Starting phenix.real_space_refine on Fri Dec 8 03:15:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/12_2023/6lxv_30007_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/12_2023/6lxv_30007.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/12_2023/6lxv_30007.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/12_2023/6lxv_30007.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/12_2023/6lxv_30007_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6lxv_30007/12_2023/6lxv_30007_updated.pdb" } resolution = 2.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.012 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 Ca 8 9.91 5 P 16 5.49 5 S 160 5.16 5 C 32917 2.51 5 N 8896 2.21 5 O 12927 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 23": "OE1" <-> "OE2" Residue "A ARG 43": "NH1" <-> "NH2" Residue "A ARG 54": "NH1" <-> "NH2" Residue "A ARG 203": "NH1" <-> "NH2" Residue "A TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 265": "OE1" <-> "OE2" Residue "A ARG 328": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 465": "OE1" <-> "OE2" Residue "A ARG 524": "NH1" <-> "NH2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A GLU 664": "OE1" <-> "OE2" Residue "A GLU 735": "OE1" <-> "OE2" Residue "A ARG 748": "NH1" <-> "NH2" Residue "A ARG 754": "NH1" <-> "NH2" Residue "A GLU 760": "OE1" <-> "OE2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 778": "OE1" <-> "OE2" Residue "A GLU 783": "OE1" <-> "OE2" Residue "B GLU 20": "OE1" <-> "OE2" Residue "B ARG 54": "NH1" <-> "NH2" Residue "B ARG 203": "NH1" <-> "NH2" Residue "B TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 265": "OE1" <-> "OE2" Residue "B GLU 314": "OE1" <-> "OE2" Residue "B ARG 328": "NH1" <-> "NH2" Residue "B ARG 383": "NH1" <-> "NH2" Residue "B ARG 428": "NH1" <-> "NH2" Residue "B PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 465": "OE1" <-> "OE2" Residue "B ARG 524": "NH1" <-> "NH2" Residue "B GLU 641": "OE1" <-> "OE2" Residue "B GLU 664": "OE1" <-> "OE2" Residue "B GLU 735": "OE1" <-> "OE2" Residue "B ARG 748": "NH1" <-> "NH2" Residue "B ARG 754": "NH1" <-> "NH2" Residue "B GLU 760": "OE1" <-> "OE2" Residue "B GLU 776": "OE1" <-> "OE2" Residue "B GLU 778": "OE1" <-> "OE2" Residue "B GLU 783": "OE1" <-> "OE2" Residue "C GLU 20": "OE1" <-> "OE2" Residue "C ARG 54": "NH1" <-> "NH2" Residue "C ARG 203": "NH1" <-> "NH2" Residue "C TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 265": "OE1" <-> "OE2" Residue "C ARG 328": "NH1" <-> "NH2" Residue "C ARG 383": "NH1" <-> "NH2" Residue "C PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 465": "OE1" <-> "OE2" Residue "C ARG 524": "NH1" <-> "NH2" Residue "C GLU 641": "OE1" <-> "OE2" Residue "C GLU 664": "OE1" <-> "OE2" Residue "C GLU 735": "OE1" <-> "OE2" Residue "C ARG 748": "NH1" <-> "NH2" Residue "C ARG 754": "NH1" <-> "NH2" Residue "C GLU 760": "OE1" <-> "OE2" Residue "C GLU 778": "OE1" <-> "OE2" Residue "C GLU 783": "OE1" <-> "OE2" Residue "D GLU 20": "OE1" <-> "OE2" Residue "D ARG 43": "NH1" <-> "NH2" Residue "D ARG 54": "NH1" <-> "NH2" Residue "D ARG 203": "NH1" <-> "NH2" Residue "D TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 265": "OE1" <-> "OE2" Residue "D ARG 328": "NH1" <-> "NH2" Residue "D ARG 383": "NH1" <-> "NH2" Residue "D PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 465": "OE1" <-> "OE2" Residue "D ARG 524": "NH1" <-> "NH2" Residue "D GLU 641": "OE1" <-> "OE2" Residue "D GLU 664": "OE1" <-> "OE2" Residue "D GLU 735": "OE1" <-> "OE2" Residue "D ARG 748": "NH1" <-> "NH2" Residue "D ARG 754": "NH1" <-> "NH2" Residue "D GLU 760": "OE1" <-> "OE2" Residue "D GLU 778": "OE1" <-> "OE2" Residue "D GLU 783": "OE1" <-> "OE2" Residue "E GLU 20": "OE1" <-> "OE2" Residue "E ARG 43": "NH1" <-> "NH2" Residue "E ARG 54": "NH1" <-> "NH2" Residue "E ARG 203": "NH1" <-> "NH2" Residue "E TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 265": "OE1" <-> "OE2" Residue "E ARG 328": "NH1" <-> "NH2" Residue "E ARG 383": "NH1" <-> "NH2" Residue "E PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 465": "OE1" <-> "OE2" Residue "E ARG 524": "NH1" <-> "NH2" Residue "E GLU 641": "OE1" <-> "OE2" Residue "E GLU 664": "OE1" <-> "OE2" Residue "E GLU 735": "OE1" <-> "OE2" Residue "E ARG 748": "NH1" <-> "NH2" Residue "E ARG 754": "NH1" <-> "NH2" Residue "E GLU 760": "OE1" <-> "OE2" Residue "E GLU 776": "OE1" <-> "OE2" Residue "E GLU 778": "OE1" <-> "OE2" Residue "E GLU 783": "OE1" <-> "OE2" Residue "F GLU 20": "OE1" <-> "OE2" Residue "F GLU 23": "OE1" <-> "OE2" Residue "F ARG 43": "NH1" <-> "NH2" Residue "F ARG 54": "NH1" <-> "NH2" Residue "F ARG 203": "NH1" <-> "NH2" Residue "F TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 265": "OE1" <-> "OE2" Residue "F ARG 328": "NH1" <-> "NH2" Residue "F ARG 383": "NH1" <-> "NH2" Residue "F ARG 428": "NH1" <-> "NH2" Residue "F PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 465": "OE1" <-> "OE2" Residue "F ARG 524": "NH1" <-> "NH2" Residue "F GLU 641": "OE1" <-> "OE2" Residue "F GLU 664": "OE1" <-> "OE2" Residue "F GLU 735": "OE1" <-> "OE2" Residue "F ARG 748": "NH1" <-> "NH2" Residue "F ARG 754": "NH1" <-> "NH2" Residue "F GLU 760": "OE1" <-> "OE2" Residue "F GLU 778": "OE1" <-> "OE2" Residue "F GLU 783": "OE1" <-> "OE2" Residue "G GLU 20": "OE1" <-> "OE2" Residue "G ARG 54": "NH1" <-> "NH2" Residue "G ARG 203": "NH1" <-> "NH2" Residue "G TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 265": "OE1" <-> "OE2" Residue "G ARG 328": "NH1" <-> "NH2" Residue "G ARG 383": "NH1" <-> "NH2" Residue "G PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 465": "OE1" <-> "OE2" Residue "G ARG 524": "NH1" <-> "NH2" Residue "G GLU 641": "OE1" <-> "OE2" Residue "G GLU 664": "OE1" <-> "OE2" Residue "G GLU 735": "OE1" <-> "OE2" Residue "G ARG 748": "NH1" <-> "NH2" Residue "G ARG 754": "NH1" <-> "NH2" Residue "G GLU 760": "OE1" <-> "OE2" Residue "G GLU 778": "OE1" <-> "OE2" Residue "G GLU 783": "OE1" <-> "OE2" Residue "H GLU 20": "OE1" <-> "OE2" Residue "H GLU 23": "OE1" <-> "OE2" Residue "H ARG 54": "NH1" <-> "NH2" Residue "H ARG 203": "NH1" <-> "NH2" Residue "H TYR 217": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 265": "OE1" <-> "OE2" Residue "H ARG 328": "NH1" <-> "NH2" Residue "H ARG 383": "NH1" <-> "NH2" Residue "H ARG 428": "NH1" <-> "NH2" Residue "H PHE 433": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 465": "OE1" <-> "OE2" Residue "H ARG 524": "NH1" <-> "NH2" Residue "H GLU 641": "OE1" <-> "OE2" Residue "H GLU 664": "OE1" <-> "OE2" Residue "H GLU 735": "OE1" <-> "OE2" Residue "H ARG 748": "NH1" <-> "NH2" Residue "H ARG 754": "NH1" <-> "NH2" Residue "H GLU 760": "OE1" <-> "OE2" Residue "H GLU 778": "OE1" <-> "OE2" Residue "H GLU 783": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 54924 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 6472 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6521 Chain: "B" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "C" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "D" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "E" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "F" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "G" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "H" Number of atoms: 6467 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} Conformer: "B" Number of residues, atoms: 806, 6411 Classifications: {'peptide': 806} Link IDs: {'PCIS': 1, 'PTRANS': 39, 'TRANS': 765} bond proxies already assigned to first conformer: 6527 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 27 Unusual residues: {' CA': 1, 'TPP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "B" Number of atoms: 370 Number of conformers: 1 Conformer: "" Number of residues, atoms: 370, 370 Classifications: {'water': 370} Link IDs: {None: 369} Chain: "C" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "D" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "E" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "F" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "G" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Chain: "H" Number of atoms: 371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 371 Classifications: {'water': 371} Link IDs: {None: 370} Residues with excluded nonbonded symmetry interactions: 48 residue: pdb=" N AARG A 428 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 428 " occ=0.50 residue: pdb=" N AGLN A 546 " occ=0.40 ... (16 atoms not shown) pdb=" NE2BGLN A 546 " occ=0.60 residue: pdb=" N AASP A 547 " occ=0.40 ... (14 atoms not shown) pdb=" OD2BASP A 547 " occ=0.60 residue: pdb=" N AHIS A 548 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS A 548 " occ=0.60 residue: pdb=" N AASN A 549 " occ=0.40 ... (14 atoms not shown) pdb=" ND2BASN A 549 " occ=0.60 residue: pdb=" N AHIS A 568 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS A 568 " occ=0.50 residue: pdb=" N AARG B 428 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG B 428 " occ=0.50 residue: pdb=" N AGLN B 546 " occ=0.40 ... (16 atoms not shown) pdb=" NE2BGLN B 546 " occ=0.60 residue: pdb=" N AASP B 547 " occ=0.40 ... (14 atoms not shown) pdb=" OD2BASP B 547 " occ=0.60 residue: pdb=" N AHIS B 548 " occ=0.40 ... (18 atoms not shown) pdb=" NE2BHIS B 548 " occ=0.60 residue: pdb=" N AASN B 549 " occ=0.40 ... (14 atoms not shown) pdb=" ND2BASN B 549 " occ=0.60 residue: pdb=" N AHIS B 568 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 568 " occ=0.50 ... (remaining 36 not shown) Time building chain proxies: 38.84, per 1000 atoms: 0.71 Number of scatterers: 54924 At special positions: 0 Unit cell: (204.45, 204.45, 113.97, 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) Ca 8 19.99 S 160 16.00 P 16 15.00 O 12927 8.00 N 8896 7.00 C 32917 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 20.39 Conformation dependent library (CDL) restraints added in 15.7 seconds 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 12018 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 311 helices and 24 sheets defined 43.8% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 9.46 Creating SS restraints... Processing helix chain 'A' and resid 19 through 41 Processing helix chain 'A' and resid 54 through 56 No H-bonds generated for 'chain 'A' and resid 54 through 56' Processing helix chain 'A' and resid 68 through 85 Processing helix chain 'A' and resid 99 through 109 Processing helix chain 'A' and resid 111 through 115 Processing helix chain 'A' and resid 123 through 132 Processing helix chain 'A' and resid 160 through 168 Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 188 through 198 removed outlier: 3.561A pdb=" N TRP A 194 " --> pdb=" O LEU A 190 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN A 195 " --> pdb=" O ALA A 191 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER A 196 " --> pdb=" O THR A 192 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN A 197 " --> pdb=" O GLY A 193 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS A 198 " --> pdb=" O TRP A 194 " (cutoff:3.500A) Processing helix chain 'A' and resid 224 through 227 No H-bonds generated for 'chain 'A' and resid 224 through 227' Processing helix chain 'A' and resid 230 through 239 Processing