H' and resid 220 through 223 No H-bonds generated for 'chain 'H' and resid 220 through 223' Processing helix chain 'H' and resid 226 through 235 Processing helix chain 'H' and resid 248 through 274 removed outlier: 4.264A pdb=" N GLY H 253 " --> pdb=" O ALA H 249 " (cutoff:3.500A) Processing helix chain 'H' and resid 310 through 312 No H-bonds generated for 'chain 'H' and resid 310 through 312' Processing helix chain 'H' and resid 324 through 337 removed outlier: 4.063A pdb=" N TYR H 337 " --> pdb=" O TRP H 333 " (cutoff:3.500A) Processing helix chain 'H' and resid 339 through 341 No H-bonds generated for 'chain 'H' and resid 339 through 341' Processing helix chain 'H' and resid 351 through 356 removed outlier: 3.868A pdb=" N ILE H 356 " --> pdb=" O GLU H 352 " (cutoff:3.500A) Processing helix chain 'H' and resid 360 through 362 No H-bonds generated for 'chain 'H' and resid 360 through 362' Processing helix chain 'H' and resid 372 through 375 Processing helix chain 'H' and resid 384 through 386 No H-bonds generated for 'chain 'H' and resid 384 through 386' Processing helix chain 'H' and resid 401 through 415 removed outlier: 4.496A pdb=" N LEU H 405 " --> pdb=" O SER H 401 " (cutoff:3.500A) Processing helix chain 'H' and resid 434 through 438 Processing helix chain 'H' and resid 450 through 455 removed outlier: 3.631A pdb=" N ASP H 454 " --> pdb=" O GLU H 451 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLY H 455 " --> pdb=" O ASP H 452 " (cutoff:3.500A) Processing helix chain 'H' and resid 470 through 482 Processing helix chain 'H' and resid 496 through 515 removed outlier: 4.691A pdb=" N SER H 501 " --> pdb=" O VAL H 498 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N VAL H 512 " --> pdb=" O TRP H 509 " (cutoff:3.500A) Processing helix chain 'H' and resid 548 through 556 removed outlier: 3.506A pdb=" N ASN H 555 " --> pdb=" O ASP H 551 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LYS H 556 " --> pdb=" O LEU H 552 " (cutoff:3.500A) Processing helix chain 'H' and resid 569 through 579 Processing helix chain 'H' and resid 602 through 611 Processing helix chain 'H' and resid 637 through 652 Processing helix chain 'H' and resid 666 through 669 Processing helix chain 'H' and resid 681 through 687 Processing helix chain 'H' and resid 702 through 708 removed outlier: 3.789A pdb=" N HIS H 706 " --> pdb=" O PRO H 702 " (cutoff:3.500A) Processing helix chain 'H' and resid 715 through 717 No H-bonds generated for 'chain 'H' and resid 715 through 717' Processing helix chain 'H' and resid 732 through 738 Processing helix chain 'H' and resid 743 through 753 Processing helix chain 'H' and resid 755 through 757 No H-bonds generated for 'chain 'H' and resid 755 through 757' Processing helix chain 'H' and resid 762 through 782 Processing helix chain 'H' and resid 787 through 790 No H-bonds generated for 'chain 'H' and resid 787 through 790' Processing helix chain 'I' and resid 15 through 37 Processing helix chain 'I' and resid 50 through 52 No H-bonds generated for 'chain 'I' and resid 50 through 52' Processing helix chain 'I' and resid 64 through 81 removed outlier: 3.672A pdb=" N HIS I 73 " --> pdb=" O PHE I 69 " (cutoff:3.500A) Processing helix chain 'I' and resid 92 through 105 Proline residue: I 96 - end of helix removed outlier: 3.576A pdb=" N GLU I 105 " --> pdb=" O ALA I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 107 through 111 Processing helix chain 'I' and resid 119 through 128 Processing helix chain 'I' and resid 156 through 164 Processing helix chain 'I' and resid 178 through 182 removed outlier: 3.501A pdb=" N GLU I 182 " --> pdb=" O ASP I 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 178 through 182' Processing helix chain 'I' and resid 184 through 195 removed outlier: 3.613A pdb=" N TRP I 190 " --> pdb=" O LEU I 186 " (cutoff:3.500A) removed outlier: 5.175A pdb=" N HIS I 191 " --> pdb=" O ALA I 187 " (cutoff:3.500A) removed outlier: 4.794A pdb=" N SER I 192 " --> pdb=" O THR I 188 " (cutoff:3.500A) removed outlier: 5.290A pdb=" N ASN I 193 " --> pdb=" O SER I 189 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N LYS I 194 " --> pdb=" O TRP I 190 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N PHE I 195 " --> pdb=" O HIS I 191 " (cutoff:3.500A) Processing helix chain 'I' and resid 220 through 223 No H-bonds generated for 'chain 'I' and resid 220 through 223' Processing helix chain 'I' and resid 226 through 235 Processing helix chain 'I' and resid 248 through 274 removed outlier: 4.318A pdb=" N GLY I 253 " --> pdb=" O ALA I 249 " (cutoff:3.500A) Processing helix chain 'I' and resid 310 through 312 No H-bonds generated for 'chain 'I' and resid 310 through 312' Processing helix chain 'I' and resid 324 through 337 removed outlier: 4.052A pdb=" N TYR I 337 " --> pdb=" O TRP I 333 " (cutoff:3.500A) Processing helix chain 'I' and resid 339 through 341 No H-bonds generated for 'chain 'I' and resid 339 through 341' Processing helix chain 'I' and resid 351 through 356 removed outlier: 3.859A pdb=" N ILE I 356 " --> pdb=" O GLU I 352 " (cutoff:3.500A) Processing helix chain 'I' and resid 360 through 362 No H-bonds generated for 'chain 'I' and resid 360 through 362' Processing helix chain 'I' and resid 372 through 375 Processing helix chain 'I' and resid 384 through 386 No H-bonds generated for 'chain 'I' and resid 384 through 386' Processing helix chain 'I' and resid 403 through 415 Processing helix chain 'I' and resid 434 through 438 Processing helix chain 'I' and resid 450 through 455 removed outlier: 3.663A pdb=" N ASP I 454 " --> pdb=" O GLU I 451 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY I 455 " --> pdb=" O ASP I 452 " (cutoff:3.500A) Processing helix chain 'I' and resid 470 through 482 Processing helix chain 'I' and resid 496 through 515 removed outlier: 4.697A pdb=" N SER I 501 " --> pdb=" O VAL I 498 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N VAL I 512 " --> pdb=" O TRP I 509 " (cutoff:3.500A) Processing helix chain 'I' and resid 548 through 555 Processing helix chain 'I' and resid 569 through 579 Processing helix chain 'I' and resid 602 through 611 Processing helix chain 'I' and resid 637 through 652 Processing helix chain 'I' and resid 666 through 669 Processing helix chain 'I' and resid 681 through 687 Processing helix chain 'I' and resid 702 through 708 Processing helix chain 'I' and resid 715 through 717 No H-bonds generated for 'chain 'I' and resid 715 through 717' Processing helix chain 'I' and resid 732 through 738 Processing helix chain 'I' and resid 743 through 753 Processing helix chain 'I' and resid 755 through 757 No H-bonds generated for 'chain 'I' and resid 755 through 757' Processing helix chain 'I' and resid 762 through 782 Processing helix chain 'I' and resid 787 through 790 No H-bonds generated for 'chain 'I' and resid 787 through 790' Processing helix chain 'J' and resid 15 through 37 Processing helix chain 'J' and resid 50 through 52 No H-bonds generated for 'chain 'J' and resid 50 through 52' Processing helix chain 'J' and resid 64 through 81 removed outlier: 3.667A pdb=" N HIS J 73 " --> pdb=" O PHE J 69 " (cutoff:3.500A) Processing helix chain 'J' and resid 92 through 105 Proline residue: J 96 - end of helix removed outlier: 3.580A pdb=" N GLU J 105 " --> pdb=" O ALA J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 107 through 111 Processing helix chain 'J' and resid 119 through 128 Processing helix chain 'J' and resid 156 through 164 Processing helix chain 'J' and resid 178 through 182 Processing helix chain 'J' and resid 184 through 195 removed outlier: 3.608A pdb=" N TRP J 190 " --> pdb=" O LEU J 186 " (cutoff:3.500A) removed outlier: 5.163A pdb=" N HIS J 191 " --> pdb=" O ALA J 187 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER J 192 " --> pdb=" O THR J 188 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN J 193 " --> pdb=" O SER J 189 " (cutoff:3.500A) removed outlier: 5.846A pdb=" N LYS J 194 " --> pdb=" O TRP J 190 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N PHE J 195 " --> pdb=" O HIS J 191 " (cutoff:3.500A) Processing helix chain 'J' and resid 220 through 223 No H-bonds generated for 'chain 'J' and resid 220 through 223' Processing helix chain 'J' and resid 226 through 235 Processing helix chain 'J' and resid 248 through 274 removed outlier: 4.286A pdb=" N GLY J 253 " --> pdb=" O ALA J 249 " (cutoff:3.500A) Processing helix chain 'J' and resid 310 through 312 No H-bonds generated for 'chain 'J' and resid 310 through 312' Processing helix chain 'J' and resid 324 through 337 removed outlier: 4.080A pdb=" N TYR J 337 " --> pdb=" O TRP J 333 " (cutoff:3.500A) Processing helix chain 'J' and resid 339 through 341 No H-bonds generated for 'chain 'J' and resid 339 through 341' Processing helix chain 'J' and resid 351 through 356 removed outlier: 3.857A pdb=" N ILE J 356 " --> pdb=" O GLU J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 360 through 362 No H-bonds generated for 'chain 'J' and resid 360 through 362' Processing helix chain 'J' and resid 372 through 375 Processing helix chain 'J' and resid 384 through 386 No H-bonds generated for 'chain 'J' and resid 384 through 386' Processing helix chain 'J' and resid 401 through 415 removed outlier: 4.503A pdb=" N LEU J 405 " --> pdb=" O