Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 22:32:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/04_2023/8ea3_27971_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/04_2023/8ea3_27971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/04_2023/8ea3_27971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/04_2023/8ea3_27971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/04_2023/8ea3_27971_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ea3_27971/04_2023/8ea3_27971_updated.pdb" } resolution = 3.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.063 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 529 5.49 5 Mg 14 5.21 5 S 170 5.16 5 C 33408 2.51 5 N 10159 2.21 5 O 11675 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 131": "OE1" <-> "OE2" Residue "A GLU 209": "OE1" <-> "OE2" Residue "B GLU 82": "OE1" <-> "OE2" Residue "B GLU 212": "OE1" <-> "OE2" Residue "C GLU 82": "OE1" <-> "OE2" Residue "C ARG 85": "NH1" <-> "NH2" Residue "C GLU 250": "OE1" <-> "OE2" Residue "C ARG 254": "NH1" <-> "NH2" Residue "D GLU 19": "OE1" <-> "OE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "D GLU 82": "OE1" <-> "OE2" Residue "D ARG 85": "NH1" <-> "NH2" Residue "D GLU 131": "OE1" <-> "OE2" Residue "D GLU 162": "OE1" <-> "OE2" Residue "D PHE 190": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 238": "OE1" <-> "OE2" Residue "E GLU 19": "OE1" <-> "OE2" Residue "E GLU 212": "OE1" <-> "OE2" Residue "E GLU 238": "OE1" <-> "OE2" Residue "E GLU 270": "OE1" <-> "OE2" Residue "F ARG 76": "NH1" <-> "NH2" Residue "F GLU 139": "OE1" <-> "OE2" Residue "F GLU 184": "OE1" <-> "OE2" Residue "G ARG 195": "NH1" <-> "NH2" Residue "G GLU 238": "OE1" <-> "OE2" Residue "H GLU 19": "OE1" <-> "OE2" Residue "H GLU 82": "OE1" <-> "OE2" Residue "H GLU 131": "OE1" <-> "OE2" Residue "H GLU 212": "OE1" <-> "OE2" Residue "H ASP 264": "OD1" <-> "OD2" Residue "H GLU 270": "OE1" <-> "OE2" Residue "I ASP 144": "OD1" <-> "OD2" Residue "I GLU 250": "OE1" <-> "OE2" Residue "J TYR 93": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 125": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 250": "OE1" <-> "OE2" Residue "O TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 130": "OE1" <-> "OE2" Residue "O TYR 182": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 230": "OE1" <-> "OE2" Residue "O PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 289": "OE1" <-> "OE2" Residue "O PHE 305": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 325": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 347": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 384": "OE1" <-> "OE2" Residue "O PHE 401": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 474": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 514": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O ARG 525": "NH1" <-> "NH2" Residue "O TYR 538": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 567": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 570": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 572": "OE1" <-> "OE2" Residue "O TYR 590": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 3": "OE1" <-> "OE2" Residue "Q PHE 12": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 17": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 20": "OE1" <-> "OE2" Residue "Q PHE 56": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 58": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q ASP 77": "OD1" <-> "OD2" Residue "Q GLU 113": "OE1" <-> "OE2" Residue "Q PHE 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S PHE 15": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 26": "OE1" <-> "OE2" Residue "S TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 30": "OE1" <-> "OE2" Residue "W ASP 57": "OD1" <-> "OD2" Residue "W TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W GLU 360": "OE1" <-> "OE2" Residue "W ARG 367": "NH1" <-> "NH2" Residue "W TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "W ARG 416": "NH1" <-> "NH2" Residue "W PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 30": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X ASP 57": "OD1" <-> "OD2" Residue "X PHE 114": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X ARG 235": "NH1" <-> "NH2" Residue "X TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 285": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 332": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 362": "OE1" <-> "OE2" Residue "X TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X TYR 439": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X PHE 448": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 462": "OE1" <-> "OE2" Residue "X GLU 480": "OE1" <-> "OE2" Residue "X GLU 525": "OE1" <-> "OE2" Residue "X ARG 526": "NH1" <-> "NH2" Residue "Y TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 269": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y PHE 324": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y ASP 378": "OD1" <-> "OD2" Residue "Y ARG 380": "NH1" <-> "NH2" Residue "Y TYR 435": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Y GLU 478": "OE1" <-> "OE2" Residue "Y ARG 523": "NH1" <-> "NH2" Residue "Z TYR 197": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z TYR 373": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z PHE 426": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 55955 Number of models: 1 Model: "" Number of chains: 44 Chain: "1" Number of atoms: 2031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 2031 Classifications: {'DNA': 99} Link IDs: {'rna3p': 98} Chain: "3" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 1022 Classifications: {'DNA': 50} Link IDs: {'rna3p': 49} Chain breaks: 1 Chain: "7" Number of atoms: 4896 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 4896 Classifications: {'RNA': 230} Modifications used: {'rna2p_pur': 20, 'rna2p_pyr': 24, 'rna3p_pur': 97, 'rna3p_pyr': 89} Link IDs: {'rna2p': 43, 'rna3p': 186} Chain breaks: 2 Chain: "A" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "B" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "C" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "D" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "E" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "F" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "G" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "H" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "I" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "J" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "K" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "L" Number of atoms: 2066 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2066 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 9, 'TRANS': 247} Chain: "O" Number of atoms: 4865 Number of conformers: 1 Conformer: "" Number of residues, atoms: 601, 4865 Classifications: {'peptide': 601} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 18, 'TRANS': 582} Chain breaks: 2 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "Q" Number of atoms: 1306 Number of conformers: 1 Conformer: "" Number of residues, atoms: 164, 1306 Classifications: {'peptide': 164} Link IDs: {'PTRANS': 13, 'TRANS': 150} Chain: "S" Number of atoms: 702 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 702 Classifications: {'peptide': 87} Link IDs: {'TRANS': 86} Chain: "w" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "x" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "y" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "z" Number of atoms: 129 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 129 Classifications: {'peptide': 14} Link IDs: {'TRANS': 13} Chain: "W" Number of atoms: 4122 Number of conformers: 1 Conformer: "" Number of residues, atoms: 514, 4122 Classifications: {'peptide': 514} Link IDs: {'PTRANS': 19, 'TRANS': 494} Chain: "X" Number of atoms: 4068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 507, 4068 Classifications: {'peptide': 507} Link IDs: {'PTRANS': 19, 'TRANS': 487} Chain breaks: 1 Chain: "Y" Number of atoms: 2453 Number of conformers: 1 Conformer: "" Number of residues, atoms: 304, 2453 Classifications: {'peptide': 304} Link IDs: {'PTRANS': 11, 'TRANS': 292} Chain breaks: 3 Chain: "Z" Number of atoms: 2426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 301, 2426 Classifications: {'peptide': 301} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 289} Chain breaks: 3 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "2" Number of atoms: 593 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 593 Classifications: {'DNA': 29} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 28} Chain: "4" Number of atoms: 941 Number of conformers: 1 Conformer: "" Number of residues, atoms: 46, 941 Classifications: {'DNA': 46} Link IDs: {'rna3p': 45} Chain: "5" Number of atoms: 573 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 573 Classifications: {'DNA': 28} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 27} Chain: "6" Number of atoms: 263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 263 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "I" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "K" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "L" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "W" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Chain: "X" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 21.53, per 1000 atoms: 0.38 Number of scatterers: 55955 At special positions: 0 Unit cell: (144.045, 146.179, 314.765, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 170 16.00 P 529 15.00 Mg 14 11.99 O 11675 8.00 N 10159 7.00 C 33408 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 Atom "ATOM 54776 O5' DT 5 3 .*. O " rejected from bonding due to valence issues. Atom "ATOM 1473 O4' DC 1 42 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 18.99 Conformation dependent library (CDL) restraints added in 5.4 seconds 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10536 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 264 helices and 26 sheets defined 50.7% alpha, 9.1% beta 181 base pairs and 326 stacking pairs defined. Time for finding SS restraints: 14.31 Creating SS restraints... Processing helix chain 'A' and resid 20 through 28 Processing helix chain 'A' and resid 37 through 51 removed outlier: 3.510A pdb=" N LYS A 51 " --> pdb=" O ASP A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 76 removed outlier: 3.570A pdb=" N ARG A 76 " --> pdb=" O ALA A 72 " (cutoff:3.500A) Processing helix chain 'A' and resid 102 through 112 Processing helix chain 'A' and resid 122 through 132 Processing helix chain 'A' and resid 146 through 148 No H-bonds generated for 'chain 'A' and resid 146 through 148' Processing helix chain 'A' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE A 154 " --> pdb=" O PRO A 151 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ARG A 158 " --> pdb=" O ALA A 155 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ALA A 161 " --> pdb=" O ARG A 158 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N ASP A 163 " --> pdb=" O ILE A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 4.176A pdb=" N ARG A 182 " --> pdb=" O ALA A 178 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 189 removed outlier: 3.727A pdb=" N ARG A 189 " --> pdb=" O GLN A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 201 through 214 removed outlier: 3.851A pdb=" N GLU A 209 " --> pdb=" O LYS A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 227 through 237 Processing helix chain 'A' and resid 241 through 257 Processing helix chain 'A' and resid 265 through 274 removed outlier: 3.915A pdb=" N GLU A 274 " --> pdb=" O GLU A 270 " (cutoff:3.500A) Processing helix chain 'B' and resid 20 through 28 Processing helix chain 'B' and resid 37 through 51 Processing helix chain 'B' and resid 66 through 74 Processing helix chain 'B' and resid 102 through 112 removed outlier: 3.609A pdb=" N PHE B 106 " --> pdb=" O PRO B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 146 through 148 No H-bonds generated for 'chain 'B' and resid 146 through 148' Processing helix chain 'B' and resid 151 through 163 removed outlier: 3.779A pdb=" N PHE B 154 " --> pdb=" O PRO B 151 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N