helix chain 'A' and resid 256 through 282 Processing helix chain 'A' and resid 317 through 319 No H-bonds generated for 'chain 'A' and resid 317 through 319' Processing helix chain 'A' and resid 331 through 344 removed outlier: 4.012A pdb=" N TYR A 344 " --> pdb=" O TRP A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 346 through 348 No H-bonds generated for 'chain 'A' and resid 346 through 348' Processing helix chain 'A' and resid 358 through 361 No H-bonds generated for 'chain 'A' and resid 358 through 361' Processing helix chain 'A' and resid 367 through 369 No H-bonds generated for 'chain 'A' and resid 367 through 369' Processing helix chain 'A' and resid 375 through 377 No H-bonds generated for 'chain 'A' and resid 375 through 377' Processing helix chain 'A' and resid 379 through 381 No H-bonds generated for 'chain 'A' and resid 379 through 381' Processing helix chain 'A' and resid 391 through 394 Processing helix chain 'A' and resid 397 through 402 removed outlier: 3.820A pdb=" N TYR A 402 " --> pdb=" O VAL A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 411 through 425 removed outlier: 3.555A pdb=" N LEU A 415 " --> pdb=" O ALA A 411 " (cutoff:3.500A) Processing helix chain 'A' and resid 444 through 448 Processing helix chain 'A' and resid 479 through 491 Processing helix chain 'A' and resid 502 through 525 removed outlier: 3.815A pdb=" N HIS A 506 " --> pdb=" O SER A 503 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N SER A 510 " --> pdb=" O VAL A 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU A 520 " --> pdb=" O LYS A 517 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL A 523 " --> pdb=" O GLU A 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 524 " --> pdb=" O ALA A 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 525 " --> pdb=" O THR A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 545 No H-bonds generated for 'chain 'A' and resid 543 through 545' Processing helix chain 'A' and resid 551 through 553 No H-bonds generated for 'chain 'A' and resid 551 through 553' Processing helix chain 'A' and resid 558 through 565 removed outlier: 3.640A pdb=" N ASN A 564 " --> pdb=" O SER A 560 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS A 565 " --> pdb=" O VAL A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 581 through 593 Processing helix chain 'A' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS A 623 " --> pdb=" O ALA A 619 " (cutoff:3.500A) Processing helix chain 'A' and resid 649 through 664 removed outlier: 3.548A pdb=" N LYS A 661 " --> pdb=" O ALA A 657 " (cutoff:3.500A) Processing helix chain 'A' and resid 677 through 680 Processing helix chain 'A' and resid 692 through 698 Processing helix chain 'A' and resid 713 through 719 Processing helix chain 'A' and resid 726 through 728 No H-bonds generated for 'chain 'A' and resid 726 through 728' Processing helix chain 'A' and resid 743 through 749 Processing helix chain 'A' and resid 754 through 766 Processing helix chain 'A' and resid 771 through 791 removed outlier: 3.576A pdb=" N ASP A 782 " --> pdb=" O GLU A 778 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 799 No H-bonds generated for 'chain 'A' and resid 796 through 799' Processing helix chain 'B' and resid 19 through 41 Processing helix chain 'B' and resid 54 through 56 No H-bonds generated for 'chain 'B' and resid 54 through 56' Processing helix chain 'B' and resid 68 through 85 Processing helix chain 'B' and resid 99 through 109 Processing helix chain 'B' and resid 111 through 115 Processing helix chain 'B' and resid 123 through 132 Processing helix chain 'B' and resid 160 through 168 Processing helix chain 'B' and resid 184 through 186 No H-bonds generated for 'chain 'B' and resid 184 through 186' Processing helix chain 'B' and resid 188 through 198 removed outlier: 3.561A pdb=" N TRP B 194 " --> pdb=" O LEU B 190 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN B 195 " --> pdb=" O ALA B 191 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER B 196 " --> pdb=" O THR B 192 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN B 197 " --> pdb=" O GLY B 193 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS B 198 " --> pdb=" O TRP B 194 " (cutoff:3.500A) Processing helix chain 'B' and resid 224 through 227 No H-bonds generated for 'chain 'B' and resid 224 through 227' Processing helix chain 'B' and resid 230 through 239 Processing helix chain 'B' and resid 256 through 282 Processing helix chain 'B' and resid 317 through 319 No H-bonds generated for 'chain 'B' and resid 317 through 319' Processing helix chain 'B' and resid 331 through 344 removed outlier: 4.014A pdb=" N TYR B 344 " --> pdb=" O TRP B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 346 through 348 No H-bonds generated for 'chain 'B' and resid 346 through 348' Processing helix chain 'B' and resid 358 through 361 No H-bonds generated for 'chain 'B' and resid 358 through 361' Processing helix chain 'B' and resid 367 through 369 No H-bonds generated for 'chain 'B' and resid 367 through 369' Processing helix chain 'B' and resid 375 through 377 No H-bonds generated for 'chain 'B' and resid 375 through 377' Processing helix chain 'B' and resid 379 through 381 No H-bonds generated for 'chain 'B' and resid 379 through 381' Processing helix chain 'B' and resid 391 through 394 Processing helix chain 'B' and resid 397 through 402 removed outlier: 3.820A pdb=" N TYR B 402 " --> pdb=" O VAL B 399 " (cutoff:3.500A) Processing helix chain 'B' and resid 411 through 425 removed outlier: 3.554A pdb=" N LEU B 415 " --> pdb=" O ALA B 411 " (cutoff:3.500A) Processing helix chain 'B' and resid 444 through 448 Processing helix chain 'B' and resid 479 through 491 Processing helix chain 'B' and resid 502 through 525 removed outlier: 3.816A pdb=" N HIS B 506 " --> pdb=" O SER B 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER B 510 " --> pdb=" O VAL B 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU B 520 " --> pdb=" O LYS B 517 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 523 " --> pdb=" O GLU B 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG B 524 " --> pdb=" O ALA B 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU B 525 " --> pdb=" O THR B 522 " (cutoff:3.500A) Processing helix chain 'B' and resid 543 through 545 No H-bonds generated for 'chain 'B' and resid 543 through 545' Processing helix chain 'B' and resid 551 through 553 No H-bonds generated for 'chain 'B' and resid 551 through 553' Processing helix chain 'B' and resid 558 through 565 removed outlier: 3.639A pdb=" N ASN B 564 " --> pdb=" O SER B 560 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS B 565 " --> pdb=" O VAL B 561 " (cutoff:3.500A) Processing helix chain 'B' and resid 581 through 593 Processing helix chain 'B' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS B 623 " --> pdb=" O ALA B 619 " (cutoff:3.500A) Processing helix chain 'B' and resid 649 through 664 removed outlier: 3.548A pdb=" N LYS B 661 " --> pdb=" O ALA B 657 " (cutoff:3.500A) Processing helix chain 'B' and resid 677 through 680 Processing helix chain 'B' and resid 692 through 698 Processing helix chain 'B' and resid 713 through 719 Processing helix chain 'B' and resid 726 through 728 No H-bonds generated for 'chain 'B' and resid 726 through 728' Processing helix chain 'B' and resid 743 through 749 Processing helix chain 'B' and resid 754 through 766 Processing helix chain 'B' and resid 771 through 791 removed outlier: 3.577A pdb=" N ASP B 782 " --> pdb=" O GLU B 778 " (cutoff:3.500A) Processing helix chain 'B' and resid 796 through 799 No H-bonds generated for 'chain 'B' and resid 796 through 799' Processing helix chain 'C' and resid 19 through 41 Processing helix chain 'C' and resid 54 through 56 No H-bonds generated for 'chain 'C' and resid 54 through 56' Processing helix chain 'C' and resid 68 through 85 Processing helix chain 'C' and resid 99 through 109 Processing helix chain 'C' and resid 111 through 115 Processing helix chain 'C' and resid 123 through 132 Processing helix chain 'C' and resid 160 through 168 Processing helix chain 'C' and resid 184 through 186 No H-bonds generated for 'chain 'C' and resid 184 through 186' Processing helix chain 'C' and resid 188 through 198 removed outlier: 3.560A pdb=" N TRP C 194 " --> pdb=" O LEU C 190 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN C 195 " --> pdb=" O ALA C 191 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N SER C 196 " --> pdb=" O THR C 192 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N ASN C 197 " --> pdb=" O GLY C 193 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS C 198 " --> pdb=" O TRP C 194 " (cutoff:3.500A) Processing helix chain 'C' and resid 224 through 227 No H-bonds generated for 'chain 'C' and resid 224 through 227' Processing helix chain 'C' and resid 230 through 239 Processing helix chain 'C' and resid 256 through 282 Processing helix chain 'C' and resid 317 through 319 No H-bonds generated for 'chain 'C' and resid 317 through 319' Processing helix chain 'C' and resid 331 through 344 removed outlier: 4.016A pdb=" N TYR C 344 " --> pdb=" O TRP C 340 " (cutoff:3.500A) Processing helix chain 'C' and resid 346 through 348 No H-bonds generated for 'chain 'C' and resid 346 through 348' Processing helix chain 'C' and resid 358 through 361 No H-bonds generated for 'chain 'C' and resid 358 through 361' Processing helix chain 'C' and resid 367 through 369 No H-bonds generated for 'chain 'C' and resid 367 through 369' Processing helix chain 'C' and resid 375 through 377 No H-bonds generated for 'chain 'C' and resid 375 through 377' Processing helix chain 'C' and resid 379 through 381 No H-bonds generated for 'chain 'C' and resid 379 through 381' Processing helix chain 'C' and resid 391 through 394 Processing helix chain 'C' and resid 397 through 402 removed outlier: 3.820A pdb=" N TYR C 402 " --> pdb=" O VAL C 399 " (cutoff:3.500A) Processing helix chain 'C' and resid 411 through 425 removed outlier: 3.556A pdb=" N LEU C 415 " --> pdb=" O ALA C 411 " (cutoff:3.500A) Processing helix chain 'C' and resid 444 through 448 Processing helix chain 'C' and resid 479 through 491 Processing helix chain 'C' and resid 502 through 525 removed outlier: 3.815A pdb=" N HIS C 506 " --> pdb=" O SER C 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER C 510 " --> pdb=" O VAL C 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU C 520 " --> pdb=" O LYS C 517 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL C 523 " --> pdb=" O GLU C 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG C 524 " --> pdb=" O ALA C 521 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU C 525 " --> pdb=" O THR C 522 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 545 No H-bonds generated for 'chain 'C' and resid 543 through 545' Processing helix chain 'C' and resid 551 through 553 No H-bonds generated for 'chain 'C' and resid 551 through 553' Processing helix chain 'C' and resid 558 through 565 removed outlier: 3.642A pdb=" N ASN C 564 " --> pdb=" O SER C 560 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS C 565 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing helix chain 