SER J 401 " (cutoff:3.500A) Processing helix chain 'J' and resid 434 through 438 Processing helix chain 'J' and resid 450 through 455 removed outlier: 3.628A pdb=" N ASP J 454 " --> pdb=" O GLU J 451 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N GLY J 455 " --> pdb=" O ASP J 452 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 482 Processing helix chain 'J' and resid 496 through 515 removed outlier: 4.710A pdb=" N SER J 501 " --> pdb=" O VAL J 498 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL J 512 " --> pdb=" O TRP J 509 " (cutoff:3.500A) Processing helix chain 'J' and resid 548 through 556 removed outlier: 3.887A pdb=" N LYS J 556 " --> pdb=" O LEU J 552 " (cutoff:3.500A) Processing helix chain 'J' and resid 569 through 579 Processing helix chain 'J' and resid 602 through 611 Processing helix chain 'J' and resid 637 through 652 Processing helix chain 'J' and resid 666 through 669 Processing helix chain 'J' and resid 681 through 687 Processing helix chain 'J' and resid 702 through 708 Processing helix chain 'J' and resid 715 through 717 No H-bonds generated for 'chain 'J' and resid 715 through 717' Processing helix chain 'J' and resid 732 through 738 Processing helix chain 'J' and resid 743 through 753 Processing helix chain 'J' and resid 755 through 757 No H-bonds generated for 'chain 'J' and resid 755 through 757' Processing helix chain 'J' and resid 762 through 782 Processing helix chain 'J' and resid 787 through 790 No H-bonds generated for 'chain 'J' and resid 787 through 790' Processing helix chain 'K' and resid 15 through 37 Processing helix chain 'K' and resid 50 through 52 No H-bonds generated for 'chain 'K' and resid 50 through 52' Processing helix chain 'K' and resid 64 through 81 removed outlier: 3.681A pdb=" N HIS K 73 " --> pdb=" O PHE K 69 " (cutoff:3.500A) Processing helix chain 'K' and resid 92 through 105 Proline residue: K 96 - end of helix removed outlier: 3.553A pdb=" N GLU K 105 " --> pdb=" O ALA K 102 " (cutoff:3.500A) Processing helix chain 'K' and resid 107 through 111 Processing helix chain 'K' and resid 119 through 128 Processing helix chain 'K' and resid 156 through 164 Processing helix chain 'K' and resid 178 through 182 removed outlier: 3.505A pdb=" N GLU K 182 " --> pdb=" O ASP K 178 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 178 through 182' Processing helix chain 'K' and resid 184 through 195 removed outlier: 3.594A pdb=" N TRP K 190 " --> pdb=" O LEU K 186 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N HIS K 191 " --> pdb=" O ALA K 187 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N SER K 192 " --> pdb=" O THR K 188 " (cutoff:3.500A) removed outlier: 5.303A pdb=" N ASN K 193 " --> pdb=" O SER K 189 " (cutoff:3.500A) removed outlier: 5.896A pdb=" N LYS K 194 " --> pdb=" O TRP K 190 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N PHE K 195 " --> pdb=" O HIS K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 220 through 223 No H-bonds generated for 'chain 'K' and resid 220 through 223' Processing helix chain 'K' and resid 226 through 235 Processing helix chain 'K' and resid 248 through 274 removed outlier: 4.282A pdb=" N GLY K 253 " --> pdb=" O ALA K 249 " (cutoff:3.500A) Processing helix chain 'K' and resid 310 through 312 No H-bonds generated for 'chain 'K' and resid 310 through 312' Processing helix chain 'K' and resid 324 through 337 removed outlier: 4.051A pdb=" N TYR K 337 " --> pdb=" O TRP K 333 " (cutoff:3.500A) Processing helix chain 'K' and resid 339 through 341 No H-bonds generated for 'chain 'K' and resid 339 through 341' Processing helix chain 'K' and resid 351 through 356 removed outlier: 3.877A pdb=" N ILE K 356 " --> pdb=" O GLU K 352 " (cutoff:3.500A) Processing helix chain 'K' and resid 360 through 362 No H-bonds generated for 'chain 'K' and resid 360 through 362' Processing helix chain 'K' and resid 372 through 375 Processing helix chain 'K' and resid 384 through 386 No H-bonds generated for 'chain 'K' and resid 384 through 386' Processing helix chain 'K' and resid 401 through 415 removed outlier: 4.487A pdb=" N LEU K 405 " --> pdb=" O SER K 401 " (cutoff:3.500A) Processing helix chain 'K' and resid 434 through 438 Processing helix chain 'K' and resid 450 through 455 removed outlier: 3.665A pdb=" N ASP K 454 " --> pdb=" O GLU K 451 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N GLY K 455 " --> pdb=" O ASP K 452 " (cutoff:3.500A) Processing helix chain 'K' and resid 470 through 482 Processing helix chain 'K' and resid 496 through 515 removed outlier: 4.691A pdb=" N SER K 501 " --> pdb=" O VAL K 498 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL K 512 " --> pdb=" O TRP K 509 " (cutoff:3.500A) Processing helix chain 'K' and resid 548 through 556 removed outlier: 4.065A pdb=" N LYS K 556 " --> pdb=" O LEU K 552 " (cutoff:3.500A) Processing helix chain 'K' and resid 569 through 579 Processing helix chain 'K' and resid 602 through 611 Processing helix chain 'K' and resid 637 through 652 Processing helix chain 'K' and resid 666 through 669 Processing helix chain 'K' and resid 681 through 687 Processing helix chain 'K' and resid 702 through 708 removed outlier: 3.730A pdb=" N HIS K 706 " --> pdb=" O PRO K 702 " (cutoff:3.500A) Processing helix chain 'K' and resid 715 through 717 No H-bonds generated for 'chain 'K' and resid 715 through 717' Processing helix chain 'K' and resid 732 through 738 Processing helix chain 'K' and resid 743 through 753 Processing helix chain 'K' and resid 755 through 757 No H-bonds generated for 'chain 'K' and resid 755 through 757' Processing helix chain 'K' and resid 762 through 782 Processing helix chain 'K' and resid 787 through 790 No H-bonds generated for 'chain 'K' and resid 787 through 790' Processing helix chain 'L' and resid 15 through 37 Processing helix chain 'L' and resid 50 through 52 No H-bonds generated for 'chain 'L' and resid 50 through 52' Processing helix chain 'L' and resid 64 through 81 removed outlier: 3.659A pdb=" N HIS L 73 " --> pdb=" O PHE L 69 " (cutoff:3.500A) Processing helix chain 'L' and resid 92 through 105 Proline residue: L 96 - end of helix removed outlier: 3.568A pdb=" N GLU L 105 " --> pdb=" O ALA L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 107 through 111 Processing helix chain 'L' and resid 119 through 128 Processing helix chain 'L' and resid 156 through 164 Processing helix chain 'L' and resid 178 through 182 Processing helix chain 'L' and resid 184 through 195 removed outlier: 3.626A pdb=" N TRP L 190 " --> pdb=" O LEU L 186 " (cutoff:3.500A) removed outlier: 5.181A pdb=" N HIS L 191 " --> pdb=" O ALA L 187 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N SER L 192 " --> pdb=" O THR L 188 " (cutoff:3.500A) removed outlier: 5.269A pdb=" N ASN L 193 " --> pdb=" O SER L 189 " (cutoff:3.500A) removed outlier: 5.860A pdb=" N LYS L 194 " --> pdb=" O TRP L 190 " (cutoff:3.500A) removed outlier: 4.603A pdb=" N PHE L 195 " --> pdb=" O HIS L 191 " (cutoff:3.500A) Processing helix chain 'L' and resid 220 through 223 No H-bonds generated for 'chain 'L' and resid 220 through 223' Processing helix chain 'L' and resid 226 through 235 Processing helix chain 'L' and resid 248 through 274 removed outlier: 4.280A pdb=" N GLY L 253 " --> pdb=" O ALA L 249 " (cutoff:3.500A) Processing helix chain 'L' and resid 310 through 312 No H-bonds generated for 'chain 'L' and resid 310 through 312' Processing helix chain 'L' and resid 324 through 337 removed outlier: 4.059A pdb=" N TYR L 337 " --> pdb=" O TRP L 333 " (cutoff:3.500A) Processing helix chain 'L' and resid 339 through 341 No H-bonds generated for 'chain 'L' and resid 339 through 341' Processing helix chain 'L' and resid 351 through 356 removed outlier: 3.883A pdb=" N ILE L 356 " --> pdb=" O GLU L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 360 through 362 No H-bonds generated for 'chain 'L' and resid 360 through 362' Processing helix chain 'L' and resid 372 through 375 Processing helix chain 'L' and resid 384 through 386 No H-bonds generated for 'chain 'L' and resid 384 through 386' Processing helix chain 'L' and resid 401 through 415 removed outlier: 4.510A pdb=" N LEU L 405 " --> pdb=" O SER L 401 " (cutoff:3.500A) Processing helix chain 'L' and resid 434 through 438 Processing helix chain 'L' and resid 450 through 455 removed outlier: 3.637A pdb=" N ASP L 454 " --> pdb=" O GLU L 451 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLY L 455 " --> pdb=" O ASP L 452 " (cutoff:3.500A) Processing helix chain 'L' and resid 470 through 482 Processing helix chain 'L' and resid 496 through 515 removed outlier: 4.699A pdb=" N SER L 501 " --> pdb=" O VAL L 498 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N VAL L 512 " --> pdb=" O TRP L 509 " (cutoff:3.500A) Processing helix chain 'L' and resid 548 through 556 removed outlier: 3.875A pdb=" N LYS L 556 " --> pdb=" O LEU L 552 " (cutoff:3.500A) Processing helix chain 'L' and resid 569 through 579 Processing helix chain 'L' and resid 602 through 611 Processing helix chain 'L' and resid 637 through 652 Processing helix chain 'L' and resid 666 through 669 Processing helix chain 'L' and resid 681 through 687 Processing helix chain 'L' and resid 702 through 708 Processing helix chain 'L' and resid 715 through 717 No H-bonds