ASP B 159 " --> pdb=" O ASP B 156 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N ILE B 160 " --> pdb=" O VAL B 157 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N ASP B 163 " --> pdb=" O ILE B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 174 through 180 Processing helix chain 'B' and resid 184 through 187 No H-bonds generated for 'chain 'B' and resid 184 through 187' Processing helix chain 'B' and resid 201 through 214 removed outlier: 3.993A pdb=" N GLU B 209 " --> pdb=" O LYS B 205 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N MET B 210 " --> pdb=" O ASN B 206 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP B 211 " --> pdb=" O THR B 207 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N GLU B 212 " --> pdb=" O VAL B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 227 through 237 removed outlier: 3.978A pdb=" N ILE B 232 " --> pdb=" O GLU B 228 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N SER B 235 " --> pdb=" O ARG B 231 " (cutoff:3.500A) Processing helix chain 'B' and resid 241 through 258 removed outlier: 3.654A pdb=" N ARG B 258 " --> pdb=" O ARG B 254 " (cutoff:3.500A) Processing helix chain 'B' and resid 265 through 274 removed outlier: 4.001A pdb=" N GLU B 274 " --> pdb=" O GLU B 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 20 through 28 removed outlier: 3.514A pdb=" N GLU C 24 " --> pdb=" O TRP C 20 " (cutoff:3.500A) Processing helix chain 'C' and resid 37 through 52 Processing helix chain 'C' and resid 66 through 75 Processing helix chain 'C' and resid 102 through 112 removed outlier: 3.875A pdb=" N PHE C 106 " --> pdb=" O PRO C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 122 through 133 Processing helix chain 'C' and resid 146 through 148 No H-bonds generated for 'chain 'C' and resid 146 through 148' Processing helix chain 'C' and resid 151 through 163 removed outlier: 3.761A pdb=" N PHE C 154 " --> pdb=" O PRO C 151 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N ARG C 158 " --> pdb=" O ALA C 155 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP C 159 " --> pdb=" O ASP C 156 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ILE C 160 " --> pdb=" O VAL C 157 " (cutoff:3.500A) Processing helix chain 'C' and resid 174 through 182 removed outlier: 4.219A pdb=" N ARG C 182 " --> pdb=" O ALA C 178 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 189 removed outlier: 3.954A pdb=" N ARG C 189 " --> pdb=" O GLN C 185 " (cutoff:3.500A) Processing helix chain 'C' and resid 201 through 214 removed outlier: 3.632A pdb=" N GLU C 209 " --> pdb=" O LYS C 205 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N MET C 210 " --> pdb=" O ASN C 206 " (cutoff:3.500A) Processing helix chain 'C' and resid 227 through 237 Processing helix chain 'C' and resid 241 through 258 removed outlier: 4.053A pdb=" N GLU C 246 " --> pdb=" O GLY C 242 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ARG C 249 " --> pdb=" O ASP C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 265 through 274 removed outlier: 3.811A pdb=" N GLU C 274 " --> pdb=" O GLU C 270 " (cutoff:3.500A) Processing helix chain 'D' and resid 20 through 28 Processing helix chain 'D' and resid 37 through 52 removed outlier: 4.111A pdb=" N LEU D 42 " --> pdb=" O GLN D 38 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 Processing helix chain 'D' and resid 102 through 112 Processing helix chain 'D' and resid 122 through 135 Processing helix chain 'D' and resid 146 through 148 No H-bonds generated for 'chain 'D' and resid 146 through 148' Processing helix chain 'D' and resid 151 through 163 removed outlier: 3.594A pdb=" N PHE D 154 " --> pdb=" O PRO D 151 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ARG D 158 " --> pdb=" O ALA D 155 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N ASP D 159 " --> pdb=" O ASP D 156 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N ASP D 163 " --> pdb=" O ILE D 160 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 182 removed outlier: 3.577A pdb=" N ALA D 178 " --> pdb=" O ASP D 174 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N ARG D 182 " --> pdb=" O ALA D 178 " (cutoff:3.500A) Processing helix chain 'D' and resid 184 through 187 No H-bonds generated for 'chain 'D' and resid 184 through 187' Processing helix chain 'D' and resid 201 through 214 removed outlier: 3.692A pdb=" N GLU D 209 " --> pdb=" O LYS D 205 " (cutoff:3.500A) Processing helix chain 'D' and resid 227 through 237 removed outlier: 4.357A pdb=" N ILE D 232 " --> pdb=" O GLU D 228 " (cutoff:3.500A) Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.768A pdb=" N GLU D 246 " --> pdb=" O GLY D 242 " (cutoff:3.500A) Processing helix chain 'D' and resid 265 through 274 removed outlier: 3.792A pdb=" N GLU D 274 " --> pdb=" O GLU D 270 " (cutoff:3.500A) Processing helix chain 'E' and resid 20 through 29 removed outlier: 3.526A pdb=" N GLU E 24 " --> pdb=" O TRP E 20 " (cutoff:3.500A) Processing helix chain 'E' and resid 37 through 52 removed outlier: 3.833A pdb=" N GLY E 48 " --> pdb=" O ASP E 44 " (cutoff:3.500A) Processing helix chain 'E' and resid 66 through 76 Processing helix chain 'E' and resid 102 through 112 Processing helix chain 'E' and resid 122 through 135 Processing helix chain 'E' and resid 146 through 148 No H-bonds generated for 'chain 'E' and resid 146 through 148' Processing helix chain 'E' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE E 154 " --> pdb=" O PRO E 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG E 158 " --> pdb=" O ALA E 155 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ASP E 159 " --> pdb=" O ASP E 156 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP E 163 " --> pdb=" O ILE E 160 " (cutoff:3.500A) Processing helix chain 'E' and resid 174 through 182 removed outlier: 4.196A pdb=" N ARG E 182 " --> pdb=" O ALA E 178 " (cutoff:3.500A) Processing helix chain 'E' and resid 184 through 189 removed outlier: 3.958A pdb=" N ARG E 189 " --> pdb=" O GLN E 185 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 214 removed outlier: 3.544A pdb=" N GLU E 209 " --> pdb=" O LYS E 205 " (cutoff:3.500A) Processing helix chain 'E' and