'C' and resid 581 through 593 Processing helix chain 'C' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS C 623 " --> pdb=" O ALA C 619 " (cutoff:3.500A) Processing helix chain 'C' and resid 649 through 664 removed outlier: 3.547A pdb=" N LYS C 661 " --> pdb=" O ALA C 657 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 680 Processing helix chain 'C' and resid 692 through 698 Processing helix chain 'C' and resid 713 through 719 Processing helix chain 'C' and resid 726 through 728 No H-bonds generated for 'chain 'C' and resid 726 through 728' Processing helix chain 'C' and resid 743 through 749 Processing helix chain 'C' and resid 754 through 766 Processing helix chain 'C' and resid 771 through 791 removed outlier: 3.579A pdb=" N ASP C 782 " --> pdb=" O GLU C 778 " (cutoff:3.500A) Processing helix chain 'C' and resid 796 through 799 No H-bonds generated for 'chain 'C' and resid 796 through 799' Processing helix chain 'D' and resid 19 through 41 Processing helix chain 'D' and resid 54 through 56 No H-bonds generated for 'chain 'D' and resid 54 through 56' Processing helix chain 'D' and resid 68 through 85 Processing helix chain 'D' and resid 99 through 109 Processing helix chain 'D' and resid 111 through 115 Processing helix chain 'D' and resid 123 through 132 Processing helix chain 'D' and resid 160 through 168 Processing helix chain 'D' and resid 184 through 186 No H-bonds generated for 'chain 'D' and resid 184 through 186' Processing helix chain 'D' and resid 188 through 198 removed outlier: 3.560A pdb=" N TRP D 194 " --> pdb=" O LEU D 190 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN D 195 " --> pdb=" O ALA D 191 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER D 196 " --> pdb=" O THR D 192 " (cutoff:3.500A) removed outlier: 5.132A pdb=" N ASN D 197 " --> pdb=" O GLY D 193 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS D 198 " --> pdb=" O TRP D 194 " (cutoff:3.500A) Processing helix chain 'D' and resid 224 through 227 No H-bonds generated for 'chain 'D' and resid 224 through 227' Processing helix chain 'D' and resid 230 through 239 Processing helix chain 'D' and resid 256 through 282 Processing helix chain 'D' and resid 317 through 319 No H-bonds generated for 'chain 'D' and resid 317 through 319' Processing helix chain 'D' and resid 331 through 344 removed outlier: 4.013A pdb=" N TYR D 344 " --> pdb=" O TRP D 340 " (cutoff:3.500A) Processing helix chain 'D' and resid 346 through 348 No H-bonds generated for 'chain 'D' and resid 346 through 348' Processing helix chain 'D' and resid 358 through 361 No H-bonds generated for 'chain 'D' and resid 358 through 361' Processing helix chain 'D' and resid 367 through 369 No H-bonds generated for 'chain 'D' and resid 367 through 369' Processing helix chain 'D' and resid 375 through 377 No H-bonds generated for 'chain 'D' and resid 375 through 377' Processing helix chain 'D' and resid 379 through 381 No H-bonds generated for 'chain 'D' and resid 379 through 381' Processing helix chain 'D' and resid 391 through 394 Processing helix chain 'D' and resid 397 through 402 removed outlier: 3.821A pdb=" N TYR D 402 " --> pdb=" O VAL D 399 " (cutoff:3.500A) Processing helix chain 'D' and resid 411 through 425 removed outlier: 3.555A pdb=" N LEU D 415 " --> pdb=" O ALA D 411 " (cutoff:3.500A) Processing helix chain 'D' and resid 444 through 448 Processing helix chain 'D' and resid 479 through 491 Processing helix chain 'D' and resid 502 through 525 removed outlier: 3.815A pdb=" N HIS D 506 " --> pdb=" O SER D 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER D 510 " --> pdb=" O VAL D 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU D 520 " --> pdb=" O LYS D 517 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL D 523 " --> pdb=" O GLU D 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG D 524 " --> pdb=" O ALA D 521 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU D 525 " --> pdb=" O THR D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 543 through 545 No H-bonds generated for 'chain 'D' and resid 543 through 545' Processing helix chain 'D' and resid 551 through 553 No H-bonds generated for 'chain 'D' and resid 551 through 553' Processing helix chain 'D' and resid 558 through 565 removed outlier: 3.639A pdb=" N ASN D 564 " --> pdb=" O SER D 560 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS D 565 " --> pdb=" O VAL D 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 581 through 593 Processing helix chain 'D' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS D 623 " --> pdb=" O ALA D 619 " (cutoff:3.500A) Processing helix chain 'D' and resid 649 through 664 removed outlier: 3.547A pdb=" N LYS D 661 " --> pdb=" O ALA D 657 " (cutoff:3.500A) Processing helix chain 'D' and resid 677 through 680 Processing helix chain 'D' and resid 692 through 698 Processing helix chain 'D' and resid 713 through 719 Processing helix chain 'D' and resid 726 through 728 No H-bonds generated for 'chain 'D' and resid 726 through 728' Processing helix chain 'D' and resid 743 through 749 Processing helix chain 'D' and resid 754 through 766 Processing helix chain 'D' and resid 771 through 791 removed outlier: 3.579A pdb=" N ASP D 782 " --> pdb=" O GLU D 778 " (cutoff:3.500A) Processing helix chain 'D' and resid 796 through 799 No H-bonds generated for 'chain 'D' and resid 796 through 799' Processing helix chain 'E' and resid 19 through 41 Processing helix chain 'E' and resid 54 through 56 No H-bonds generated for 'chain 'E' and resid 54 through 56' Processing helix chain 'E' and resid 68 through 85 Processing helix chain 'E' and resid 99 through 109 Processing helix chain 'E' and resid 111 through 115 Processing helix chain 'E' and resid 123 through 132 Processing helix chain 'E' and resid 160 through 168 Processing helix chain 'E' and resid 184 through 186 No H-bonds generated for 'chain 'E' and resid 184 through 186' Processing helix chain 'E' and resid 188 through 198 removed outlier: 3.561A pdb=" N TRP E 194 " --> pdb=" O LEU E 190 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN E 195 " --> pdb=" O ALA E 191 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER E 196 " --> pdb=" O THR E 192 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN E 197 " --> pdb=" O GLY E 193 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS E 198 " --> pdb=" O TRP E 194 " (cutoff:3.500A) Processing helix chain 'E' and resid 224 through 227 No H-bonds generated for 'chain 'E' and resid 224 through 227' Processing helix chain 'E' and resid 230 through 239 Processing helix chain 'E' and resid 256 through 282 Processing helix chain 'E' and resid 317 through 319 No H-bonds generated for 'chain 'E' and resid 317 through 319' Processing helix chain 'E' and resid 331 through 344 removed outlier: 4.013A pdb=" N TYR E 344 " --> pdb=" O TRP E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 358 through 361 No H-bonds generated for 'chain 'E' and resid 358 through 361' Processing helix chain 'E' and resid 367 through 369 No H-bonds generated for 'chain 'E' and resid 367 through 369' Processing helix chain 'E' and resid 375 through 377 No H-bonds generated for 'chain 'E' and resid 375 through 377' Processing helix chain 'E' and resid 379 through 381 No H-bonds generated for 'chain 'E' and resid 379 through 381' Processing helix chain 'E' and resid 391 through 394 Processing helix chain 'E' and resid 397 through 402 removed outlier: 3.822A pdb=" N TYR E 402 " --> pdb=" O VAL E 399 " (cutoff:3.500A) Processing helix chain 'E' and resid 411 through 425 removed outlier: 3.555A pdb=" N LEU E 415 " --> pdb=" O ALA E 411 " (cutoff:3.500A) Processing helix chain 'E' and resid 444 through 448 Processing helix chain 'E' and resid 479 through 491 Processing helix chain 'E' and resid 502 through 525 removed outlier: 3.815A pdb=" N HIS E 506 " --> pdb=" O SER E 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER E 510 " --> pdb=" O VAL E 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU E 520 " --> pdb=" O LYS E 517 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL E 523 " --> pdb=" O GLU E 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG E 524 " --> pdb=" O ALA E 521 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU E 525 " --> pdb=" O THR E 522 " (cutoff:3.500A) Processing helix chain 'E' and resid 543 through 545 No H-bonds generated for 'chain 'E' and resid 543 through 545' Processing helix chain 'E' and resid 551 through 553 No H-bonds generated for 'chain 'E' and resid 551 through 553' Processing helix chain 'E' and resid 558 through 565 removed outlier: 3.639A pdb=" N ASN E 564 " --> pdb=" O SER E 560 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LYS E 565 " --> pdb=" O VAL E 561 " (cutoff:3.500A) Processing helix chain 'E' and resid 581 through 593 Processing helix chain 'E' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS E 623 " --> pdb=" O ALA E 619 " (cutoff:3.500A) Processing helix chain 'E' and resid 649 through 664 removed outlier: 3.547A pdb=" N LYS E 661 " --> pdb=" O ALA E 657 " (cutoff:3.500A) Processing helix chain 'E' and resid 677 through 680 Processing helix chain 'E' and resid 692 through 698 Processing helix chain 'E' and resid 713 through 719 Processing helix chain 'E' and resid 726 through 728 No H-bonds generated for 'chain 'E' and resid 726 through 728' Processing helix chain 'E' and resid 743 through 749 Processing helix chain 'E' and resid 754 through 766 Processing helix chain 'E' and resid 771 through 791 removed outlier: 3.577A pdb=" N ASP E 782 " --> pdb=" O GLU E 778 " (cutoff:3.500A) Processing helix chain 'E' and resid 796 through 799 No H-bonds generated for 'chain 'E' and resid 796 through 799' Processing helix chain 'F' and resid 19 through 41 Processing helix chain 'F' and resid 54 through 56 No H-bonds generated for 'chain 'F' and resid 54 through 56' Processing helix chain 'F' and resid 68 through 85 Processing helix chain 'F' and resid 99 through 109 Processing helix chain 'F' and resid 111 through 115 Processing helix chain 'F' and resid 123 through 132 Processing helix chain 'F' and resid 160 through 168 Processing helix chain 'F' and resid 184 through 186 No H-bonds generated for 'chain 'F' and resid 184 through 186' Processing helix chain 'F' and resid 188 through 198 removed outlier: 3.561A pdb=" N TRP F 194 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLN F 195 " --> pdb=" O ALA F 191 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER F 196 " --> pdb=" O THR F 192 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN F 197 " --> pdb=" O GLY F 193 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS F 198 " --> pdb=" O TRP F 194 " (cutoff:3.500A) Processing helix chain 'F' and resid 224 through 227 No H-bonds generated for 'chain 'F' and resid 224 through 227' Processing helix chain 'F' and resid 230 through 239 Processing helix chain 'F' and resid 256 through 282 Processing helix chain 'F' and resid 317 through 319 No H-bonds generated for 'chain 'F' and resid 317 through 319' Processing helix chain 'F' and resid 331 through 344 removed outlier: 4.012A pdb=" N TYR F 344 " --> pdb=" O TRP F 340 " (cutoff:3.500A) Processing helix