generated for 'chain 'L' and resid 715 through 717' Processing helix chain 'L' and resid 732 through 738 Processing helix chain 'L' and resid 743 through 753 Processing helix chain 'L' and resid 755 through 757 No H-bonds generated for 'chain 'L' and resid 755 through 757' Processing helix chain 'L' and resid 762 through 782 Processing helix chain 'L' and resid 787 through 790 No H-bonds generated for 'chain 'L' and resid 787 through 790' Processing sheet with id= A, first strand: chain 'A' and resid 84 through 89 removed outlier: 6.930A pdb=" N ALA A 203 " --> pdb=" O VAL A 172 " (cutoff:3.500A) removed outlier: 7.502A pdb=" N CYS A 174 " --> pdb=" O ALA A 203 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N LEU A 205 " --> pdb=" O CYS A 174 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE A 176 " --> pdb=" O LEU A 205 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N ILE A 207 " --> pdb=" O ILE A 176 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 397 through 400 removed outlier: 4.875A pdb=" N SER A 397 " --> pdb=" O GLN A 598 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 464 through 466 removed outlier: 6.528A pdb=" N LEU A 422 " --> pdb=" O MET A 465 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N PHE A 488 " --> pdb=" O PHE A 423 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 613 through 616 removed outlier: 4.643A pdb=" N PHE A 660 " --> pdb=" O TRP A 616 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL A 629 " --> pdb=" O ARG A 659 " (cutoff:3.500A) removed outlier: 7.674A pdb=" N VAL A 661 " --> pdb=" O VAL A 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE A 631 " --> pdb=" O VAL A 661 " (cutoff:3.500A) removed outlier: 7.706A pdb=" N VAL A 663 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER A 633 " --> pdb=" O VAL A 663 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 84 through 89 removed outlier: 6.918A pdb=" N ALA B 203 " --> pdb=" O VAL B 172 " (cutoff:3.500A) removed outlier: 7.494A pdb=" N CYS B 174 " --> pdb=" O ALA B 203 " (cutoff:3.500A) removed outlier: 6.046A pdb=" N LEU B 205 " --> pdb=" O CYS B 174 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N ILE B 176 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N ILE B 207 " --> pdb=" O ILE B 176 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 397 through 400 removed outlier: 4.863A pdb=" N SER B 397 " --> pdb=" O GLN B 598 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'B' and resid 464 through 466 removed outlier: 6.520A pdb=" N LEU B 422 " --> pdb=" O MET B 465 " (cutoff:3.500A) removed outlier: 6.499A pdb=" N PHE B 488 " --> pdb=" O PHE B 423 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'B' and resid 613 through 616 removed outlier: 4.652A pdb=" N PHE B 660 " --> pdb=" O TRP B 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL B 629 " --> pdb=" O ARG B 659 " (cutoff:3.500A) removed outlier: 7.690A pdb=" N VAL B 661 " --> pdb=" O VAL B 629 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE B 631 " --> pdb=" O VAL B 661 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N VAL B 663 " --> pdb=" O ILE B 631 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER B 633 " --> pdb=" O VAL B 663 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 84 through 89 removed outlier: 6.889A pdb=" N ALA C 203 " --> pdb=" O VAL C 172 " (cutoff:3.500A) removed outlier: 7.480A pdb=" N CYS C 174 " --> pdb=" O ALA C 203 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N LEU C 205 " --> pdb=" O CYS C 174 " (cutoff:3.500A) removed outlier: 7.153A pdb=" N ILE C 176 " --> pdb=" O LEU C 205 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N ILE C 207 " --> pdb=" O ILE C 176 " (cutoff:3.500A) removed outlier: 8.795A pdb=" N LEU C 208 " --> pdb=" O PRO C 285 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ILE C 287 " --> pdb=" O LEU C 208 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'C' and resid 397 through 400 removed outlier: 4.852A pdb=" N SER C 397 " --> pdb=" O GLN C 598 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'C' and resid 464 through 466 removed outlier: 6.545A pdb=" N LEU C 422 " --> pdb=" O MET C 465 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE C 488 " --> pdb=" O PHE C 423 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'C' and resid 613 through 616 removed outlier: 4.626A pdb=" N PHE C 660 " --> pdb=" O TRP C 616 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N VAL C 629 " --> pdb=" O ARG C 659 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL C 661 " --> pdb=" O VAL C 629 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N ILE C 631 " --> pdb=" O VAL C 661 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL C 663 " --> pdb=" O ILE C 631 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N SER C 633 " --> pdb=" O VAL C 663 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'D' and resid 84 through 89 removed outlier: 6.872A pdb=" N ALA D 203 " --> pdb=" O VAL D 172 " (cutoff:3.500A) removed outlier: 7.452A pdb=" N CYS D 174 " --> pdb=" O ALA D 203 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N LEU D 205 " --> pdb=" O CYS D 174 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N ILE D 176 " --> pdb=" O LEU D 205 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ILE D 207 " --> pdb=" O ILE D 176 " (cutoff:3.500A) removed outlier: 8.788A pdb=" N LEU D 208 " --> pdb=" O PRO D 285 " (cutoff:3.500A) removed outlier: 7.000A pdb=" N ILE D 287 " --> pdb=" O LEU D 208 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'D' and resid 397 through 400 removed outlier: 4.861A pdb=" N SER D 397 " --> pdb=" O GLN D 598 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'D' and resid 464 through 466 removed outlier: 6.575A pdb=" N LEU D 422 " --> pdb=" O MET D 465 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N PHE D 488 " --> pdb=" O PHE D 423 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'D' and resid 613 through 616 removed outlier: 4.638A pdb=" N PHE D 660 " --> pdb=" O TRP D 616 " (cutoff:3.500A) removed outlier: 6.641A pdb=" N VAL D 629 " --> pdb=" O ARG D 659 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL D 661 " --> pdb=" O VAL D 629 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N ILE D 631 " --> pdb=" O VAL D 661 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL D 663 " --> pdb=" O ILE D 631 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N SER D 633 " --> pdb=" O VAL D 663 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'E' and resid 84 through 89 removed outlier: 6.904A pdb=" N ALA E 203 " --> pdb=" O VAL E 172 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N CYS E 174 " --> pdb=" O ALA E 203 " (cutoff:3.500A) removed outlier: 6.090A pdb=" N LEU E 205 " --> pdb=" O CYS E 174 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N ILE E 176 " --> pdb=" O LEU E 205 " (cutoff:3.500A) removed outlier: 6.226A pdb=" N ILE E 207 " --> pdb=" O ILE E 176 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'E' and resid 397 through 400 removed outlier: 4.857A pdb=" N SER E 397 " --> pdb=" O GLN E 598 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'E' and resid 464 through 466 removed outlier: 6.518A pdb=" N LEU E 422 " --> pdb=" O MET E 465 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE E 488 " --> pdb=" O PHE E 423 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'E' and resid 613 through 616 removed outlier: 4.651A pdb=" N PHE E 660 " --> pdb=" O TRP E 616 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N VAL E 629 " --> pdb=" O ARG E 659 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL E 661 " --> pdb=" O VAL E 629 " (cutoff:3.500A) removed outlier: 6.180A pdb=" N ILE E 631 " --> pdb=" O VAL E 661 " (cutoff:3.500A) removed outlier: 7.707A pdb=" N VAL E 663 " --> pdb=" O ILE E 631 " (cutoff:3.500A) removed outlier: 6.512A pdb=" N SER E 633 " --> pdb=" O VAL E 663 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'F' and resid 84 through 89 removed outlier: 6.923A pdb=" N ALA F 203 " --> pdb=" O VAL F 172 " (cutoff:3.500A) removed outlier: 7.501A pdb=" N CYS F 174 " --> pdb=" O ALA F 203 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU F 205 " --> pdb=" O CYS F 174 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N ILE F 176 " --> pdb=" O LEU F 205 " (cutoff:3.500A) removed outlier: 6.206A pdb=" N ILE F 207 " --> pdb=" O ILE F 176 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'F' and resid 397 through 400 removed outlier: 4.876A pdb=" N SER F 397 " --> pdb=" O GLN F 598 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'F' and resid 464 through 466 removed outlier: 6.561A pdb=" N LEU F 422 " --> pdb=" O MET F 465 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N PHE F 488 " --> pdb=" O PHE F 423 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'F' and resid 613 through 616 removed outlier: 4.623A pdb=" N PHE F 660 " --> pdb=" O TRP F 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL F 629 " --> pdb=" O ARG F 659 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL F 661 " --> pdb=" O VAL F 629 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE F 631 " --> pdb=" O VAL F 661 " (cutoff:3.500A) removed outlier: 7.718A pdb=" N VAL F 663 " --> pdb=" O ILE F 631 