resid 227 through 237 removed outlier: 3.802A pdb=" N ILE E 232 " --> pdb=" O GLU E 228 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 235 " --> pdb=" O ARG E 231 " (cutoff:3.500A) Processing helix chain 'E' and resid 241 through 258 Processing helix chain 'E' and resid 265 through 274 removed outlier: 4.139A pdb=" N GLU E 274 " --> pdb=" O GLU E 270 " (cutoff:3.500A) Processing helix chain 'F' and resid 20 through 28 Processing helix chain 'F' and resid 37 through 52 Processing helix chain 'F' and resid 66 through 76 removed outlier: 3.835A pdb=" N ARG F 76 " --> pdb=" O ALA F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 102 through 112 removed outlier: 3.872A pdb=" N PHE F 106 " --> pdb=" O PRO F 102 " (cutoff:3.500A) Processing helix chain 'F' and resid 122 through 133 Processing helix chain 'F' and resid 146 through 148 No H-bonds generated for 'chain 'F' and resid 146 through 148' Processing helix chain 'F' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE F 154 " --> pdb=" O PRO F 151 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ARG F 158 " --> pdb=" O ALA F 155 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ASP F 159 " --> pdb=" O ASP F 156 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE F 160 " --> pdb=" O VAL F 157 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 182 removed outlier: 4.318A pdb=" N ARG F 182 " --> pdb=" O ALA F 178 " (cutoff:3.500A) Processing helix chain 'F' and resid 184 through 189 removed outlier: 3.622A pdb=" N GLU F 188 " --> pdb=" O GLU F 184 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ARG F 189 " --> pdb=" O GLN F 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 184 through 189' Processing helix chain 'F' and resid 201 through 214 removed outlier: 3.764A pdb=" N GLU F 209 " --> pdb=" O LYS F 205 " (cutoff:3.500A) Processing helix chain 'F' and resid 227 through 237 removed outlier: 4.357A pdb=" N ILE F 232 " --> pdb=" O GLU F 228 " (cutoff:3.500A) Processing helix chain 'F' and resid 241 through 258 removed outlier: 3.697A pdb=" N ARG F 258 " --> pdb=" O ARG F 254 " (cutoff:3.500A) Processing helix chain 'F' and resid 265 through 274 removed outlier: 4.208A pdb=" N GLU F 274 " --> pdb=" O GLU F 270 " (cutoff:3.500A) Processing helix chain 'G' and resid 20 through 29 Processing helix chain 'G' and resid 37 through 52 removed outlier: 3.572A pdb=" N GLY G 48 " --> pdb=" O ASP G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 66 through 76 removed outlier: 3.744A pdb=" N ARG G 76 " --> pdb=" O ALA G 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 102 through 112 Processing helix chain 'G' and resid 122 through 133 Processing helix chain 'G' and resid 146 through 148 No H-bonds generated for 'chain 'G' and resid 146 through 148' Processing helix chain 'G' and resid 151 through 163 removed outlier: 3.800A pdb=" N PHE G 154 " --> pdb=" O PRO G 151 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ARG G 158 " --> pdb=" O ALA G 155 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE G 160 " --> pdb=" O VAL G 157 " (cutoff:3.500A) Processing helix chain 'G' and resid 174 through 182 removed outlier: 4.194A pdb=" N ARG G 182 " --> pdb=" O ALA G 178 " (cutoff:3.500A) Processing helix chain 'G' and resid 184 through 187 No H-bonds generated for 'chain 'G' and resid 184 through 187' Processing helix chain 'G' and resid 201 through 214 removed outlier: 3.526A pdb=" N LYS G 205 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASN G 206 " --> pdb=" O ASP G 203 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU G 212 " --> pdb=" O GLU G 209 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N GLN G 213 " --> pdb=" O MET G 210 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N MET G 214 " --> pdb=" O TRP G 211 " (cutoff:3.500A) Processing helix chain 'G' and resid 227 through 237 removed outlier: 3.550A pdb=" N ILE G 232 " --> pdb=" O GLU G 228 " (cutoff:3.500A) Processing helix chain 'G' and resid 241 through 258 removed outlier: 3.801A pdb=" N ARG G 258 " --> pdb=" O ARG G 254 " (cutoff:3.500A) Processing helix chain 'G' and resid 265 through 274 removed outlier: 4.216A pdb=" N GLU G 274 " --> pdb=" O GLU G 270 " (cutoff:3.500A) Processing helix chain 'H' and resid 20 through 28 Processing helix chain 'H' and resid 37 through 51 Processing helix chain 'H' and resid 66 through 76 removed outlier: 3.555A pdb=" N ARG H 76 " --> pdb=" O ALA H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 102 through 112 Processing helix chain 'H' and resid 122 through 133 Processing helix chain 'H' and resid 146 through 148 No H-bonds generated for 'chain 'H' and resid 146 through 148' Processing helix chain 'H' and resid 151 through 163 removed outlier: 3.759A pdb=" N PHE H 154 " --> pdb=" O PRO H 151 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG H 158 " --> pdb=" O ALA H 155 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASP H 159 " --> pdb=" O ASP H 156 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ASP H 163 " --> pdb=" O ILE H 160 " (cutoff:3.500A) Processing helix chain 'H' and resid 174 through 182 removed outlier: 4.230A pdb=" N ARG H 182 " --> pdb=" O ALA H 178 " (cutoff:3.500A) Processing helix chain 'H' and resid 184 through 189 removed outlier: 3.883A pdb=" N ARG H 189 " --> pdb=" O GLN H 185 " (cutoff:3.500A) Processing helix chain 'H' and resid 201 through 214 removed outlier: 3.664A pdb=" N GLU H 209 " --> pdb=" O LYS H 205 " (cutoff:3.500A) Processing helix chain 'H' and resid 227 through 237 removed outlier: 3.707A pdb=" N ILE H 232 " --> pdb=" O GLU H 228 " (cutoff:3.500A) Processing helix chain 'H' and resid 241 through 258 removed outlier: 3.561A pdb=" N ARG H 258 " --> pdb=" O ARG H 254 " (cutoff:3.500A) Processing helix chain 'H' and resid 265 through 274 removed outlier: 3.893A pdb=" N GLU H 274 " --> pdb=" O GLU H 270 " (cutoff:3.500A) Processing helix chain 'I' and resid 20 through 29 removed outlier: 3.508A pdb=" N GLU I 24 " --> pdb=" O TRP I 20 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) Processing helix chain 'I' and resid 37 through 52 removed outlier: 3.611A pdb=" N LYS I 51 " --> pdb=" O ASP