chain 'F' and resid 346 through 348 No H-bonds generated for 'chain 'F' and resid 346 through 348' Processing helix chain 'F' and resid 358 through 361 No H-bonds generated for 'chain 'F' and resid 358 through 361' Processing helix chain 'F' and resid 367 through 369 No H-bonds generated for 'chain 'F' and resid 367 through 369' Processing helix chain 'F' and resid 375 through 377 No H-bonds generated for 'chain 'F' and resid 375 through 377' Processing helix chain 'F' and resid 379 through 381 No H-bonds generated for 'chain 'F' and resid 379 through 381' Processing helix chain 'F' and resid 391 through 394 Processing helix chain 'F' and resid 397 through 402 removed outlier: 3.820A pdb=" N TYR F 402 " --> pdb=" O VAL F 399 " (cutoff:3.500A) Processing helix chain 'F' and resid 411 through 425 removed outlier: 3.555A pdb=" N LEU F 415 " --> pdb=" O ALA F 411 " (cutoff:3.500A) Processing helix chain 'F' and resid 444 through 448 Processing helix chain 'F' and resid 479 through 491 Processing helix chain 'F' and resid 502 through 525 removed outlier: 3.815A pdb=" N HIS F 506 " --> pdb=" O SER F 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER F 510 " --> pdb=" O VAL F 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU F 520 " --> pdb=" O LYS F 517 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N VAL F 523 " --> pdb=" O GLU F 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG F 524 " --> pdb=" O ALA F 521 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU F 525 " --> pdb=" O THR F 522 " (cutoff:3.500A) Processing helix chain 'F' and resid 543 through 545 No H-bonds generated for 'chain 'F' and resid 543 through 545' Processing helix chain 'F' and resid 551 through 553 No H-bonds generated for 'chain 'F' and resid 551 through 553' Processing helix chain 'F' and resid 558 through 565 removed outlier: 3.641A pdb=" N ASN F 564 " --> pdb=" O SER F 560 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS F 565 " --> pdb=" O VAL F 561 " (cutoff:3.500A) Processing helix chain 'F' and resid 581 through 593 Processing helix chain 'F' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS F 623 " --> pdb=" O ALA F 619 " (cutoff:3.500A) Processing helix chain 'F' and resid 649 through 664 removed outlier: 3.549A pdb=" N LYS F 661 " --> pdb=" O ALA F 657 " (cutoff:3.500A) Processing helix chain 'F' and resid 677 through 680 Processing helix chain 'F' and resid 692 through 698 Processing helix chain 'F' and resid 713 through 719 Processing helix chain 'F' and resid 726 through 728 No H-bonds generated for 'chain 'F' and resid 726 through 728' Processing helix chain 'F' and resid 743 through 749 Processing helix chain 'F' and resid 754 through 766 Processing helix chain 'F' and resid 771 through 791 removed outlier: 3.580A pdb=" N ASP F 782 " --> pdb=" O GLU F 778 " (cutoff:3.500A) Processing helix chain 'F' and resid 796 through 799 No H-bonds generated for 'chain 'F' and resid 796 through 799' Processing helix chain 'G' and resid 19 through 41 Processing helix chain 'G' and resid 54 through 56 No H-bonds generated for 'chain 'G' and resid 54 through 56' Processing helix chain 'G' and resid 68 through 85 Processing helix chain 'G' and resid 99 through 109 Processing helix chain 'G' and resid 111 through 115 Processing helix chain 'G' and resid 123 through 132 Processing helix chain 'G' and resid 160 through 168 Processing helix chain 'G' and resid 184 through 186 No H-bonds generated for 'chain 'G' and resid 184 through 186' Processing helix chain 'G' and resid 188 through 198 removed outlier: 3.560A pdb=" N TRP G 194 " --> pdb=" O LEU G 190 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N GLN G 195 " --> pdb=" O ALA G 191 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N SER G 196 " --> pdb=" O THR G 192 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N ASN G 197 " --> pdb=" O GLY G 193 " (cutoff:3.500A) removed outlier: 5.720A pdb=" N LYS G 198 " --> pdb=" O TRP G 194 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 227 No H-bonds generated for 'chain 'G' and resid 224 through 227' Processing helix chain 'G' and resid 230 through 239 Processing helix chain 'G' and resid 256 through 282 Processing helix chain 'G' and resid 317 through 319 No H-bonds generated for 'chain 'G' and resid 317 through 319' Processing helix chain 'G' and resid 331 through 344 removed outlier: 4.012A pdb=" N TYR G 344 " --> pdb=" O TRP G 340 " (cutoff:3.500A) Processing helix chain 'G' and resid 346 through 348 No H-bonds generated for 'chain 'G' and resid 346 through 348' Processing helix chain 'G' and resid 358 through 361 No H-bonds generated for 'chain 'G' and resid 358 through 361' Processing helix chain 'G' and resid 367 through 369 No H-bonds generated for 'chain 'G' and resid 367 through 369' Processing helix chain 'G' and resid 375 through 377 No H-bonds generated for 'chain 'G' and resid 375 through 377' Processing helix chain 'G' and resid 379 through 381 No H-bonds generated for 'chain 'G' and resid 379 through 381' Processing helix chain 'G' and resid 391 through 394 Processing helix chain 'G' and resid 397 through 402 removed outlier: 3.822A pdb=" N TYR G 402 " --> pdb=" O VAL G 399 " (cutoff:3.500A) Processing helix chain 'G' and resid 411 through 425 removed outlier: 3.554A pdb=" N LEU G 415 " --> pdb=" O ALA G 411 " (cutoff:3.500A) Processing helix chain 'G' and resid 444 through 448 Processing helix chain 'G' and resid 479 through 491 Processing helix chain 'G' and resid 502 through 525 removed outlier: 3.815A pdb=" N HIS G 506 " --> pdb=" O SER G 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER G 510 " --> pdb=" O VAL G 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU G 520 " --> pdb=" O LYS G 517 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL G 523 " --> pdb=" O GLU G 520 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG G 524 " --> pdb=" O ALA G 521 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU G 525 " --> pdb=" O THR G 522 " (cutoff:3.500A) Processing helix chain 'G' and resid 543 through 545 No H-bonds generated for 'chain 'G' and resid 543 through 545' Processing helix chain 'G' and resid 551 through 553 No H-bonds generated for 'chain 'G' and resid 551 through 553' Processing helix chain 'G' and resid 558 through 565 removed outlier: 3.642A pdb=" N ASN G 564 " --> pdb=" O SER G 560 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N LYS G 565 " --> pdb=" O VAL G 561 " (cutoff:3.500A) Processing helix chain 'G' and resid 581 through 593 Processing helix chain 'G' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS G 623 " --> pdb=" O ALA G 619 " (cutoff:3.500A) Processing helix chain 'G' and resid 649 through 664 removed outlier: 3.548A pdb=" N LYS G 661 " --> pdb=" O ALA G 657 " (cutoff:3.500A) Processing helix chain 'G' and resid 677 through 680 Processing helix chain 'G' and resid 692 through 698 Processing helix chain 'G' and resid 713 through 719 Processing helix chain 'G' and resid 726 through 728 No H-bonds generated for 'chain 'G' and resid 726 through 728' Processing helix chain 'G' and resid 743 through 749 Processing helix chain 'G' and resid 754 through 766 Processing helix chain 'G' and resid 771 through 791 removed outlier: 3.579A pdb=" N ASP G 782 " --> pdb=" O GLU G 778 " (cutoff:3.500A) Processing helix chain 'G' and resid 796 through 799 No H-bonds generated for 'chain 'G' and resid 796 through 799' Processing helix chain 'H' and resid 19 through 41 Processing helix chain 'H' and resid 54 through 56 No H-bonds generated for 'chain 'H' and resid 54 through 56' Processing helix chain 'H' and resid 68 through 85 Processing helix chain 'H' and resid 99 through 109 Processing helix chain 'H' and resid 111 through 115 Processing helix chain 'H' and resid 123 through 132 Processing helix chain 'H' and resid 160 through 168 Processing helix chain 'H' and resid 184 through 186 No H-bonds generated for 'chain 'H' and resid 184 through 186' Processing helix chain 'H' and resid 188 through 198 removed outlier: 3.561A pdb=" N TRP H 194 " --> pdb=" O LEU H 190 " (cutoff:3.500A) removed outlier: 4.876A pdb=" N GLN H 195 " --> pdb=" O ALA H 191 " (cutoff:3.500A) removed outlier: 4.306A pdb=" N SER H 196 " --> pdb=" O THR H 192 " (cutoff:3.500A) removed outlier: 5.122A pdb=" N ASN H 197 " --> pdb=" O GLY H 193 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N LYS H 198 " --> pdb=" O TRP H 194 " (cutoff:3.500A) Processing helix chain 'H' and resid 224 through 227 No H-bonds generated for 'chain 'H' and resid 224 through 227' Processing helix chain 'H' and resid 230 through 239 Processing helix chain 'H' and resid 256 through 282 Processing helix chain 'H' and resid 317 through 319 No H-bonds generated for 'chain 'H' and resid 317 through 319' Processing helix chain 'H' and resid 331 through 344 removed outlier: 4.012A pdb=" N TYR H 344 " --> pdb=" O TRP H 340 " (cutoff:3.500A) Processing helix chain 'H' and resid 346 through 348 No H-bonds generated for 'chain 'H' and resid 346 through 348' Processing helix chain 'H' and resid 358 through 361 No H-bonds generated for 'chain 'H' and resid 358 through 361' Processing helix chain 'H' and resid 367 through 369 No H-bonds generated for 'chain 'H' and resid 367 through 369' Processing helix chain 'H' and resid 375 through 377 No H-bonds generated for 'chain 'H' and resid 375 through 377' Processing helix chain 'H' and resid 379 through 381 No H-bonds generated for 'chain 'H' and resid 379 through 381' Processing helix chain 'H' and resid 391 through 394 Processing helix chain 'H' and resid 397 through 402 removed outlier: 3.820A pdb=" N TYR H 402 " --> pdb=" O VAL H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 411 through 425 removed outlier: 3.555A pdb=" N LEU H 415 " --> pdb=" O ALA H 411 " (cutoff:3.500A) Processing helix chain 'H' and resid 444 through 448 Processing helix chain 'H' and resid 479 through 491 Processing helix chain 'H' and resid 502 through 525 removed outlier: 3.816A pdb=" N HIS H 506 " --> pdb=" O SER H 503 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N SER H 510 " --> pdb=" O VAL H 507 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU H 520 " --> pdb=" O LYS H 517 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL H 523 " --> pdb=" O GLU H 520 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG H 524 " --> pdb=" O ALA H 521 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLU H 525 " --> pdb=" O THR H 522 " (cutoff:3.500A) Processing helix chain 'H' and resid 543 through 545 No H-bonds generated for 'chain 'H' and resid 543 through 545' Processing helix chain 'H' and resid 551 through 553 No H-bonds generated for 'chain 'H' and resid 551 through 553' Processing helix chain 'H' and resid 558 through 565 removed outlier: 3.641A pdb=" N ASN H 564 " --> pdb=" O SER H 560 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LYS H 565 " --> pdb=" O VAL H 561 " (cutoff:3.500A) Processing helix chain 'H' and resid 581 through 593 Processing helix chain 'H' and resid 614 through 623 removed outlier: 3.658A pdb=" N LYS H 623 " --> pdb=" O ALA H 619 " (cutoff:3.500A) Processing helix chain 'H' and resid 649 through 664 removed