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N SER F 633 " --> pdb=" O VAL F 663 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'G' and resid 84 through 89 removed outlier: 6.922A pdb=" N ALA G 203 " --> pdb=" O VAL G 172 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N CYS G 174 " --> pdb=" O ALA G 203 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N LEU G 205 " --> pdb=" O CYS G 174 " (cutoff:3.500A) removed outlier: 7.159A pdb=" N ILE G 176 " --> pdb=" O LEU G 205 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N ILE G 207 " --> pdb=" O ILE G 176 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'G' and resid 397 through 400 removed outlier: 4.874A pdb=" N SER G 397 " --> pdb=" O GLN G 598 " (cutoff:3.500A) Processing sheet with id= AA, first strand: chain 'G' and resid 464 through 466 removed outlier: 6.528A pdb=" N LEU G 422 " --> pdb=" O MET G 465 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N PHE G 488 " --> pdb=" O PHE G 423 " (cutoff:3.500A) Processing sheet with id= AB, first strand: chain 'G' and resid 613 through 616 removed outlier: 4.619A pdb=" N PHE G 660 " --> pdb=" O TRP G 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL G 629 " --> pdb=" O ARG G 659 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL G 661 " --> pdb=" O VAL G 629 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE G 631 " --> pdb=" O VAL G 661 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL G 663 " --> pdb=" O ILE G 631 " (cutoff:3.500A) removed outlier: 6.504A pdb=" N SER G 633 " --> pdb=" O VAL G 663 " (cutoff:3.500A) Processing sheet with id= AC, first strand: chain 'H' and resid 84 through 89 removed outlier: 6.910A pdb=" N ALA H 203 " --> pdb=" O VAL H 172 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N CYS H 174 " --> pdb=" O ALA H 203 " (cutoff:3.500A) removed outlier: 6.043A pdb=" N LEU H 205 " --> pdb=" O CYS H 174 " (cutoff:3.500A) removed outlier: 7.131A pdb=" N ILE H 176 " --> pdb=" O LEU H 205 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N ILE H 207 " --> pdb=" O ILE H 176 " (cutoff:3.500A) Processing sheet with id= AD, first strand: chain 'H' and resid 397 through 400 removed outlier: 4.864A pdb=" N SER H 397 " --> pdb=" O GLN H 598 " (cutoff:3.500A) Processing sheet with id= AE, first strand: chain 'H' and resid 464 through 466 removed outlier: 6.516A pdb=" N LEU H 422 " --> pdb=" O MET H 465 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N PHE H 488 " --> pdb=" O PHE H 423 " (cutoff:3.500A) Processing sheet with id= AF, first strand: chain 'H' and resid 613 through 616 removed outlier: 4.651A pdb=" N PHE H 660 " --> pdb=" O TRP H 616 " (cutoff:3.500A) removed outlier: 6.634A pdb=" N VAL H 629 " --> pdb=" O ARG H 659 " (cutoff:3.500A) removed outlier: 7.689A pdb=" N VAL H 661 " --> pdb=" O VAL H 629 " (cutoff:3.500A) removed outlier: 6.181A pdb=" N ILE H 631 " --> pdb=" O VAL H 661 " (cutoff:3.500A) removed outlier: 7.709A pdb=" N VAL H 663 " --> pdb=" O ILE H 631 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N SER H 633 " --> pdb=" O VAL H 663 " (cutoff:3.500A) Processing sheet with id= AG, first strand: chain 'I' and resid 84 through 89 removed outlier: 6.890A pdb=" N ALA I 203 " --> pdb=" O VAL I 172 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N CYS I 174 " --> pdb=" O ALA I 203 " (cutoff:3.500A) removed outlier: 6.053A pdb=" N LEU I 205 " --> pdb=" O CYS I 174 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ILE I 176 " --> pdb=" O LEU I 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE I 207 " --> pdb=" O ILE I 176 " (cutoff:3.500A) Processing sheet with id= AH, first strand: chain 'I' and resid 397 through 400 removed outlier: 4.853A pdb=" N SER I 397 " --> pdb=" O GLN I 598 " (cutoff:3.500A) Processing sheet with id= AI, first strand: chain 'I' and resid 464 through 466 removed outlier: 6.546A pdb=" N LEU I 422 " --> pdb=" O MET I 465 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N PHE I 488 " --> pdb=" O PHE I 423 " (cutoff:3.500A) Processing sheet with id= AJ, first strand: chain 'I' and resid 613 through 616 removed outlier: 4.625A pdb=" N PHE I 660 " --> pdb=" O TRP I 616 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL I 629 " --> pdb=" O ARG I 659 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N VAL I 661 " --> pdb=" O VAL I 629 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE I 631 " --> pdb=" O VAL I 661 " (cutoff:3.500A) removed outlier: 7.701A pdb=" N VAL I 663 " --> pdb=" O ILE I 631 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N SER I 633 " --> pdb=" O VAL I 663 " (cutoff:3.500A) Processing sheet with id= AK, first strand: chain 'J' and resid 84 through 89 removed outlier: 6.862A pdb=" N ALA J 203 " --> pdb=" O VAL J 172 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N CYS J 174 " --> pdb=" O ALA J 203 " (cutoff:3.500A) removed outlier: 6.023A pdb=" N LEU J 205 " --> pdb=" O CYS J 174 " (cutoff:3.500A) removed outlier: 7.147A pdb=" N ILE J 176 " --> pdb=" O LEU J 205 " (cutoff:3.500A) removed outlier: 6.203A pdb=" N ILE J 207 " --> pdb=" O ILE J 176 " (cutoff:3.500A) removed outlier: 8.796A pdb=" N LEU J 208 " --> pdb=" O PRO J 285 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N ILE J 287 " --> pdb=" O LEU J 208 " (cutoff:3.500A) Processing sheet with id= AL, first strand: chain 'J' and resid 397 through 400 removed outlier: 4.862A pdb=" N SER J 397 " --> pdb=" O GLN J 598 " (cutoff:3.500A) Processing sheet with id= AM, first strand: chain 'J' and resid 464 through 466 removed outlier: 8.602A pdb=" N MET J 465 " --> pdb=" O PHE J 420 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N LEU J 422 " --> pdb=" O MET J 465 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N HIS J 486 " --> pdb=" O ARG J 421 " (cutoff:3.500A) removed outlier: 8.317A pdb=" N PHE J 423 " --> pdb=" O HIS J 486 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N PHE J 488 " --> pdb=" O PHE J 423 " (cutoff:3.500A) removed outlier: 4.616A pdb=" N ASN J 527 " --> pdb=" O GLY J 487 " (cutoff:3.500A) Processing sheet with id= AN, first strand: chain 'J' and resid 613 through 616 removed outlier: 4.635A pdb=" N PHE J 660 " --> pdb=" O TRP J 616 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N VAL J 629 " --> pdb=" O ARG J 659 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL J 661 " --> pdb=" O VAL J 629 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE J 631 " --> pdb=" O VAL J 661 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N VAL J 663 " --> pdb=" O ILE J 631 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER J 633 " --> pdb=" O VAL J 663 " (cutoff:3.500A) Processing sheet with id= AO, first strand: chain 'K' and resid 84 through 89 removed outlier: 6.902A pdb=" N ALA K 203 " --> pdb=" O VAL K 172 " (cutoff:3.500A) removed outlier: 7.506A pdb=" N CYS K 174 " --> pdb=" O ALA K 203 " (cutoff:3.500A) removed outlier: 6.056A pdb=" N LEU K 205 " --> pdb=" O CYS K 174 " (cutoff:3.500A) removed outlier: 7.143A pdb=" N ILE K 176 " --> pdb=" O LEU K 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE K 207 " --> pdb=" O ILE K 176 " (cutoff:3.500A) Processing sheet with id= AP, first strand: chain 'K' and resid 397 through 400 removed outlier: 4.861A pdb=" N SER K 397 " --> pdb=" O GLN K 598 " (cutoff:3.500A) Processing sheet with id= AQ, first strand: chain 'K' and resid 464 through 466 removed outlier: 6.518A pdb=" N LEU K 422 " --> pdb=" O MET K 465 " (cutoff:3.500A) removed outlier: 6.494A pdb=" N PHE K 488 " --> pdb=" O PHE K 423 " (cutoff:3.500A) Processing sheet with id= AR, first strand: chain 'K' and resid 613 through 616 removed outlier: 4.639A pdb=" N PHE K 660 " --> pdb=" O TRP K 616 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL K 629 " --> pdb=" O ARG K 659 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL K 661 " --> pdb=" O VAL K 629 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ILE K 631 " --> pdb=" O VAL K 661 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL K 663 " --> pdb=" O ILE K 631 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N SER K 633 " --> pdb=" O VAL K 663 " (cutoff:3.500A) Processing sheet with id= AS, first strand: chain 'L' and resid 84 through 89 removed outlier: 6.918A pdb=" N ALA L 203 " --> pdb=" O VAL L 172 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N CYS L 174 " --> pdb=" O ALA L 203 " (cutoff:3.500A) removed outlier: 6.058A pdb=" N LEU L 205 " --> pdb=" O CYS L 174 " (cutoff:3.500A) removed outlier: 7.152A pdb=" N ILE L 176 " --> pdb=" O LEU L 205 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N ILE L 207 " --> pdb=" O ILE L 176 " (cutoff:3.500A) Processing sheet with id= AT, first strand: chain 'L' and resid 397 through 400 removed outlier: 4.875A pdb=" N SER L 397 " --> pdb=" O GLN L 598 " (cutoff:3.500A) Processing sheet with id= AU, first strand: chain 'L' and resid 464 through 466 removed outlier: 6.563A pdb=" N LEU L 422 " --> pdb=" O MET L 465 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N PHE L 488 " --> pdb=" O PHE L 423 " (cutoff:3.500A) Processing sheet with id= AV, first strand: chain 'L' and resid 613 through 616 removed outlier: 4.639A pdb=" N PHE L 660 " --> pdb=" O TRP L 616 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N VAL L 629 " --> pdb=" O ARG L 659 " (cutoff:3.500A) removed outlier: 7.672A pdb=" N VAL L 661 " --> pdb=" O VAL L 629 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ILE L 631 " --> pdb=" O VAL L 661 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N VAL L 663 " --> pdb=" O ILE L 631 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N SER L 633 " --> pdb=" O VAL L 663 " (cutoff:3.500A) 2790 hydrogen bonds defined for protein. 