I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 66 through 76 removed outlier: 3.778A pdb=" N ARG I 76 " --> pdb=" O ALA I 72 " (cutoff:3.500A) Processing helix chain 'I' and resid 102 through 112 removed outlier: 3.602A pdb=" N PHE I 106 " --> pdb=" O PRO I 102 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 135 Processing helix chain 'I' and resid 146 through 148 No H-bonds generated for 'chain 'I' and resid 146 through 148' Processing helix chain 'I' and resid 151 through 163 removed outlier: 3.548A pdb=" N PHE I 154 " --> pdb=" O PRO I 151 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N ALA I 155 " --> pdb=" O GLU I 152 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP I 159 " --> pdb=" O ASP I 156 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N ASP I 163 " --> pdb=" O ILE I 160 " (cutoff:3.500A) Processing helix chain 'I' and resid 174 through 182 removed outlier: 4.021A pdb=" N ARG I 182 " --> pdb=" O ALA I 178 " (cutoff:3.500A) Processing helix chain 'I' and resid 184 through 189 removed outlier: 3.555A pdb=" N GLU I 188 " --> pdb=" O GLU I 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG I 189 " --> pdb=" O GLN I 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 184 through 189' Processing helix chain 'I' and resid 201 through 214 Processing helix chain 'I' and resid 227 through 237 Processing helix chain 'I' and resid 241 through 258 removed outlier: 3.786A pdb=" N GLU I 246 " --> pdb=" O GLY I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 265 through 274 removed outlier: 3.758A pdb=" N GLU I 270 " --> pdb=" O ALA I 266 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N GLU I 274 " --> pdb=" O GLU I 270 " (cutoff:3.500A) Processing helix chain 'J' and resid 20 through 29 removed outlier: 3.630A pdb=" N GLU J 24 " --> pdb=" O TRP J 20 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE J 25 " --> pdb=" O LEU J 21 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA J 26 " --> pdb=" O GLN J 22 " (cutoff:3.500A) Processing helix chain 'J' and resid 37 through 52 removed outlier: 3.693A pdb=" N GLY J 48 " --> pdb=" O ASP J 44 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N LYS J 51 " --> pdb=" O ASP J 47 " (cutoff:3.500A) Processing helix chain 'J' and resid 66 through 75 Processing helix chain 'J' and resid 102 through 112 removed outlier: 3.612A pdb=" N PHE J 106 " --> pdb=" O PRO J 102 " (cutoff:3.500A) Processing helix chain 'J' and resid 122 through 135 removed outlier: 3.658A pdb=" N ASP J 127 " --> pdb=" O SER J 123 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 148 No H-bonds generated for 'chain 'J' and resid 146 through 148' Processing helix chain 'J' and resid 151 through 163 removed outlier: 3.786A pdb=" N PHE J 154 " --> pdb=" O PRO J 151 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N ARG J 158 " --> pdb=" O ALA J 155 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP J 159 " --> pdb=" O ASP J 156 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N GLU J 162 " --> pdb=" O ASP J 159 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ASP J 163 " --> pdb=" O ILE J 160 " (cutoff:3.500A) Processing helix chain 'J' and resid 174 through 182 removed outlier: 3.571A pdb=" N ALA J 178 " --> pdb=" O ASP J 174 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ARG J 182 " --> pdb=" O ALA J 178 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 189 removed outlier: 3.571A pdb=" N GLU J 188 " --> pdb=" O GLU J 184 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ARG J 189 " --> pdb=" O GLN J 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 184 through 189' Processing helix chain 'J' and resid 201 through 214 removed outlier: 3.501A pdb=" N LYS J 205 " --> pdb=" O GLY J 201 " (cutoff:3.500A) Processing helix chain 'J' and resid 227 through 237 removed outlier: 4.004A pdb=" N ILE J 232 " --> pdb=" O GLU J 228 " (cutoff:3.500A) Processing helix chain 'J' and resid 241 through 257 Processing helix chain 'J' and resid 265 through 274 removed outlier: 4.398A pdb=" N GLU J 274 " --> pdb=" O GLU J 270 " (cutoff:3.500A) Processing helix chain 'K' and resid 20 through 29 removed outlier: 3.699A pdb=" N GLU K 24 " --> pdb=" O TRP K 20 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ILE K 25 " --> pdb=" O LEU K 21 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA K 26 " --> pdb=" O GLN K 22 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N LEU K 28 " --> pdb=" O GLU K 24 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 52 Processing helix chain 'K' and resid 66 through 76 removed outlier: 3.857A pdb=" N ARG K 76 " --> pdb=" O ALA K 72 " (cutoff:3.500A) Processing helix chain 'K' and resid 102 through 112 Processing helix chain 'K' and resid 122 through 133 Processing helix chain 'K' and resid 146 through 148 No H-bonds generated for 'chain 'K' and resid 146 through 148' Processing helix chain 'K' and resid 154 through 163 Processing helix chain 'K' and resid 174 through 182 removed outlier: 4.109A pdb=" N ARG K 182 " --> pdb=" O ALA K 178 " (cutoff:3.500A) Processing helix chain 'K' and resid 184 through 189 removed outlier: 3.553A pdb=" N GLU K 188 " --> pdb=" O GLU K 184 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG K 189 " --> pdb=" O GLN K 185 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 184 through 189' Processing helix chain 'K' and resid 201 through 214 Processing helix chain 'K' and resid 227 through 237 removed outlier: 3.695A pdb=" N ILE K 232 " --> pdb=" O GLU K 228 " (cutoff:3.500A) Processing helix chain 'K' and resid 241 through 257 Processing helix chain 'K' and resid 265 through 274 removed outlier: 3.632A pdb=" N GLU K 274 " --> pdb=" O GLU K 270 " (cutoff:3.500A) Processing helix chain 'L' and resid 20 through 29 removed outlier: 3.521A pdb=" N ALA L 26 " --> pdb=" O GLN L 22 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG L 27 " --> pdb=" O ALA L 23 " (cutoff:3.500A) Processing helix chain 'L' and resid 37 through 52 removed outlier: 4.029A pdb=" N GLY L 48 " --> pdb=" O ASP L 44 " (cutoff:3.500A) Processing helix chain 'L' and resid 66 through 76 Processing helix chain 'L' and resid 102 