outlier: 3.548A pdb=" N LYS H 661 " --> pdb=" O ALA H 657 " (cutoff:3.500A) Processing helix chain 'H' and resid 677 through 680 Processing helix chain 'H' and resid 692 through 698 Processing helix chain 'H' and resid 713 through 719 Processing helix chain 'H' and resid 726 through 728 No H-bonds generated for 'chain 'H' and resid 726 through 728' Processing helix chain 'H' and resid 743 through 749 Processing helix chain 'H' and resid 754 through 766 Processing helix chain 'H' and resid 771 through 791 removed outlier: 3.578A pdb=" N ASP H 782 " --> pdb=" O GLU H 778 " (cutoff:3.500A) Processing helix chain 'H' and resid 796 through 799 No H-bonds generated for 'chain 'H' and resid 796 through 799' Processing sheet with id= A, first strand: chain 'A' and resid 89 through 93 removed outlier: 6.402A pdb=" N PHE A 175 " --> pdb=" O VAL A 90 " (cutoff:3.500A) removed outlier: 7.447A pdb=" N ILE A 92 " --> pdb=" O PHE A 175 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE A 207 " --> pdb=" O VAL A 176 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ALA A 178 " --> pdb=" O ILE A 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU A 209 " --> pdb=" O ALA A 178 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL A 180 " --> pdb=" O LEU A 209 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE A 211 " --> pdb=" O VAL A 180 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR A 298 " --> pdb=" O LEU A 214 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL A 474 " --> pdb=" O PHE A 430 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N ILE A 432 " --> pdb=" O VAL A 474 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS A 495 " --> pdb=" O ARG A 431 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE A 433 " --> pdb=" O HIS A 495 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE A 497 " --> pdb=" O PHE A 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN A 536 " --> pdb=" O GLY A 496 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL A 642 " --> pdb=" O LYS A 670 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL A 672 " --> pdb=" O VAL A 642 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU A 644 " --> pdb=" O VAL A 672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL A 674 " --> pdb=" O LEU A 644 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA A 646 " --> pdb=" O VAL A 674 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA A 645 " --> pdb=" O PRO A 704 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU A 706 " --> pdb=" O ALA A 645 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA A 647 " --> pdb=" O LEU A 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA A 708 " --> pdb=" O ALA A 647 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 89 through 93 removed outlier: 6.401A pdb=" N PHE B 175 " --> pdb=" O VAL B 90 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE B 92 " --> pdb=" O PHE B 175 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE B 207 " --> pdb=" O VAL B 176 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ALA B 178 " --> pdb=" O ILE B 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU B 209 " --> pdb=" O ALA B 178 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL B 180 " --> pdb=" O LEU B 209 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE B 211 " --> pdb=" O VAL B 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR B 298 " --> pdb=" O LEU B 214 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 473 through 475 removed outlier: 8.509A pdb=" N VAL B 474 " --> pdb=" O PHE B 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE B 432 " --> pdb=" O VAL B 474 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS B 495 " --> pdb=" O ARG B 431 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE B 433 " --> pdb=" O HIS B 495 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE B 497 " --> pdb=" O PHE B 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN B 536 " --> pdb=" O GLY B 496 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL B 642 " --> pdb=" O LYS B 670 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL B 672 " --> pdb=" O VAL B 642 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU B 644 " --> pdb=" O VAL B 672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL B 674 " --> pdb=" O LEU B 644 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA B 646 " --> pdb=" O VAL B 674 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA B 645 " --> pdb=" O PRO B 704 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU B 706 " --> pdb=" O ALA B 645 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA B 647 " --> pdb=" O LEU B 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA B 708 " --> pdb=" O ALA B 647 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 89 through 93 removed outlier: 6.401A pdb=" N PHE C 175 " --> pdb=" O VAL C 90 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE C 92 " --> pdb=" O PHE C 175 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE C 207 " --> pdb=" O VAL C 176 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA C 178 " --> pdb=" O ILE C 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU C 209 " --> pdb=" O ALA C 178 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL C 180 " --> pdb=" O LEU C 209 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE C 211 " --> pdb=" O VAL C 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR C 298 " --> pdb=" O LEU C 214 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 473 through 475 removed outlier: 8.507A pdb=" N VAL C 474 " --> pdb=" O PHE C 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE C 432 " --> pdb=" O VAL C 474 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N HIS C 495 " --> pdb=" O ARG C 431 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE C 433 " --> pdb=" O HIS C 495 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE C 497 " --> pdb=" O PHE C 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN C 536 " --> pdb=" O GLY C 496 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL C 642 " --> pdb=" O LYS C 670 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL C 672 " --> pdb=" O VAL C 642 " (cutoff:3.500A) removed outlier: 6.328A pdb=" N LEU C 644 " --> pdb=" O VAL C 672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL C 674 " --> pdb=" O LEU C 644 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA C 646 " --> pdb=" O VAL C 674 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA C 645 " --> pdb=" O PRO C 704 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU C 706 " --> pdb=" O ALA C 645 " (cutoff:3.500A) removed outlier: 7.989A pdb=" N ALA C 647 " --> pdb=" O LEU C 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA C 708 " --> pdb=" O ALA C 647 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'D' and resid 89 through 93 removed outlier: 6.401A pdb=" N PHE D 175 " --> pdb=" O VAL D 90 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE D 92 " --> pdb=" O PHE D 175 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE D 207 " --> pdb=" O VAL D 176 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA D 178 " --> pdb=" O ILE D 207 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU D 209 " --> pdb=" O ALA D 178 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL D 180 " --> pdb=" O LEU D 209 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N ILE D 211 " --> pdb=" O VAL D 180 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR D 298 " --> pdb=" O LEU D 214 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'D' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL D 474 " --> pdb=" O PHE D 430 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE D 432 " --> pdb=" O VAL D 474 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS D 495 " --> pdb=" O ARG D 431 " (cutoff:3.500A) removed outlier: 7.949A pdb=" N PHE D 433 " --> pdb=" O HIS D 495 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ILE D 497 " --> pdb=" O PHE D 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN D 536 " --> pdb=" O GLY D 496 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'D' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL D 642 " --> pdb=" O LYS D 670 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL D 672 " --> pdb=" O VAL D 642 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU D 644 " --> pdb=" O VAL D 672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL D 674 " --> pdb=" O LEU D 644 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA D 646 " --> pdb=" O VAL D 674 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA D 645 " --> pdb=" O PRO D 704 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU D 706 " --> pdb=" O ALA D 645 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA D 647 " --> pdb=" O LEU D 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA D 708 " --> pdb=" O ALA D 647 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'E' and resid 89 through 93 removed outlier: 6.401A pdb=" N PHE E 175 " --> pdb=" O VAL E 90 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE E 92 " --> pdb=" O PHE E 175 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE E 207 " --> pdb=" O VAL E 176 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA E 178 " --> pdb=" O ILE E 207 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU E 209 " --> pdb=" O ALA E 178 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N VAL E 180 " --> pdb=" O LEU E 209 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N ILE E 211 " --> pdb=" O VAL E 180 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N THR E 298 " --> pdb=" O LEU E 214 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'E' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL E 474 " --> pdb=" O PHE E 430 " (cutoff:3.500A) removed outlier: 6.562A pdb=" N ILE E 432 " --> pdb=" O VAL E 474 " (cutoff:3.500A) removed outlier: 6.847A pdb=" N HIS E 495 " --> pdb=" O ARG E 431 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE E 433 " --> pdb=" O HIS E 495 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE E 497 " --> pdb=" O PHE E 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN E 536 " --> pdb=" O GLY E 496 " (cutoff:3.500A) Processing sheet with id= O, first strand: chain 'E' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL E 642 " --> pdb=" O LYS E 670 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL E 672 " --> pdb=" O VAL E 642 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU E 644 " --> pdb=" O VAL E 672 " (cutoff:3.500A) removed outlier: 7.749A pdb=" N VAL E 674 " --> pdb=" O LEU E 644 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA E 646 " --> pdb=" O VAL E 674 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA E 645 " --> pdb=" O PRO E 704 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU E 706 " --> pdb=" O ALA E 645 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA E 647 " --> pdb=" O LEU E 706 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA E 708 " --> pdb=" O ALA E 647 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'F' and resid 89 through 93 removed outlier: 6.401A pdb=" N PHE F 175 " --> pdb=" O VAL F 90 