7308 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: 30.38 Time building geometry restraints manager: 26.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 25528 1.34 - 1.46: 12877 1.46 - 1.57: 39148 1.57 - 1.69: 87 1.69 - 1.81: 276 Bond restraints: 77916 Sorted by residual: bond pdb=" O3A ANP L 901 " pdb=" PB ANP L 901 " ideal model delta sigma weight residual 1.700 1.551 0.149 2.00e-02 2.50e+03 5.52e+01 bond pdb=" O3A ANP I 901 " pdb=" PB ANP I 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O3A ANP F 901 " pdb=" PB ANP F 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.51e+01 bond pdb=" O3A ANP H 901 " pdb=" PB ANP H 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 bond pdb=" O3A ANP G 901 " pdb=" PB ANP G 901 " ideal model delta sigma weight residual 1.700 1.552 0.148 2.00e-02 2.50e+03 5.49e+01 ... (remaining 77911 not shown) Histogram of bond angle deviations from ideal: 91.24 - 100.97: 94 100.97 - 110.71: 27259 110.71 - 120.45: 47891 120.45 - 130.18: 30311 130.18 - 139.92: 885 Bond angle restraints: 106440 Sorted by residual: angle pdb=" O2B TPP B 902 " pdb=" PB TPP B 902 " pdb=" O3A TPP B 902 " ideal model delta sigma weight residual 104.26 111.30 -7.04 1.33e+00 5.64e-01 2.79e+01 angle pdb=" O2B TPP D 902 " pdb=" PB TPP D 902 " pdb=" O3A TPP D 902 " ideal model delta sigma weight residual 104.26 111.27 -7.01 1.33e+00 5.64e-01 2.77e+01 angle pdb=" O2B TPP H 902 " pdb=" PB TPP H 902 " pdb=" O3A TPP H 902 " ideal model delta sigma weight residual 104.26 111.26 -7.00 1.33e+00 5.64e-01 2.76e+01 angle pdb=" O2B TPP L 902 " pdb=" PB TPP L 902 " pdb=" O3A TPP L 902 " ideal model delta sigma weight residual 104.26 111.17 -6.91 1.33e+00 5.64e-01 2.69e+01 angle pdb=" O2B TPP J 902 " pdb=" PB TPP J 902 " pdb=" O3A TPP J 902 " ideal model delta sigma weight residual 104.26 111.16 -6.90 1.33e+00 5.64e-01 2.68e+01 ... (remaining 106435 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.87: 43120 17.87 - 35.73: 2138 35.73 - 53.60: 364 53.60 - 71.47: 168 71.47 - 89.33: 62 Dihedral angle restraints: 45852 sinusoidal: 18552 harmonic: 27300 Sorted by residual: dihedral pdb=" CA GLY L 294 " pdb=" C GLY L 294 " pdb=" N TRP L 295 " pdb=" CA TRP L 295 " ideal model delta harmonic sigma weight residual 180.00 -157.27 -22.73 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA GLY F 294 " pdb=" C GLY F 294 " pdb=" N TRP F 295 " pdb=" CA TRP F 295 " ideal model delta harmonic sigma weight residual 180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA GLY G 294 " pdb=" C GLY G 294 " pdb=" N TRP G 295 " pdb=" CA TRP G 295 " ideal model delta harmonic sigma weight residual -180.00 -157.33 -22.67 0 5.00e+00 4.00e-02 2.06e+01 ... (remaining 45849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.070: 10160 0.070 - 0.140: 1175 0.140 - 0.209: 17 0.209 - 0.279: 10 0.279 - 0.349: 2 Chirality restraints: 11364 Sorted by residual: chirality pdb=" C3' ANP B 901 " pdb=" C2' ANP B 901 " pdb=" C4' ANP B 901 " pdb=" O3' ANP B 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.71 0.35 2.00e-01 2.50e+01 3.05e+00 chirality pdb=" C3' ANP D 901 " pdb=" C2' ANP D 901 " pdb=" C4' ANP D 901 " pdb=" O3' ANP D 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.70 0.35 2.00e-01 2.50e+01 2.99e+00 chirality pdb=" C3' ANP I 901 " pdb=" C2' ANP I 901 " pdb=" C4' ANP I 901 " pdb=" O3' ANP I 901 " both_signs ideal model delta sigma weight residual False -2.36 -2.62 0.26 2.00e-01 2.50e+01 1.67e+00 ... (remaining 11361 not shown) Planarity restraints: 13944 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY K 184 " -0.034 5.00e-02 4.00e+02 5.17e-02 4.27e+00 pdb=" N PRO K 185 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO K 185 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO K 185 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY E 184 " -0.034 5.00e-02 4.00e+02 5.11e-02 4.17e+00 pdb=" N PRO E 185 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO E 185 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO E 185 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY B 184 " 0.033 5.00e-02 4.00e+02 5.01e-02 4.01e+00 pdb=" N PRO B 185 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO B 185 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO B 185 " 0.028 5.00e-02 4.00e+02 ... (remaining 13941 not shown) Histogram of nonbonded interaction distances: 1.99 - 2.57: 895 2.57 - 3.15: 64316 3.15 - 3.73: 127306 3.73 - 4.32: 189218 4.32 - 4.90: 305643 Nonbonded interactions: 687378 Sorted by model distance: nonbonded pdb=" O2A TPP A 902 " pdb="MG MG A 903 " model vdw 1.987 2.170 nonbonded pdb=" O1A TPP J 902 " pdb="MG MG J 903 " model vdw 1.989 2.170 nonbonded pdb=" O2A TPP G 902 " pdb="MG MG G 903 " model vdw 1.992 2.170 nonbonded pdb=" O1A TPP L 902 " pdb="MG MG L 903 " model vdw 1.992 2.170 nonbonded pdb=" O1A TPP F 902 " pdb="MG MG F 903 " model vdw 1.992 2.170 ... (remaining 687373 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' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'B' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'C' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'D' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'E' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'F' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'G' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'H' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'I' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'J' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'K' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) selection = (chain 'L' and (resid 9 through 702 or resid 704 through 796 or resid 901 throug \ h 903)) } 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=0.38 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.060 Extract box with map and model: 14.380 Check model and map are aligned: 0.860 Set scattering table: 0.550 Process input model: 200.460 Find NCS groups from input model: 4.650 Set up NCS constraints: 0.690 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:13.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 238.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 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 : 0.005 0.149 77916 Z= 0.349 Angle : 0.599 15.285 106440 Z= 0.288 Chirality : 0.044 0.349 11364 Planarity : 0.004 0.052 13944 Dihedral : 12.120 89.332 28284 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.48 % Allowed : 3.19 % Favored : 96.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.34 (0.09), residues: 9468 helix: 0.89 (0.08), residues: 4242 sheet: 0.22 (0.15), residues: 1128 loop : -0.38 (0.09), residues: 4098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 61 HIS 0.004 0.001 HIS E 596 PHE 0.012 0.002 PHE I 233 TYR 0.009 0.001 TYR A 723 ARG 0.004 0.000 ARG C 520 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 327 time to evaluate : 6.709 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: C 217 ASN cc_start: 0.7526 (m-40) cc_final: 0.6954 (m110) REVERT: D 217 ASN cc_start: 0.7424 (m-40) cc_final: 0.6811 (m110) REVERT: E 217 ASN cc_start: 0.7524 (m-40) cc_final: 0.6908 (m110) REVERT: J 217 ASN cc_start: 0.7496 (m-40) cc_final: 0.6894 (m110) REVERT: K 217 ASN cc_start: 0.7536 (m-40) cc_final: 0.6932 (m110) outliers start: 26 outliers final: 7 residues processed: 353 average time/residue: 1.5232 time to fit residues: 723.4379 Evaluate side-chains 189 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 182 time to evaluate : 6.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain K residue 305 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 790 optimal weight: 9.9990 chunk 709 optimal weight: 0.7980 chunk 393 optimal weight: 8.9990 chunk 242 optimal weight: 5.9990 chunk 478 optimal weight: 0.9980 chunk 379 optimal weight: 0.9990 chunk 733 optimal weight: 0.4980 chunk 283 optimal weight: 4.9990 chunk 446 optimal weight: 0.0270 chunk 546 optimal weight: 30.0000 chunk 849 optimal weight: 0.6980 overall best weight: 0.6038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8102 moved from start: 0.0938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 77916 Z= 0.144 Angle : 0.491 6.285 106440 Z= 0.250 Chirality : 0.042 0.153 11364 Planarity : 0.005 0.047 13944 Dihedral : 8.418 67.917 10796 Min Nonbonded Distance : 1.995 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.10 % Allowed : 5.71 % Favored : 93.