through 112 Processing helix chain 'L' and resid 122 through 133 Processing helix chain 'L' and resid 146 through 148 No H-bonds generated for 'chain 'L' and resid 146 through 148' Processing helix chain 'L' and resid 151 through 163 removed outlier: 3.784A pdb=" N PHE L 154 " --> pdb=" O PRO L 151 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N ARG L 158 " --> pdb=" O ALA L 155 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE L 160 " --> pdb=" O VAL L 157 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASP L 163 " --> pdb=" O ILE L 160 " (cutoff:3.500A) Processing helix chain 'L' and resid 174 through 182 removed outlier: 4.057A pdb=" N ARG L 182 " --> pdb=" O ALA L 178 " (cutoff:3.500A) Processing helix chain 'L' and resid 184 through 189 removed outlier: 3.764A pdb=" N ARG L 189 " --> pdb=" O GLN L 185 " (cutoff:3.500A) Processing helix chain 'L' and resid 201 through 214 Processing helix chain 'L' and resid 227 through 237 removed outlier: 3.721A pdb=" N ILE L 232 " --> pdb=" O GLU L 228 " (cutoff:3.500A) Processing helix chain 'L' and resid 241 through 258 Processing helix chain 'L' and resid 265 through 274 removed outlier: 4.094A pdb=" N GLU L 274 " --> pdb=" O GLU L 270 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 39 removed outlier: 3.885A pdb=" N THR O 29 " --> pdb=" O ALA O 25 " (cutoff:3.500A) Proline residue: O 30 - end of helix removed outlier: 3.912A pdb=" N LEU O 35 " --> pdb=" O LEU O 31 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLN O 38 " --> pdb=" O GLU O 34 " (cutoff:3.500A) Processing helix chain 'O' and resid 45 through 51 Processing helix chain 'O' and resid 58 through 66 Proline residue: O 65 - end of helix Processing helix chain 'O' and resid 77 through 114 removed outlier: 3.906A pdb=" N ALA O 96 " --> pdb=" O LYS O 92 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N ARG O 100 " --> pdb=" O ALA O 96 " (cutoff:3.500A) removed outlier: 4.271A pdb=" N TRP O 111 " --> pdb=" O GLY O 107 " (cutoff:3.500A) Processing helix chain 'O' and resid 118 through 125 Processing helix chain 'O' and resid 129 through 143 Processing helix chain 'O' and resid 174 through 183 Processing helix chain 'O' and resid 190 through 199 removed outlier: 3.724A pdb=" N LYS O 199 " --> pdb=" O TYR O 196 " (cutoff:3.500A) Processing helix chain 'O' and resid 211 through 232 Processing helix chain 'O' and resid 245 through 256 Processing helix chain 'O' and resid 262 through 272 Processing helix chain 'O' and resid 288 through 290 No H-bonds generated for 'chain 'O' and resid 288 through 290' Processing helix chain 'O' and resid 322 through 338 removed outlier: 3.580A pdb=" N LEU O 329 " --> pdb=" O PHE O 325 " (cutoff:3.500A) Processing helix chain 'O' and resid 344 through 346 No H-bonds generated for 'chain 'O' and resid 344 through 346' Processing helix chain 'O' and resid 365 through 368 No H-bonds generated for 'chain 'O' and resid 365 through 368' Processing helix chain 'O' and resid 379 through 381 No H-bonds generated for 'chain 'O' and resid 379 through 381' Processing helix chain 'O' and resid 384 through 405 removed outlier: 3.670A pdb=" N ILE O 389 " --> pdb=" O GLU O 385 " (cutoff:3.500A) Processing helix chain 'O' and resid 413 through 430 removed outlier: 4.074A pdb=" N ALA O 417 " --> pdb=" O ASP O 413 " (cutoff:3.500A) removed outlier: 4.733A pdb=" N ASN O 430 " --> pdb=" O LEU O 426 " (cutoff:3.500A) Processing helix chain 'O' and resid 477 through 480 No H-bonds generated for 'chain 'O' and resid 477 through 480' Processing helix chain 'O' and resid 482 through 508 removed outlier: 4.752A pdb=" N GLU O 486 " --> pdb=" O ASP O 483 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N GLN O 495 " --> pdb=" O ARG O 492 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N LEU O 498 " --> pdb=" O GLN O 495 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER O 499 " --> pdb=" O GLN O 496 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LYS O 507 " --> pdb=" O LYS O 504 " (cutoff:3.500A) Processing helix chain 'O' and resid 517 through 537 Processing helix chain 'O' and resid 551 through 565 removed outlier: 4.033A pdb=" N GLN O 565 " --> pdb=" O ALA O 561 " (cutoff:3.500A) Processing helix chain 'O' and resid 571 through 575 Processing helix chain 'O' and resid 579 through 586 Processing helix chain 'O' and resid 590 through 604 Processing helix chain 'O' and resid 619 through 634 removed outlier: 3.839A pdb=" N ARG O 634 " --> pdb=" O ALA O 630 " (cutoff:3.500A) Processing helix chain 'Q' and resid 22 through 32 Processing helix chain 'Q' and resid 37 through 44 Processing helix chain 'Q' and resid 47 through 55 removed outlier: 4.051A pdb=" N VAL Q 50 " --> pdb=" O GLY Q 47 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N GLU Q 54 " --> pdb=" O ALA Q 51 " (cutoff:3.500A) Processing helix chain 'Q' and resid 64 through 74 removed outlier: 3.589A pdb=" N VAL Q 73 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) Processing helix chain 'Q' and resid 78 through 84 removed outlier: 3.653A pdb=" N GLN Q 83 " --> pdb=" O GLN Q 79 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N MET Q 84 " --> pdb=" O ARG Q 80 " (cutoff:3.500A) Processing helix chain 'Q' and resid 112 through 115 Processing helix chain 'Q' and resid 143 through 145 No H-bonds generated for 'chain 'Q' and resid 143 through 145' Processing helix chain 'Q' and resid 158 through 163 removed outlier: 3.869A pdb=" N ALA Q 162 " --> pdb=" O ALA Q 159 " (cutoff:3.500A) Processing helix chain 'S' and resid 5 through 15 removed outlier: 3.527A pdb=" N GLU S 14 " --> pdb=" O LYS S 10 " (cutoff:3.500A) Processing helix chain 'S' and resid 25 through 45 removed outlier: 3.558A pdb=" N GLY S 41 " --> pdb=" O ASN S 37 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N HIS S 42 " --> pdb=" O HIS S 38 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLU S 45 " --> pdb=" O GLY S 41 " (cutoff:3.500A) Processing helix chain 'S' and resid 52 through 73 removed outlier: 3.521A pdb=" N ARG S 72 " --> pdb=" O ASP S 68 " (cutoff:3.500A) Processing helix chain 'S' and resid 75 through 85 Processing helix chain 'w' and resid 575 through 