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N ILE F 92 " --> pdb=" O PHE F 175 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE F 207 " --> pdb=" O VAL F 176 " (cutoff:3.500A) removed outlier: 7.260A pdb=" N ALA F 178 " --> pdb=" O ILE F 207 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N LEU F 209 " --> pdb=" O ALA F 178 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL F 180 " --> pdb=" O LEU F 209 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE F 211 " --> pdb=" O VAL F 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR F 298 " --> pdb=" O LEU F 214 " (cutoff:3.500A) Processing sheet with id= Q, first strand: chain 'F' and resid 473 through 475 removed outlier: 8.509A pdb=" N VAL F 474 " --> pdb=" O PHE F 430 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ILE F 432 " --> pdb=" O VAL F 474 " (cutoff:3.500A) removed outlier: 6.851A pdb=" N HIS F 495 " --> pdb=" O ARG F 431 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N PHE F 433 " --> pdb=" O HIS F 495 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE F 497 " --> pdb=" O PHE F 433 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N ASN F 536 " --> pdb=" O GLY F 496 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'F' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL F 642 " --> pdb=" O LYS F 670 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL F 672 " --> pdb=" O VAL F 642 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU F 644 " --> pdb=" O VAL F 672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL F 674 " --> pdb=" O LEU F 644 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N ALA F 646 " --> pdb=" O VAL F 674 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA F 645 " --> pdb=" O PRO F 704 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU F 706 " --> pdb=" O ALA F 645 " (cutoff:3.500A) removed outlier: 7.990A pdb=" N ALA F 647 " --> pdb=" O LEU F 706 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N ALA F 708 " --> pdb=" O ALA F 647 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'G' and resid 89 through 93 removed outlier: 6.401A pdb=" N PHE G 175 " --> pdb=" O VAL G 90 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N ILE G 92 " --> pdb=" O PHE G 175 " (cutoff:3.500A) removed outlier: 6.581A pdb=" N ILE G 207 " --> pdb=" O VAL G 176 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ALA G 178 " --> pdb=" O ILE G 207 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N LEU G 209 " --> pdb=" O ALA G 178 " (cutoff:3.500A) removed outlier: 7.232A pdb=" N VAL G 180 " --> pdb=" O LEU G 209 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N ILE G 211 " --> pdb=" O VAL G 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR G 298 " --> pdb=" O LEU G 214 " (cutoff:3.500A) Processing sheet with id= T, first strand: chain 'G' and resid 473 through 475 removed outlier: 8.508A pdb=" N VAL G 474 " --> pdb=" O PHE G 430 " (cutoff:3.500A) removed outlier: 6.563A pdb=" N ILE G 432 " --> pdb=" O VAL G 474 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N HIS G 495 " --> pdb=" O ARG G 431 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE G 433 " --> pdb=" O HIS G 495 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE G 497 " --> pdb=" O PHE G 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN G 536 " --> pdb=" O GLY G 496 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'G' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL G 642 " --> pdb=" O LYS G 670 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N VAL G 672 " --> pdb=" O VAL G 642 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N LEU G 644 " --> pdb=" O VAL G 672 " (cutoff:3.500A) removed outlier: 7.748A pdb=" N VAL G 674 " --> pdb=" O LEU G 644 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N ALA G 646 " --> pdb=" O VAL G 674 " (cutoff:3.500A) removed outlier: 7.417A pdb=" N ALA G 645 " --> pdb=" O PRO G 704 " (cutoff:3.500A) removed outlier: 6.228A pdb=" N LEU G 706 " --> pdb=" O ALA G 645 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA G 647 " --> pdb=" O LEU G 706 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N ALA G 708 " --> pdb=" O ALA G 647 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'H' and resid 89 through 93 removed outlier: 6.402A pdb=" N PHE H 175 " --> pdb=" O VAL H 90 " (cutoff:3.500A) removed outlier: 7.424A pdb=" N ILE H 92 " --> pdb=" O PHE H 175 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N ILE H 207 " --> pdb=" O VAL H 176 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA H 178 " --> pdb=" O ILE H 207 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N LEU H 209 " --> pdb=" O ALA H 178 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N VAL H 180 " --> pdb=" O LEU H 209 " (cutoff:3.500A) removed outlier: 6.298A pdb=" N ILE H 211 " --> pdb=" O VAL H 180 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N THR H 298 " --> pdb=" O LEU H 214 " (cutoff:3.500A) Processing sheet with id= W, first strand: chain 'H' and resid 473 through 475 removed outlier: 8.507A pdb=" N VAL H 474 " --> pdb=" O PHE H 430 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N ILE H 432 " --> pdb=" O VAL H 474 " (cutoff:3.500A) removed outlier: 6.848A pdb=" N HIS H 495 " --> pdb=" O ARG H 431 " (cutoff:3.500A) removed outlier: 7.948A pdb=" N PHE H 433 " --> pdb=" O HIS H 495 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE H 497 " --> pdb=" O PHE H 433 " (cutoff:3.500A) removed outlier: 4.456A pdb=" N ASN H 536 " --> pdb=" O GLY H 496 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'H' and resid 625 through 627 removed outlier: 6.467A pdb=" N VAL H 642 " --> pdb=" O LYS H 670 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N VAL H 672 " --> pdb=" O VAL H 642 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N LEU H 644 " --> pdb=" O VAL H 672 " (cutoff:3.500A) removed outlier: 7.750A pdb=" N VAL H 674 " --> pdb=" O LEU H 644 " (cutoff:3.500A) removed outlier: 6.558A pdb=" N ALA H 646 " --> pdb=" O VAL H 674 " (cutoff:3.500A) removed outlier: 7.416A pdb=" N ALA H 645 " --> pdb=" O PRO H 704 " (cutoff:3.500A) removed outlier: 6.229A pdb=" N LEU H 706 " --> pdb=" O ALA H 645 " (cutoff:3.500A) removed outlier: 7.988A pdb=" N ALA H 647 " --> pdb=" O LEU H 706 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N ALA H 708 " --> pdb=" O ALA H 647 " (cutoff:3.500A) 1776 hydrogen bonds defined for protein. 4824 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: 17.79 Time building geometry restraints manager: 21.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.14 - 1.27: 9039 1.27 - 1.41: 14776 1.41 - 1.54: 28355 1.54 - 1.68: 972 1.68 - 1.82: 272 Bond restraints: 53414 Sorted by residual: bond pdb=" C5 TPP H 900 " pdb=" S1 TPP H 900 " ideal model delta sigma weight residual 1.727 1.587 0.140 1.00e-02 1.00e+04 1.95e+02 bond pdb=" C5 TPP B 900 " pdb=" S1 TPP B 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.94e+02 bond pdb=" C5 TPP E 900 " pdb=" S1 TPP E 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.94e+02 bond pdb=" C5 TPP G 900 " pdb=" S1 TPP G 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.93e+02 bond pdb=" C5 TPP C 900 " pdb=" S1 TPP C 900 " ideal model delta sigma weight residual 1.727 1.588 0.139 1.00e-02 1.00e+04 1.93e+02 ... (remaining 53409 not shown) Histogram of bond angle deviations from ideal: 83.66 - 93.84: 16 93.84 - 104.03: 924 104.03 - 114.21: 28807 114.21 - 124.40: 40677 124.40 - 134.59: 2282 Bond angle restraints: 72706 Sorted by residual: angle pdb=" N3 TPP A 900 " pdb=" C2 TPP A 900 " pdb=" S1 TPP A 900 " ideal model delta sigma weight residual 112.34 122.29 -9.95 1.00e+00 1.00e+00 9.89e+01 angle pdb=" N3 TPP C 900 " pdb=" C2 TPP C 900 " pdb=" S1 TPP C 900 " ideal model delta sigma weight residual 112.34 122.11 -9.77 1.00e+00 1.00e+00 9.54e+01 angle pdb=" N3 TPP F 900 " pdb=" C2 TPP F 900 " pdb=" S1 TPP F 900 " ideal model delta sigma weight residual 112.34 122.07 -9.73 1.00e+00 1.00e+00 9.47e+01 angle pdb=" N3 TPP D 900 " pdb=" C2 TPP D 900 " pdb=" S1 TPP D 900 " ideal model delta sigma weight residual 112.34 122.04 -9.70 1.00e+00 1.00e+00 9.40e+01 angle pdb=" N3 TPP B 900 " pdb=" C2 TPP B 900 " pdb=" S1 TPP B 900 " ideal model delta sigma weight residual 112.34 122.00 -9.66 1.00e+00 1.00e+00 9.34e+01 ... (remaining 72701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.84: 27920 17.84 - 35.67: 2519 35.67 - 53.51: 518 53.51 - 71.34: 197 71.34 - 89.18: 92 Dihedral angle restraints: 31246 sinusoidal: 12450 harmonic: 18796 Sorted by residual: dihedral pdb=" CA PHE F 699 " pdb=" C PHE F 699 " pdb=" N THR F 700 " pdb=" CA THR F 700 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.46e+01 dihedral pdb=" CA PHE C 699 " pdb=" C PHE C 699 " pdb=" N THR C 700 " pdb=" CA THR C 700 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.45e+01 dihedral pdb=" CA PHE G 699 " pdb=" C PHE G 699 " pdb=" N THR G 700 " pdb=" CA THR G 700 " ideal model delta harmonic sigma weight residual 180.00 143.07 36.93 0 5.00e+00 4.00e-02 5.45e+01 ... (remaining 31243 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.154: 6357 0.154 - 0.308: 1141 0.308 - 0.461: 88 0.461 - 0.615: 8 0.615 - 0.769: 8 Chirality restraints: 7602 Sorted by residual: chirality pdb=" CG LEU F 477 " pdb=" CB LEU F 477 " pdb=" CD1 LEU F 477 " pdb=" CD2 LEU F 477 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CG LEU C 477 " pdb=" CB LEU C 477 " pdb=" CD1 LEU C 477 " pdb=" CD2 LEU C 477 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.48e+01 chirality pdb=" CG LEU H 477 " pdb=" CB LEU H 477 " pdb=" CD1 LEU H 477 " pdb=" CD2 LEU H 477 " both_signs ideal model delta sigma weight residual False -2.59 -1.82 -0.77 2.00e-01 2.50e+01 1.47e+01 ... (remaining 7599 not shown) Planarity restraints: 9577 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 217 " -0.072 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR D 217 " 0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR D 217 " 0.024 2.00e-02 2.50e+03 pdb=" CD2 TYR D 217 " 0.048 2.00e-02 2.50e+03 pdb=" CE1 TYR D 217 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR D 217 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR D 217 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR D 217 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR G 217 " -0.072 2.00e-02 2.50e+03 3.74e-02 2.80e+01 pdb=" CG TYR G 217 " 0.046 2.00e-02 2.50e+03 pdb=" CD1 TYR G 217 " 0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR G 217 " 0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR G 217 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR G 217 " -0.011 2.00e-02 2.50e+03 pdb=" CZ TYR G 217 " -0.007 2.00e-02 2.50e+03 pdb=" OH TYR G 217 " -0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 217 " 0.071 2.00e-02 2.50e+03 3.73e-02 2.79e+01 pdb=" CG TYR C 217 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 TYR C 217 " -0.023 2.00e-02 2.50e+03 pdb=" CD2 TYR C 217 " -0.047 2.00e-02 2.50e+03 pdb=" CE1 TYR C 217 " -0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR C 217 " 0.011 2.00e-02 2.50e+03 pdb=" CZ TYR C 217 " 0.007 2.00e-02 2.50e+03 pdb=" OH TYR C 217 " 0.032 2.00e-02 2.50e+03 ... (remaining 9574 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 7882 2.74 - 3.28: 56964 3.28 - 3.82: 115662 3.82 - 4.36: 142334 4.36 - 4.90: 220047 Nonbonded interactions: 542889 Sorted by model distance: nonbonded pdb=" OE1 GLU E 153 " pdb=" O HOH E1001 " model vdw 2.196 2.440 nonbonded pdb=" OE1 GLU H 153 " pdb=" O HOH H1001 " model vdw 2.196 2.440 nonbonded pdb=" OE1 GLU A 153 " pdb=" O HOH A1001 " model vdw 2.196 2.440 nonbonded pdb=" OE1 GLU F 153 " pdb=" O HOH F1001 " model vdw 2.196 2.440 nonbonded pdb=" OE1 GLU C 153 " pdb=" O HOH C1001 " model vdw 2.196 2.440 ... (remaining 542884 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 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'B' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'C' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'D' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'E' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'F' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'G' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ selection = (chain 'H' and (resid 2 through 90 or resid 92 through 427 or resid 429 through \ 545 or resid 550 through 567 or resid 569 through 807 or resid 900 through 901)) \ } 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=0.40 max=1.00 mean=0.99 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 11.210 Check model and map are aligned: 0.620 Set scattering table: 0.380 Process input model: 144.910 Find NCS groups from input model: 2.940 Set up NCS constraints: 0.270 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:8.