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.09), residues: 9468 helix: 1.09 (0.08), residues: 4244 sheet: 0.20 (0.15), residues: 1128 loop : -0.39 (0.09), residues: 4096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP J 476 HIS 0.005 0.001 HIS D 706 PHE 0.013 0.001 PHE D 489 TYR 0.021 0.001 TYR I 723 ARG 0.004 0.000 ARG C 274 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 76 poor density : 249 time to evaluate : 6.663 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: B 274 ARG cc_start: 0.7405 (OUTLIER) cc_final: 0.7126 (mtt180) REVERT: C 217 ASN cc_start: 0.7379 (m-40) cc_final: 0.6831 (m110) REVERT: D 283 MET cc_start: 0.6718 (OUTLIER) cc_final: 0.6479 (tpt) REVERT: F 142 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8162 (mt-10) REVERT: H 274 ARG cc_start: 0.7387 (OUTLIER) cc_final: 0.7179 (mtt180) REVERT: I 217 ASN cc_start: 0.7389 (m-40) cc_final: 0.6844 (m110) REVERT: J 283 MET cc_start: 0.6711 (OUTLIER) cc_final: 0.6470 (tpt) REVERT: L 142 GLU cc_start: 0.8464 (OUTLIER) cc_final: 0.8160 (mt-10) outliers start: 76 outliers final: 10 residues processed: 283 average time/residue: 1.3475 time to fit residues: 534.2042 Evaluate side-chains 203 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 187 time to evaluate : 6.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain G residue 758 ARG Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 283 MET Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 472 optimal weight: 6.9990 chunk 263 optimal weight: 2.9990 chunk 707 optimal weight: 20.0000 chunk 578 optimal weight: 0.9990 chunk 234 optimal weight: 30.0000 chunk 851 optimal weight: 6.9990 chunk 919 optimal weight: 9.9990 chunk 758 optimal weight: 4.9990 chunk 844 optimal weight: 0.9980 chunk 290 optimal weight: 0.6980 chunk 683 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 45 GLN L 45 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8121 moved from start: 0.1034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 77916 Z= 0.183 Angle : 0.469 9.699 106440 Z= 0.238 Chirality : 0.042 0.147 11364 Planarity : 0.004 0.042 13944 Dihedral : 7.395 72.813 10791 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 8.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.22 % Allowed : 6.25 % Favored : 92.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.49 (0.09), residues: 9468 helix: 1.17 (0.08), residues: 4240 sheet: 0.22 (0.15), residues: 1152 loop : -0.48 (0.09), residues: 4076 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 476 HIS 0.003 0.001 HIS C 699 PHE 0.013 0.001 PHE H 69 TYR 0.016 0.001 TYR C 723 ARG 0.005 0.000 ARG F 758 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 209 time to evaluate : 6.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8467 (OUTLIER) cc_final: 0.8134 (mt-10) REVERT: A 217 ASN cc_start: 0.7503 (m-40) cc_final: 0.7006 (m110) REVERT: B 274 ARG cc_start: 0.7525 (OUTLIER) cc_final: 0.7167 (mtt180) REVERT: G 142 GLU cc_start: 0.8461 (OUTLIER) cc_final: 0.8123 (mt-10) REVERT: G 217 ASN cc_start: 0.7424 (m-40) cc_final: 0.6930 (m110) REVERT: H 274 ARG cc_start: 0.7426 (OUTLIER) cc_final: 0.7113 (mtt180) REVERT: H 465 MET cc_start: 0.8290 (OUTLIER) cc_final: 0.8052 (mtp) REVERT: I 217 ASN cc_start: 0.7352 (m-40) cc_final: 0.6794 (m110) outliers start: 85 outliers final: 20 residues processed: 248 average time/residue: 1.3590 time to fit residues: 478.8669 Evaluate side-chains 214 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 189 time to evaluate : 6.582 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 465 MET Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 305 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 841 optimal weight: 8.9990 chunk 640 optimal weight: 1.9990 chunk 441 optimal weight: 7.9990 chunk 94 optimal weight: 2.9990 chunk 406 optimal weight: 9.9990 chunk 571 optimal weight: 3.9990 chunk 854 optimal weight: 0.0570 chunk 904 optimal weight: 8.9990 chunk 446 optimal weight: 4.9990 chunk 809 optimal weight: 4.9990 chunk 243 optimal weight: 10.0000 overall best weight: 2.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 45 GLN B 45 GLN E 45 GLN ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 45 GLN H 45 GLN ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 45 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8136 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 77916 Z= 0.226 Angle : 0.472 9.105 106440 Z= 0.242 Chirality : 0.043 0.148 11364 Planarity : 0.004 0.041 13944 Dihedral : 7.013 77.113 10791 Min Nonbonded Distance : 1.938 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 1.32 % Allowed : 6.28 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.53 (0.09), residues: 9468 helix: 1.20 (0.08), residues: 4182 sheet: 0.20 (0.16), residues: 1152 loop : -0.41 (0.09), residues: 4134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 476 HIS 0.003 0.001 HIS G 226 PHE 0.013 0.001 PHE F 69 TYR 0.016 0.001 TYR J 723 ARG 0.003 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 194 time to evaluate : 6.692 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8470 (OUTLIER) cc_final: 0.8130 (mt-10) REVERT: A 217 ASN cc_start: 0.7476 (m-40) cc_final: 0.6973 (m110) REVERT: B 274 ARG cc_start: 0.7479 (OUTLIER) cc_final: 0.7144 (mtt180) REVERT: C 711 ARG cc_start: 0.7191 (OUTLIER) cc_final: 0.6979 (mtp180) REVERT: D 122 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8392 (tt) REVERT: E 742 ASP cc_start: 0.8211 (p0) cc_final: 0.7998 (p0) REVERT: G 142 GLU cc_start: 0.8462 (OUTLIER) cc_final: 0.8119 (mt-10) REVERT: H 274 ARG cc_start: 0.7378 (OUTLIER) cc_final: 0.7107 (mtt180) REVERT: I 217 ASN cc_start: 0.7358 (m-40) cc_final: 0.6817 (m110) REVERT: I 283 MET cc_start: 0.6512 (OUTLIER) cc_final: 0.6282 (tpt) REVERT: J 122 LEU cc_start: 0.8693 (OUTLIER) cc_final: 0.8415 (tt) outliers start: 93 outliers final: 21 residues processed: 243 average time/residue: 1.3818 time to fit residues: 470.7069 Evaluate side-chains 217 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 188 time to evaluate : 6.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain I residue 283 MET Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 122 LEU Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 305 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 753 optimal weight: 10.0000 chunk 513 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 673 optimal weight: 0.8980 chunk 373 optimal weight: 7.9990 chunk 772 optimal weight: 3.9990 chunk 625 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 461 optimal weight: 4.9990 chunk 812 optimal weight: 2.9990 chunk 228 optimal weight: 2.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 77916 Z= 0.210 Angle : 0.461 8.772 106440 Z= 0.235 Chirality : 0.042 0.146 11364 Planarity : 0.004 0.041 13944 Dihedral : 6.906 77.244 10791 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.50 % Favored : 96.50 % Rotamer: Outliers : 1.24 % Allowed : 6.65 % Favored : 92.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.56 (0.09), residues: 9468 helix: 1.24 (0.08), residues: 4170 sheet: 0.18 (0.16), residues: 1154 loop : -0.40 (0.09), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 61 HIS 0.003 0.001 HIS A 226 PHE 0.012 0.001 PHE K 69 TYR 0.013 0.001 TYR C 723 ARG 0.003 0.000 ARG A 758 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 88 poor density : 204 time to evaluate : 6.786 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8456 (OUTLIER) cc_final: 0.8112 (mt-10) REVERT: A 217 ASN cc_start: 0.7484 (m-40) cc_final: 0.6905 (m110) REVERT: A 514 LYS cc_start: 0.8615 (ttpt) cc_final: 0.8322 (mtpt) REVERT: B 274 ARG cc_start: 0.7505 (OUTLIER) cc_final: 0.7179 (mtt180) REVERT: C 711 ARG cc_start: 0.7186 (OUTLIER) cc_final: 0.6983 (mtp180) REVERT: D 122 LEU cc_start: 0.8696 (OUTLIER) cc_final: 0.8404 (tt) REVERT: D 283 MET cc_start: 0.6515 (OUTLIER) cc_final: 0.6286 (tpt) REVERT: E 742 ASP cc_start: 0.8206 (p0) cc_final: 0.7975 (p0) REVERT: F 217 ASN cc_start: 0.7455 (m-40) cc_final: 0.6786 (m110) REVERT: F 514 LYS cc_start: 0.8645 (ttpt) cc_final: 0.8387 (mtpt) REVERT: G 142 GLU cc_start: 0.8452 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: G 514 LYS cc_start: 0.8616 (ttpt) cc_final: 0.8346 (mtpt) REVERT: H 274 ARG cc_start: 0.7425 (OUTLIER) cc_final: 0.7173 (mtt180) REVERT: J 283 MET cc_start: 0.6510 (OUTLIER) cc_final: 0.6285 (tpt) REVERT: L 514 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8353 (mtpt) outliers start: 88 outliers final: 33 residues processed: 249 average time/residue: 1.3297 time to fit residues: 475.9739 Evaluate side-chains 225 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 184 time to evaluate : 6.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 283 MET Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain H residue 274 ARG Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 283 MET Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 551 ASP Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 304 optimal weight: 10.0000 chunk 814 optimal weight: 20.0000 chunk 178 optimal weight: 9.9990 chunk 531 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 905 optimal weight: 10.0000 chunk 751 optimal weight: 4.9990 chunk 419 optimal weight: 9.9990 chunk 75 optimal weight: 6.9990 chunk 299 optimal weight: 5.9990 chunk 475 optimal weight: 0.8980 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 60 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.1201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 77916 Z= 0.285 Angle : 0.497 8.821 106440 Z= 0.255 Chirality : 0.044 0.145 11364 Planarity : 0.004 0.040 13944 Dihedral : 7.111 77.759 10791 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.39 % Allowed : 6.71 % Favored : 91.