581 Processing helix chain 'x' and resid 575 through 581 Processing helix chain 'y' and resid 575 through 581 Processing helix chain 'z' and resid 575 through 581 removed outlier: 3.629A pdb=" N ARG z 579 " --> pdb=" O TYR z 575 " (cutoff:3.500A) Processing helix chain 'W' and resid 40 through 52 Processing helix chain 'W' and resid 58 through 72 Processing helix chain 'W' and resid 76 through 88 Processing helix chain 'W' and resid 91 through 93 No H-bonds generated for 'chain 'W' and resid 91 through 93' Processing helix chain 'W' and resid 109 through 123 Processing helix chain 'W' and resid 131 through 145 Processing helix chain 'W' and resid 153 through 159 Processing helix chain 'W' and resid 161 through 172 removed outlier: 4.049A pdb=" N GLN W 167 " --> pdb=" O ILE W 163 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLN W 168 " --> pdb=" O LEU W 164 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS W 169 " --> pdb=" O GLU W 165 " (cutoff:3.500A) removed outlier: 4.288A pdb=" N SER W 172 " --> pdb=" O GLN W 168 " (cutoff:3.500A) Processing helix chain 'W' and resid 249 through 260 Processing helix chain 'W' and resid 267 through 269 No H-bonds generated for 'chain 'W' and resid 267 through 269' Processing helix chain 'W' and resid 295 through 304 Processing helix chain 'W' and resid 314 through 330 removed outlier: 3.669A pdb=" N GLY W 318 " --> pdb=" O SER W 315 " (cutoff:3.500A) removed outlier: 4.879A pdb=" N VAL W 319 " --> pdb=" O GLU W 316 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG W 322 " --> pdb=" O VAL W 319 " (cutoff:3.500A) Proline residue: W 323 - end of helix removed outlier: 3.700A pdb=" N GLN W 330 " --> pdb=" O LEU W 327 " (cutoff:3.500A) Processing helix chain 'W' and resid 332 through 334 No H-bonds generated for 'chain 'W' and resid 332 through 334' Processing helix chain 'W' and resid 343 through 345 No H-bonds generated for 'chain 'W' and resid 343 through 345' Processing helix chain 'W' and resid 358 through 371 Processing helix chain 'W' and resid 373 through 375 No H-bonds generated for 'chain 'W' and resid 373 through 375' Processing helix chain 'W' and resid 386 through 393 Processing helix chain 'W' and resid 403 through 409 removed outlier: 3.917A pdb=" N ILE W 408 " --> pdb=" O ASP W 405 " (cutoff:3.500A) Processing helix chain 'W' and resid 420 through 422 No H-bonds generated for 'chain 'W' and resid 420 through 422' Processing helix chain 'W' and resid 436 through 439 Processing helix chain 'W' and resid 484 through 497 Processing helix chain 'W' and resid 503 through 519 Processing helix chain 'W' and resid 526 through 540 Processing helix chain 'X' and resid 39 through 52 removed outlier: 6.015A pdb=" N VAL X 44 " --> pdb=" O GLU X 40 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N LYS X 45 " --> pdb=" O GLU X 41 " (cutoff:3.500A) Processing helix chain 'X' and resid 58 through 71 removed outlier: 4.177A pdb=" N GLY X 62 " --> pdb=" O ARG X 58 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N GLN X 63 " --> pdb=" O THR X 59 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU X 70 " --> pdb=" O ARG X 66 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N LYS X 71 " --> pdb=" O GLU X 67 " (cutoff:3.500A) Processing helix chain 'X' and resid 76 through 94 removed outlier: 8.134A pdb=" N LEU X 91 " --> pdb=" O GLU X 87 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N VAL X 92 " --> pdb=" O GLN X 88 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N GLY X 93 " --> pdb=" O ASP X 89 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N LEU X 94 " --> pdb=" O GLY X 90 " (cutoff:3.500A) Processing helix chain 'X' and resid 109 through 123 Processing helix chain 'X' and resid 131 through 144 Processing helix chain 'X' and resid 153 through 172 Proline residue: X 162 - end of helix removed outlier: 4.021A pdb=" N GLN X 167 " --> pdb=" O ILE X 163 " (cutoff:3.500A) Processing helix chain 'X' and resid 249 through 260 Processing helix chain 'X' and resid 267 through 269 No H-bonds generated for 'chain 'X' and resid 267 through 269' Processing helix chain 'X' and resid 295 through 304 Processing helix chain 'X' and resid 318 through 330 Proline residue: X 323 - end of helix Processing helix chain 'X' and resid 332 through 334 No H-bonds generated for 'chain 'X' and resid 332 through 334' Processing helix chain 'X' and resid 358 through 371 removed outlier: 3.821A pdb=" N ARG X 367 " --> pdb=" O GLN X 363 " (cutoff:3.500A) Processing helix chain 'X' and resid 373 through 375 No H-bonds generated for 'chain 'X' and resid 373 through 375' Processing helix chain 'X' and resid 386 through 393 Processing helix chain 'X' and resid 403 through 409 removed outlier: 3.527A pdb=" N ILE X 408 " --> pdb=" O ASP X 405 " (cutoff:3.500A) Processing helix chain 'X' and resid 436 through 439 Processing helix chain 'X' and resid 484 through 497 Processing helix chain 'X' and resid 503 through 515 removed outlier: 3.785A pdb=" N ASP X 512 " --> pdb=" O GLN X 508 " (cutoff:3.500A) removed outlier: 4.885A pdb=" N ARG X 513 " --> pdb=" O GLU X 509 " (cutoff:3.500A) Processing helix chain 'X' and resid 526 through 540 Processing helix chain 'Y' and resid 252 through 260 Processing helix chain 'Y' and resid 267 through 269 No H-bonds generated for 'chain 'Y' and resid 267 through 269' Processing helix chain 'Y' and resid 296 through 304 Processing helix chain 'Y' and resid 324 through 330 Processing helix chain 'Y' and resid 332 through 334 No H-bonds generated for 'chain 'Y' and resid 332 through 334' Processing helix chain 'Y' and resid 358 through 371 Processing helix chain 'Y' and resid 379 through 381 No H-bonds generated for 'chain 'Y' and resid 379 through 381' Processing helix chain 'Y' and resid 386 through 392 Processing helix chain 'Y' and resid 403 through 409 removed outlier: 4.342A pdb=" N ILE Y 408 " --> pdb=" O ASP Y 405 " (cutoff:3.500A) Processing helix chain 'Y' and resid 436 through 439 Processing helix chain 'Y' and resid 484 through 500 Processing helix chain 'Y' and resid 505 through 517 removed outlier: 5.071A pdb=" N VAL Y 510 " --> pdb=" O LEU Y 507 