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 170.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8877 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 : 0.025 0.198 53414 Z= 1.671 Angle : 1.662 20.909 72706 Z= 0.963 Chirality : 0.120 0.769 7602 Planarity : 0.011 0.055 9577 Dihedral : 16.070 89.175 19228 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.93 % Favored : 95.94 % Rotamer: Outliers : 2.81 % Allowed : 4.96 % Favored : 92.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.13 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 6529 helix: -1.54 (0.08), residues: 2736 sheet: -1.45 (0.17), residues: 801 loop : -0.53 (0.11), residues: 2992 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.010 TRP D 65 HIS 0.028 0.008 HIS B 320 PHE 0.045 0.009 PHE B 237 TYR 0.072 0.011 TYR G 217 ARG 0.022 0.003 ARG D 494 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 721 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 137 poor density : 584 time to evaluate : 4.740 Fit side-chains outliers start: 137 outliers final: 93 residues processed: 671 average time/residue: 1.7763 time to fit residues: 1450.6494 Evaluate side-chains 671 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 578 time to evaluate : 4.748 Switching outliers to nearest non-outliers outliers start: 93 outliers final: 61 residues processed: 32 average time/residue: 1.4265 time to fit residues: 63.9200 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 540 optimal weight: 5.9990 chunk 485 optimal weight: 0.6980 chunk 269 optimal weight: 3.9990 chunk 165 optimal weight: 0.7980 chunk 327 optimal weight: 5.9990 chunk 259 optimal weight: 0.8980 chunk 501 optimal weight: 0.8980 chunk 194 optimal weight: 5.9990 chunk 305 optimal weight: 5.9990 chunk 373 optimal weight: 5.9990 chunk 581 optimal weight: 0.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN A 39 GLN A 105 GLN A 321 GLN A 466 HIS ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** A 653 GLN B 14 ASN B 39 GLN B 105 GLN B 132 GLN B 321 GLN B 466 HIS ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** B 653 GLN C 14 ASN C 39 GLN C 105 GLN C 466 HIS ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 653 GLN D 14 ASN D 39 GLN D 105 GLN D 321 GLN D 466 HIS ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 653 GLN E 14 ASN E 39 GLN E 105 GLN E 321 GLN E 466 HIS ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** E 653 GLN F 14 ASN F 39 GLN F 105 GLN F 132 GLN F 321 GLN F 466 HIS ** F 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** F 653 GLN G 14 ASN G 39 GLN G 105 GLN G 321 GLN G 466 HIS ** G 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** G 653 GLN H 14 ASN H 39 GLN H 105 GLN H 132 GLN H 321 GLN H 466 HIS ** H 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** H 653 GLN Total number of N/Q/H flips: 50 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1196 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 53414 Z= 0.165 Angle : 0.583 8.943 72706 Z= 0.314 Chirality : 0.045 0.237 7602 Planarity : 0.004 0.036 9577 Dihedral : 6.055 46.255 7098 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 2.04 % Allowed : 7.36 % Favored : 90.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.06 (0.10), residues: 6529 helix: 0.49 (0.09), residues: 2744 sheet: -0.79 (0.18), residues: 841 loop : 0.05 (0.12), residues: 2944 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 10 HIS 0.005 0.001 HIS B 152 PHE 0.018 0.002 PHE A 699 TYR 0.019 0.002 TYR E 744 ARG 0.003 0.000 ARG A 203 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 729 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 95 poor density : 634 time to evaluate : 4.830 Fit side-chains outliers start: 95 outliers final: 16 residues processed: 698 average time/residue: 1.7174 time to fit residues: 1470.4457 Evaluate side-chains 579 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 563 time to evaluate : 4.742 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 16 residues processed: 0 time to fit residues: 6.2860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 322 optimal weight: 6.9990 chunk 180 optimal weight: 6.9990 chunk 483 optimal weight: 9.9990 chunk 395 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 582 optimal weight: 0.9990 chunk 628 optimal weight: 0.8980 chunk 518 optimal weight: 4.9990 chunk 577 optimal weight: 4.9990 chunk 198 optimal weight: 1.9990 chunk 467 optimal weight: 9.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 53414 Z= 0.250 Angle : 0.635 6.960 72706 Z= 0.344 Chirality : 0.048 0.258 7602 Planarity : 0.005 0.055 9577 Dihedral : 6.038 49.836 7098 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.74 % Favored : 97.26 % Rotamer: Outliers : 1.32 % Allowed : 9.43 % Favored : 89.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.46 (0.11), residues: 6529 helix: 0.92 (0.10), residues: 2760 sheet: -0.89 (0.18), residues: 801 loop : 0.25 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 65 HIS 0.006 0.001 HIS D 320 PHE 0.019 0.003 PHE H 237 TYR 0.022 0.003 TYR C 217 ARG 0.003 0.000 ARG C 262 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 649 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 593 time to evaluate : 4.739 Fit side-chains outliers start: 56 outliers final: 32 residues processed: 609 average time/residue: 1.7770 time to fit residues: 1323.3702 Evaluate side-chains 605 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 573 time to evaluate : 4.690 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 16 residues processed: 16 average time/residue: 1.1413 time to fit residues: 30.8265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 575 optimal weight: 5.9990 chunk 437 optimal weight: 0.0770 chunk 302 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 277 optimal weight: 0.9990 chunk 390 optimal weight: 20.0000 chunk 584 optimal weight: 5.9990 chunk 618 optimal weight: 2.9990 chunk 305 optimal weight: 10.0000 chunk 553 optimal weight: 7.9990 chunk 166 optimal weight: 10.0000 overall best weight: 2.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8803 moved from start: 0.1258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 53414 Z= 0.222 Angle : 0.602 6.934 72706 Z= 0.325 Chirality : 0.046 0.206 7602 Planarity : 0.004 0.050 9577 Dihedral : 5.878 50.159 7098 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.38 % Allowed : 9.56 % Favored : 89.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.63 (0.11), residues: 6529 helix: 1.08 (0.10), residues: 2760 sheet: -0.83 (0.18), residues: 801 loop : 0.33 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 65 HIS 0.005 0.001 HIS E 320 PHE 0.018 0.002 PHE B 237 TYR 0.018 0.002 TYR D 217 ARG 0.002 0.000 ARG F 262 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 637 time to evaluate : 4.749 Fit side-chains outliers start: 59 outliers final: 39 residues processed: 672 average time/residue: 1.8266 time to fit residues: 1496.5798 Evaluate side-chains 641 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 602 time to evaluate : 4.747 Switching outliers to nearest non-outliers outliers start: 39 outliers final: 23 residues processed: 16 average time/residue: 1.1108 time to fit residues: 30.3334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 515 optimal weight: 3.9990 chunk 351 optimal weight: 9.9990 chunk 8 optimal weight: 2.9990 chunk 460 optimal weight: 8.9990 chunk 255 optimal weight: 10.0000 chunk 527 optimal weight: 4.9990 chunk 427 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 315 optimal weight: 9.9990 chunk 555 optimal weight: 9.9990 chunk 156 optimal weight: 0.3980 overall best weight: 4.2788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 548 HIS B ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 548 HIS B ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS ** F 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS ** H 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8827 moved from start: 0.1095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 53414 Z= 0.351 Angle : 0.701 7.008 72706 Z= 0.381 Chirality : 0.052 0.244 7602 Planarity : 0.005 0.072 9577 Dihedral : 6.171 50.667 7098 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.60 % Allowed : 9.71 % Favored : 88.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.50 (0.11), residues: 6529 helix: 0.97 (0.10), residues: 2760 sheet: -0.96 (0.18), residues: 817 loop : 0.29 (0.12), residues: 2952 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP E 65 HIS 0.007 0.002 HIS C 320 PHE 0.027 0.003 PHE H 237 TYR 0.026 0.003 TYR H 217 ARG 0.003 0.001 ARG D 494 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 71 poor density : 577 time to evaluate : 4.894 Fit side-chains outliers start: 71 outliers final: 33 residues processed: 608 average time/residue: 1.7961 time to fit residues: 1335.3874 Evaluate side-chains 622 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 589 time to evaluate : 4.851 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 17 residues processed: 16 average time/residue: 1.1128 time to fit residues: 30.4742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 208 optimal weight: 2.9990 chunk 557 optimal weight: 4.9990 chunk 122 optimal weight: 0.8980 chunk 363 optimal weight: 0.5980 chunk 152 optimal weight: 0.0980 chunk 619 optimal weight: 0.9990 chunk 514 optimal weight: 1.9990 chunk 286 optimal weight: 1.9990 chunk 51 optimal weight: 8.9990 chunk 204 optimal weight: 1.9990 chunk 325 optimal weight: 6.