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.47 (0.09), residues: 9468 helix: 1.16 (0.08), residues: 4170 sheet: 0.12 (0.16), residues: 1154 loop : -0.43 (0.09), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 61 HIS 0.003 0.001 HIS K 699 PHE 0.013 0.002 PHE I 233 TYR 0.014 0.001 TYR I 723 ARG 0.003 0.000 ARG J 520 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 191 time to evaluate : 6.703 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: B 274 ARG cc_start: 0.7568 (OUTLIER) cc_final: 0.7262 (mtt180) REVERT: C 283 MET cc_start: 0.5900 (tpt) cc_final: 0.5661 (tpt) REVERT: C 711 ARG cc_start: 0.7212 (OUTLIER) cc_final: 0.7001 (mtp180) REVERT: D 122 LEU cc_start: 0.8716 (OUTLIER) cc_final: 0.8394 (tt) REVERT: E 742 ASP cc_start: 0.8231 (p0) cc_final: 0.8016 (p0) REVERT: F 286 MET cc_start: 0.6336 (OUTLIER) cc_final: 0.5741 (ttp) REVERT: F 514 LYS cc_start: 0.8638 (ttpt) cc_final: 0.8354 (mtpt) REVERT: G 286 MET cc_start: 0.6320 (OUTLIER) cc_final: 0.5730 (ttp) REVERT: G 514 LYS cc_start: 0.8636 (ttpt) cc_final: 0.8407 (mtpt) REVERT: H 601 ASP cc_start: 0.7603 (OUTLIER) cc_final: 0.7224 (p0) REVERT: I 217 ASN cc_start: 0.7368 (m-40) cc_final: 0.6815 (m110) REVERT: L 514 LYS cc_start: 0.8633 (ttpt) cc_final: 0.8407 (mtpt) outliers start: 100 outliers final: 41 residues processed: 239 average time/residue: 1.3259 time to fit residues: 450.6705 Evaluate side-chains 223 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 176 time to evaluate : 6.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 551 ASP Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 122 LEU Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 364 MET Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 364 MET Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 364 MET Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 286 MET Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 601 ASP Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 465 MET Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 364 MET Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 364 MET Chi-restraints excluded: chain L residue 551 ASP Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 873 optimal weight: 4.9990 chunk 102 optimal weight: 0.2980 chunk 515 optimal weight: 6.9990 chunk 661 optimal weight: 9.9990 chunk 512 optimal weight: 0.0010 chunk 762 optimal weight: 0.9980 chunk 505 optimal weight: 10.0000 chunk 902 optimal weight: 0.4980 chunk 564 optimal weight: 6.9990 chunk 550 optimal weight: 7.9990 chunk 416 optimal weight: 8.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8113 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 77916 Z= 0.151 Angle : 0.442 8.270 106440 Z= 0.225 Chirality : 0.041 0.146 11364 Planarity : 0.004 0.044 13944 Dihedral : 6.729 76.966 10791 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.22 % Allowed : 6.93 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 9468 helix: 1.32 (0.08), residues: 4170 sheet: 0.16 (0.16), residues: 1134 loop : -0.33 (0.10), residues: 4164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP I 476 HIS 0.004 0.001 HIS D 706 PHE 0.013 0.001 PHE K 69 TYR 0.012 0.001 TYR C 723 ARG 0.003 0.000 ARG F 758 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 301 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 86 poor density : 215 time to evaluate : 6.869 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 217 ASN cc_start: 0.7408 (m-40) cc_final: 0.6907 (m110) REVERT: A 514 LYS cc_start: 0.8597 (ttpt) cc_final: 0.8391 (mtpt) REVERT: A 601 ASP cc_start: 0.7602 (OUTLIER) cc_final: 0.7315 (p0) REVERT: A 665 ASP cc_start: 0.8154 (OUTLIER) cc_final: 0.7713 (t0) REVERT: B 274 ARG cc_start: 0.7547 (OUTLIER) cc_final: 0.7220 (mtt180) REVERT: B 665 ASP cc_start: 0.8216 (OUTLIER) cc_final: 0.7949 (t0) REVERT: D 601 ASP cc_start: 0.7641 (OUTLIER) cc_final: 0.7330 (p0) REVERT: E 665 ASP cc_start: 0.8213 (OUTLIER) cc_final: 0.7993 (t0) REVERT: F 142 GLU cc_start: 0.8468 (OUTLIER) cc_final: 0.8161 (mt-10) REVERT: F 286 MET cc_start: 0.6304 (OUTLIER) cc_final: 0.5705 (ttp) REVERT: F 665 ASP cc_start: 0.8180 (OUTLIER) cc_final: 0.7731 (t0) REVERT: G 217 ASN cc_start: 0.7425 (m-40) cc_final: 0.6919 (m110) REVERT: G 514 LYS cc_start: 0.8586 (ttpt) cc_final: 0.8370 (mtpt) REVERT: G 601 ASP cc_start: 0.7635 (OUTLIER) cc_final: 0.7271 (p0) REVERT: H 601 ASP cc_start: 0.7570 (OUTLIER) cc_final: 0.7227 (p0) REVERT: H 665 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7976 (t0) REVERT: J 516 GLU cc_start: 0.8195 (mm-30) cc_final: 0.7914 (mp0) REVERT: L 514 LYS cc_start: 0.8607 (ttpt) cc_final: 0.8395 (mtpt) outliers start: 86 outliers final: 37 residues processed: 255 average time/residue: 1.2561 time to fit residues: 466.7094 Evaluate side-chains 249 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 200 time to evaluate : 6.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 364 MET Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 551 ASP Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 665 ASP Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain F residue 665 ASP Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 364 MET Chi-restraints excluded: chain H residue 601 ASP Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 665 ASP Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 364 MET Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 551 ASP Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 558 optimal weight: 0.2980 chunk 360 optimal weight: 6.9990 chunk 538 optimal weight: 4.9990 chunk 271 optimal weight: 7.9990 chunk 177 optimal weight: 0.0040 chunk 174 optimal weight: 9.9990 chunk 573 optimal weight: 8.9990 chunk 614 optimal weight: 3.9990 chunk 446 optimal weight: 0.1980 chunk 84 optimal weight: 2.9990 chunk 709 optimal weight: 0.9990 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 77916 Z= 0.131 Angle : 0.433 8.986 106440 Z= 0.218 Chirality : 0.041 0.140 11364 Planarity : 0.004 0.044 13944 Dihedral : 6.512 76.908 10791 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.12 % Allowed : 7.17 % Favored : 91.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.75 (0.09), residues: 9468 helix: 1.44 (0.08), residues: 4170 sheet: 0.23 (0.16), residues: 1158 loop : -0.33 (0.10), residues: 4140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 476 HIS 0.004 0.001 HIS D 706 PHE 0.016 0.001 PHE K 69 TYR 0.013 0.001 TYR I 723 ARG 0.003 0.000 ARG A 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 317 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 79 poor density : 238 time to evaluate : 6.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8481 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: A 217 ASN cc_start: 0.7343 (m-40) cc_final: 0.6878 (m110) REVERT: A 514 LYS cc_start: 0.8561 (ttpt) cc_final: 0.8312 (mtpt) REVERT: A 665 ASP cc_start: 0.8144 (OUTLIER) cc_final: 0.7743 (t0) REVERT: B 274 ARG cc_start: 0.7475 (OUTLIER) cc_final: 0.7174 (mtt180) REVERT: B 665 ASP cc_start: 0.8153 (OUTLIER) cc_final: 0.7809 (t0) REVERT: D 283 MET cc_start: 0.5980 (tpt) cc_final: 0.5544 (tpt) REVERT: E 665 ASP cc_start: 0.8202 (OUTLIER) cc_final: 0.7915 (t0) REVERT: F 142 GLU cc_start: 0.8503 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: F 286 MET cc_start: 0.6299 (OUTLIER) cc_final: 0.5701 (ttp) REVERT: G 217 ASN cc_start: 0.7346 (m-40) cc_final: 0.6888 (m110) REVERT: G 514 LYS cc_start: 0.8543 (ttpt) cc_final: 0.8282 (mtpt) REVERT: G 601 ASP cc_start: 0.7485 (OUTLIER) cc_final: 0.7150 (p0) REVERT: H 665 ASP cc_start: 0.8191 (OUTLIER) cc_final: 0.7844 (t0) REVERT: I 283 MET cc_start: 0.6084 (tpt) cc_final: 0.5877 (tpt) REVERT: J 516 GLU cc_start: 0.8181 (mm-30) cc_final: 0.7899 (mp0) REVERT: J 601 ASP cc_start: 0.7552 (OUTLIER) cc_final: 0.7216 (p0) REVERT: L 142 GLU cc_start: 0.8496 (OUTLIER) cc_final: 0.8174 (mt-10) REVERT: L 514 LYS cc_start: 0.8552 (ttpt) cc_final: 0.8294 (mtpt) outliers start: 79 outliers final: 30 residues processed: 279 average time/residue: 1.2777 time to fit residues: 513.6668 Evaluate side-chains 245 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 204 time to evaluate : 6.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain B residue 665 ASP Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 551 ASP Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 665 ASP Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 286 MET Chi-restraints excluded: chain F residue 613 ILE Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 665 ASP Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 601 ASP Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 820 optimal weight: 4.9990 chunk 864 optimal weight: 1.9990 chunk 788 optimal weight: 5.9990 chunk 840 optimal weight: 10.0000 chunk 506 optimal weight: 0.2980 chunk 366 optimal weight: 0.5980 chunk 660 optimal weight: 9.9990 chunk 257 optimal weight: 3.9990 chunk 759 optimal weight: 10.0000 chunk 795 optimal weight: 4.9990 chunk 837 optimal weight: 6.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 555 ASN F 555 ASN G 555 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8120 moved from start: 0.1467 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 77916 Z= 0.199 Angle : 0.454 11.269 106440 Z= 0.229 Chirality : 0.042 0.141 11364 Planarity : 0.004 0.043 13944 Dihedral : 6.652 77.553 10791 Min Nonbonded Distance : 1.946 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 1.07 % Allowed : 7.35 % Favored : 91.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.69 (0.09), residues: 9468 helix: 1.38 (0.08), residues: 4172 sheet: 0.23 (0.16), residues: 1154 loop : -0.36 (0.10), residues: 4142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 476 HIS 0.003 0.001 HIS B 719 PHE 0.016 0.001 PHE E 69 TYR 0.016 0.001 TYR C 723 ARG 0.002 0.000 ARG L 758 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 195 time to evaluate : 6.708 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8138 (mt-10) REVERT: A 217 ASN cc_start: 0.7398 (m-40) cc_final: 0.6896 (m110) REVERT: A 665 ASP cc_start: 0.8232 (OUTLIER) cc_final: 0.7742 (t0) REVERT: B 274 ARG cc_start: 0.7524 (OUTLIER) cc_final: 0.7222 (mtt180) REVERT: C 711 ARG cc_start: 0.7221 (OUTLIER) cc_final: 0.7005 (mtp180) REVERT: D 601 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7241 (p0) REVERT: G 142 GLU cc_start: 0.8483 (OUTLIER) cc_final: 0.8136 (mt-10) REVERT: G 514 LYS cc_start: 0.8548 (ttpt) cc_final: 0.8334 (mtpt) REVERT: G 601 ASP cc_start: 0.7529 (OUTLIER) cc_final: 0.7179 (p0) REVERT: H 665 ASP cc_start: 0.8256 (OUTLIER) cc_final: 0.8036 (t0) REVERT: I 283 MET cc_start: 0.6171 (tpt) cc_final: 0.5960 (tpt) REVERT: J 283 MET cc_start: 0.6015 (tpt) cc_final: 0.5658 (tpt) REVERT: J 516 GLU cc_start: 0.8192 (mm-30) cc_final: 0.7890 (mp0) REVERT: J 601 ASP cc_start: 0.7593 (OUTLIER) cc_final: 0.7261 (p0) REVERT: L 514 LYS cc_start: 0.8544 (ttpt) cc_final: 0.8331 (mtpt) outliers start: 75 outliers final: 40 residues processed: 237 average time/residue: 1.3146 time to fit residues: 445.6461 Evaluate side-chains 241 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 192 time to evaluate : 6.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 255 MET Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 274 ARG Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 315 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain F residue 255 MET Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 255 MET Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 665 ASP Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 465 MET Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 465 MET Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 601 ASP Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 552 optimal weight: 4.9990 chunk 888 optimal weight: 0.9980 chunk 542 optimal weight: 0.7980 chunk 421 optimal weight: 4.9990 chunk 617 optimal weight: 0.9980 chunk 932 optimal weight: 6.9990 chunk 858 optimal weight: 30.0000 chunk 742 optimal weight: 5.9990 chunk 77 optimal weight: 0.0670 chunk 573 optimal weight: 2.9990 chunk 455 optimal weight: 3.9990 overall best weight: 1.1720 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.1589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 77916 Z= 0.140 Angle : 0.435 10.935 106440 Z= 0.218 Chirality : 0.041 0.141 11364 Planarity : 0.004 0.044 13944 Dihedral : 6.496 77.122 10791 Min Nonbonded Distance : 1.990 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.79 % Allowed : 7.71 % Favored : 91.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.74 (0.09), residues: 9468 helix: 1.43 (0.08), residues: 4170 sheet: 0.23 (0.16), residues: 1154 loop : -0.33 (0.10), residues: 4144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 476 HIS 0.004 0.001 HIS D 706 PHE 0.014 0.001 PHE E 69 TYR 0.014 0.001 TYR D 723 ARG 0.002 0.000 ARG A 758 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18936 Ramachandran restraints generated. 9468 Oldfield, 0 Emsley, 9468 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 256 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 53 poor density : 203 time to evaluate : 6.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 142 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8137 (mt-10) REVERT: A 665 ASP cc_start: 0.8164 (OUTLIER) cc_final: 0.7698 (t0) REVERT: C 516 GLU cc_start: 0.8151 (mm-30) cc_final: 0.7887 (mp0) REVERT: C 711 ARG cc_start: 0.7181 (OUTLIER) cc_final: 0.6942 (mtp180) REVERT: D 516 GLU cc_start: 0.8157 (mm-30) cc_final: 0.7897 (mp0) REVERT: D 601 ASP cc_start: 0.7509 (OUTLIER) cc_final: 0.7180 (p0) REVERT: E 665 ASP cc_start: 0.8207 (OUTLIER) cc_final: 0.7933 (t0) REVERT: F 142 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8187 (mt-10) REVERT: G 142 GLU cc_start: 0.8485 (OUTLIER) cc_final: 0.8135 (mt-10) REVERT: G 217 ASN cc_start: 0.7322 (m-40) cc_final: 0.6892 (m110) REVERT: G 601 ASP cc_start: 0.7493 (OUTLIER) cc_final: 0.7220 (p0) REVERT: H 665 ASP cc_start: 0.8223 (OUTLIER) cc_final: 0.7918 (t0) REVERT: I 516 GLU cc_start: 0.8154 (mm-30) cc_final: 0.7889 (mp0) REVERT: I 665 ASP cc_start: 0.8171 (OUTLIER) cc_final: 0.7650 (t0) REVERT: J 516 GLU cc_start: 0.8175 (mm-30) cc_final: 0.7881 (mp0) REVERT: J 601 ASP cc_start: 0.7520 (OUTLIER) cc_final: 0.7188 (p0) REVERT: L 142 GLU cc_start: 0.8480 (OUTLIER) cc_final: 0.8185 (mt-10) outliers start: 53 outliers final: 33 residues processed: 243 average time/residue: 1.2615 time to fit residues: 443.2970 Evaluate side-chains 241 residues out of total 7944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 196 time to evaluate : 6.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 305 VAL Chi-restraints excluded: chain A residue 315 VAL Chi-restraints excluded: chain A residue 613 ILE Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain A residue 665 ASP Chi-restraints excluded: chain B residue 305 VAL Chi-restraints excluded: chain B residue 315 VAL Chi-restraints excluded: chain B residue 663 VAL Chi-restraints excluded: chain C residue 305 VAL Chi-restraints excluded: chain C residue 613 ILE Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 711 ARG Chi-restraints excluded: chain D residue 305 VAL Chi-restraints excluded: chain D residue 551 ASP Chi-restraints excluded: chain D residue 601 ASP Chi-restraints excluded: chain D residue 613 ILE Chi-restraints excluded: chain D residue 663 VAL Chi-restraints excluded: chain E residue 305 VAL Chi-restraints excluded: chain E residue 613 ILE Chi-restraints excluded: chain E residue 663 VAL Chi-restraints excluded: chain E residue 665 ASP Chi-restraints excluded: chain F residue 142 GLU Chi-restraints excluded: chain G residue 142 GLU Chi-restraints excluded: chain G residue 305 VAL Chi-restraints excluded: chain G residue 601 ASP Chi-restraints excluded: chain H residue 305 VAL Chi-restraints excluded: chain H residue 663 VAL Chi-restraints excluded: chain H residue 665 ASP Chi-restraints excluded: chain I residue 305 VAL Chi-restraints excluded: chain I residue 364 MET Chi-restraints excluded: chain I residue 551 ASP Chi-restraints excluded: chain I residue 663 VAL Chi-restraints excluded: chain I residue 665 ASP Chi-restraints excluded: chain J residue 305 VAL Chi-restraints excluded: chain J residue 551 ASP Chi-restraints excluded: chain J residue 601 ASP Chi-restraints excluded: chain J residue 663 VAL Chi-restraints excluded: chain J residue 711 ARG Chi-restraints excluded: chain K residue 305 VAL Chi-restraints excluded: chain K residue 551 ASP Chi-restraints excluded: chain L residue 142 GLU Chi-restraints excluded: chain L residue 255 MET Chi-restraints excluded: chain L residue 305 VAL Chi-restraints excluded: chain L residue 663 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 936 random chunks: chunk 589 optimal weight: 7.9990 chunk 790 optimal weight: 0.4980 chunk 227 optimal weight: 0.8980 chunk 684 optimal weight: 7.9990 chunk 109 optimal weight: 0.6980 chunk 206 optimal weight: 7.9990 chunk 743 optimal weight: 0.6980 chunk 311 optimal weight: 0.8980 chunk 763 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 136 optimal weight: 5.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.111944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3651 r_free = 0.3651 target = 0.088436 restraints weight = 390866.014| |-----------------------------------------------------------------------------| r_work (start): 0.3556 rms_B_bonded: 4.28 r_work: 0.3396 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3397 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3397 r_free = 0.3397 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.38 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3395 r_free = 0.3395 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.14 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3395 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 77916 Z= 0.122 Angle : 0.425 10.909 106440 Z= 0.213 Chirality : 0.041 0.137 11364 Planarity : 0.004 0.044 13944 Dihedral : 6.311 77.428 10791 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.73 % Allowed : 7.84 % Favored : 91.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 0.84 (0.09), residues: 9468 helix: 1.54 (0.08), residues: 4170 sheet: 0.29 (0.16), residues: 1182 loop : -0.32 (0.10), residues: 4116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 476 HIS 0.004 0.001 HIS D 706 PHE 0.015 0.001 PHE E 69 TYR 0.018 0.001 TYR C 723 ARG 0.004 0.000 ARG L 223 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14238.73 seconds wall clock time: 254 minutes 22.40 seconds (15262.40 seconds total)