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 333 HIS ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 333 HIS ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 333 HIS ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 333 HIS ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 333 HIS ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 333 HIS F 546 GLN B F 549 ASN B ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 333 HIS ** G 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 333 HIS H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.1431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 53414 Z= 0.159 Angle : 0.548 8.465 72706 Z= 0.293 Chirality : 0.044 0.243 7602 Planarity : 0.004 0.036 9577 Dihedral : 5.643 47.537 7098 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 0.90 % Allowed : 10.63 % Favored : 88.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.86 (0.11), residues: 6529 helix: 1.36 (0.10), residues: 2704 sheet: -0.63 (0.18), residues: 841 loop : 0.35 (0.12), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP F 498 HIS 0.005 0.001 HIS B 152 PHE 0.013 0.002 PHE E 334 TYR 0.016 0.002 TYR C 744 ARG 0.002 0.000 ARG G 262 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 617 time to evaluate : 4.760 Fit side-chains outliers start: 41 outliers final: 31 residues processed: 640 average time/residue: 1.7912 time to fit residues: 1405.6554 Evaluate side-chains 630 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 599 time to evaluate : 5.784 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 1.9047 time to fit residues: 24.8203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 597 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 352 optimal weight: 4.9990 chunk 452 optimal weight: 0.6980 chunk 350 optimal weight: 7.9990 chunk 521 optimal weight: 9.9990 chunk 345 optimal weight: 10.0000 chunk 616 optimal weight: 8.9990 chunk 386 optimal weight: 0.9990 chunk 376 optimal weight: 5.9990 chunk 284 optimal weight: 0.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 53414 Z= 0.192 Angle : 0.571 7.749 72706 Z= 0.306 Chirality : 0.046 0.318 7602 Planarity : 0.004 0.046 9577 Dihedral : 5.674 49.534 7098 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.99 % Allowed : 10.33 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.82 (0.11), residues: 6529 helix: 1.26 (0.10), residues: 2760 sheet: -0.76 (0.18), residues: 801 loop : 0.42 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP F 544 HIS 0.004 0.001 HIS H 553 PHE 0.015 0.002 PHE E 237 TYR 0.017 0.002 TYR C 744 ARG 0.002 0.000 ARG B 494 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 669 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 621 time to evaluate : 4.839 Fit side-chains outliers start: 48 outliers final: 31 residues processed: 652 average time/residue: 1.8427 time to fit residues: 1466.1851 Evaluate side-chains 636 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 605 time to evaluate : 4.747 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 23 residues processed: 8 average time/residue: 1.7663 time to fit residues: 23.5544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 381 optimal weight: 5.9990 chunk 246 optimal weight: 6.9990 chunk 368 optimal weight: 4.9990 chunk 185 optimal weight: 3.9990 chunk 121 optimal weight: 9.9990 chunk 119 optimal weight: 9.9990 chunk 392 optimal weight: 6.9990 chunk 420 optimal weight: 7.9990 chunk 304 optimal weight: 5.9990 chunk 57 optimal weight: 0.0980 chunk 484 optimal weight: 10.0000 overall best weight: 4.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8823 moved from start: 0.1168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 53414 Z= 0.350 Angle : 0.700 7.844 72706 Z= 0.378 Chirality : 0.052 0.353 7602 Planarity : 0.005 0.071 9577 Dihedral : 6.071 50.648 7098 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 4.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 0.95 % Allowed : 10.39 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.70 (0.11), residues: 6529 helix: 1.19 (0.10), residues: 2712 sheet: -0.91 (0.18), residues: 817 loop : 0.36 (0.12), residues: 3000 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP D 65 HIS 0.007 0.002 HIS D 320 PHE 0.028 0.003 PHE D 237 TYR 0.025 0.003 TYR G 217 ARG 0.003 0.001 ARG A 262 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 592 time to evaluate : 5.248 Fit side-chains outliers start: 42 outliers final: 34 residues processed: 615 average time/residue: 1.8858 time to fit residues: 1414.0352 Evaluate side-chains 601 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 567 time to evaluate : 4.730 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 23 residues processed: 11 average time/residue: 1.4149 time to fit residues: 26.1177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 561 optimal weight: 0.9990 chunk 590 optimal weight: 4.9990 chunk 539 optimal weight: 0.9980 chunk 574 optimal weight: 2.9990 chunk 345 optimal weight: 8.9990 chunk 250 optimal weight: 0.6980 chunk 451 optimal weight: 0.9990 chunk 176 optimal weight: 6.9990 chunk 519 optimal weight: 10.0000 chunk 543 optimal weight: 0.4980 chunk 572 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B C 132 GLN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 408 GLN ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 ASN D 132 GLN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN B E 549 ASN B ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 53414 Z= 0.151 Angle : 0.543 9.056 72706 Z= 0.287 Chirality : 0.044 0.352 7602 Planarity : 0.004 0.035 9577 Dihedral : 5.525 46.927 7098 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 3.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 0.75 % Allowed : 10.72 % Favored : 88.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.93 (0.11), residues: 6529 helix: 1.42 (0.10), residues: 2704 sheet: -0.61 (0.18), residues: 841 loop : 0.41 (0.12), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 498 HIS 0.005 0.001 HIS C 152 PHE 0.011 0.001 PHE E 296 TYR 0.016 0.002 TYR E 744 ARG 0.002 0.000 ARG C 494 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 660 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 624 time to evaluate : 5.016 Fit side-chains outliers start: 36 outliers final: 36 residues processed: 647 average time/residue: 1.8704 time to fit residues: 1479.9868 Evaluate side-chains 661 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 625 time to evaluate : 4.747 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 23 residues processed: 13 average time/residue: 1.2456 time to fit residues: 27.6167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 377 optimal weight: 10.0000 chunk 607 optimal weight: 0.0170 chunk 371 optimal weight: 8.9990 chunk 288 optimal weight: 3.9990 chunk 422 optimal weight: 3.9990 chunk 637 optimal weight: 0.9980 chunk 586 optimal weight: 9.9990 chunk 507 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 392 optimal weight: 0.0270 chunk 311 optimal weight: 8.9990 overall best weight: 1.8080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 546 GLN B ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 549 ASN B ** both conformations clash, **PLEASE CHECK MANUALLY** D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN B E 549 ASN B E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 53414 Z= 0.199 Angle : 0.587 8.801 72706 Z= 0.312 Chirality : 0.047 0.416 7602 Planarity : 0.004 0.046 9577 Dihedral : 5.646 49.726 7098 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 3.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 0.70 % Allowed : 11.30 % Favored : 88.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % 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: 0.85 (0.11), residues: 6529 helix: 1.25 (0.10), residues: 2760 sheet: -0.72 (0.18), residues: 801 loop : 0.46 (0.12), residues: 2968 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 544 HIS 0.004 0.001 HIS G 553 PHE 0.016 0.002 PHE E 237 TYR 0.016 0.002 TYR E 744 ARG 0.002 0.000 ARG C 763 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 13058 Ramachandran restraints generated. 6529 Oldfield, 0 Emsley, 6529 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 658 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 625 time to evaluate : 5.074 Fit side-chains outliers start: 33 outliers final: 23 residues processed: 648 average time/residue: 1.8218 time to fit residues: 1441.1367 Evaluate side-chains 643 residues out of total 5351 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 620 time to evaluate : 4.750 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 6.2911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 640 random chunks: chunk 403 optimal weight: 3.9990 chunk 540 optimal weight: 0.7980 chunk 155 optimal weight: 10.0000 chunk 468 optimal weight: 0.1980 chunk 74 optimal weight: 5.9990 chunk 141 optimal weight: 6.9990 chunk 508 optimal weight: 0.0050 chunk 212 optimal weight: 0.9990 chunk 522 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 93 optimal weight: 3.9990 overall best weight: 0.7998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 546 GLN B A 549 ASN B A 636 ASN ** B 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 546 GLN B B 549 ASN B B 636 ASN ** C 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 546 GLN B C 549 ASN B C 636 ASN ** D 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 546 GLN B D 549 ASN B D 636 ASN ** E 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 546 GLN B E 549 ASN B E 636 ASN ** F 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 546 GLN B F 549 ASN B F 636 ASN ** G 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 546 GLN B G 549 ASN B G 636 ASN ** H 321 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 546 GLN B H 549 ASN B Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.118543 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.093551 restraints weight = 137348.220| |-----------------------------------------------------------------------------| r_work (start): 0.2924 rms_B_bonded: 1.65 r_work: 0.2789 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2684 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2675 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2675 r_free = 0.2675 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.45 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2675 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8978 moved from start: 0.1643 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 53414 Z= 0.144 Angle : 0.531 9.189 72706 Z= 0.280 Chirality : 0.044 0.401 7602 Planarity : 0.004 0.036 9577 Dihedral : 5.367 47.342 7098 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Rotamer: Outliers : 0.77 % Allowed : 11.10 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.50 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.11), residues: 6529 helix: 1.47 (0.10), residues: 2704 sheet: -0.52 (0.18), residues: 841 loop : 0.48 (0.12), residues: 2984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP F 498 HIS 0.004 0.001 HIS G 152 PHE 0.012 0.001 PHE E 296 TYR 0.016 0.001 TYR C 744 ARG 0.002 0.000 ARG E 494 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 21308.68 seconds wall clock time: 370 minutes 57.60 seconds (22257.60 seconds total)