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP Y 512 " --> pdb=" O GLU Y 509 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N ASP Y 514 " --> pdb=" O VAL Y 511 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL Y 517 " --> pdb=" O ASP Y 514 " (cutoff:3.500A) Processing helix chain 'Z' and resid 249 through 260 Processing helix chain 'Z' and resid 267 through 269 No H-bonds generated for 'chain 'Z' and resid 267 through 269' Processing helix chain 'Z' and resid 296 through 304 Processing helix chain 'Z' and resid 324 through 330 Processing helix chain 'Z' and resid 332 through 334 No H-bonds generated for 'chain 'Z' and resid 332 through 334' Processing helix chain 'Z' and resid 358 through 371 Processing helix chain 'Z' and resid 373 through 375 No H-bonds generated for 'chain 'Z' and resid 373 through 375' Processing helix chain 'Z' and resid 386 through 392 Processing helix chain 'Z' and resid 403 through 409 removed outlier: 4.564A pdb=" N ILE Z 408 " --> pdb=" O ASP Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 437 through 439 No H-bonds generated for 'chain 'Z' and resid 437 through 439' Processing helix chain 'Z' and resid 484 through 501 Processing helix chain 'Z' and resid 504 through 523 removed outlier: 3.576A pdb=" N GLU Z 509 " --> pdb=" O LEU Z 506 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N ASP Z 514 " --> pdb=" O VAL Z 511 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N VAL Z 517 " --> pdb=" O ASP Z 514 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 193 through 196 removed outlier: 6.727A pdb=" N ARG A 57 " --> pdb=" O LEU A 194 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N PHE A 196 " --> pdb=" O ARG A 57 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL A 59 " --> pdb=" O PHE A 196 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG B 57 " --> pdb=" O LEU B 194 " (cutoff:3.500A) removed outlier: 8.078A pdb=" N PHE B 196 " --> pdb=" O ARG B 57 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N VAL B 59 " --> pdb=" O PHE B 196 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 193 through 196 removed outlier: 6.727A pdb=" N ARG C 57 " --> pdb=" O LEU C 194 " (cutoff:3.500A) removed outlier: 8.068A pdb=" N PHE C 196 " --> pdb=" O ARG C 57 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N VAL C 59 " --> pdb=" O PHE C 196 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'D' and resid 193 through 196 removed outlier: 6.810A pdb=" N ARG D 57 " --> pdb=" O LEU D 194 " (cutoff:3.500A) removed outlier: 7.932A pdb=" N PHE D 196 " --> pdb=" O ARG D 57 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N VAL D 59 " --> pdb=" O PHE D 196 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'E' and resid 193 through 196 removed outlier: 6.577A pdb=" N ARG E 57 " --> pdb=" O LEU E 194 " (cutoff:3.500A) removed outlier: 7.800A pdb=" N PHE E 196 " --> pdb=" O ARG E 57 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL E 59 " --> pdb=" O PHE E 196 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'F' and resid 193 through 196 removed outlier: 6.569A pdb=" N ARG F 57 " --> pdb=" O LEU F 194 " (cutoff:3.500A) removed outlier: 7.882A pdb=" N PHE F 196 " --> pdb=" O ARG F 57 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N VAL F 59 " --> pdb=" O PHE F 196 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'G' and resid 193 through 196 removed outlier: 6.777A pdb=" N ARG G 57 " --> pdb=" O LEU G 194 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N PHE G 196 " --> pdb=" O ARG G 57 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N VAL G 59 " --> pdb=" O PHE G 196 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'H' and resid 193 through 195 removed outlier: 6.847A pdb=" N ARG H 57 " --> pdb=" O LEU H 194 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'I' and resid 193 through 196 removed outlier: 6.729A pdb=" N ARG I 57 " --> pdb=" O LEU I 194 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N PHE I 196 " --> pdb=" O ARG I 57 " (cutoff:3.500A) removed outlier: 7.020A pdb=" N VAL I 59 " --> pdb=" O PHE I 196 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'J' and resid 193 through 196 removed outlier: 6.749A pdb=" N ARG J 57 " --> pdb=" O LEU J 194 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N PHE J 196 " --> pdb=" O ARG J 57 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N VAL J 59 " --> pdb=" O PHE J 196 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'K' and resid 193 through 196 removed outlier: 6.780A pdb=" N ARG K 57 " --> pdb=" O LEU K 194 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N PHE K 196 " --> pdb=" O ARG K 57 " (cutoff:3.500A) removed outlier: 6.919A pdb=" N VAL K 59 " --> pdb=" O PHE K 196 " (cutoff:3.500A) Processing sheet with id= L, first strand: chain 'L' and resid 193 through 196 removed outlier: 6.785A pdb=" N ARG L 57 " --> pdb=" O LEU L 194 " (cutoff:3.500A) removed outlier: 7.999A pdb=" N PHE L 196 " --> pdb=" O ARG L 57 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N VAL L 59 " --> pdb=" O PHE L 196 " (cutoff:3.500A) Processing sheet with id= M, first strand: chain 'O' and resid 314 through 316 removed outlier: 4.832A pdb=" N LEU O 371 " --> pdb=" O LEU O 10 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ASN O 351 " --> pdb=" O CYS O 376 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N ASP O 378 " --> pdb=" O LEU O 349 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N LEU O 349 " --> pdb=" O ASP O 378 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'O' and resid 291 through 295 Processing sheet with id= O, first strand: chain 'O' and resid 607 through 611 removed outlier: 3.583A pdb=" N GLY O 611 " --> pdb=" O LEU O 545 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N SER O 542 " --> pdb=" O ILE O 447 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA O 473 " --> pdb=" O VAL O 463 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ASP O 465 " --> pdb=" O VAL O 471 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N VAL O 471 " --> pdb=" O ASP O 465 " (cutoff:3.500A) Processing sheet with id= P, first strand: chain 'W' and resid 184 through 186 Processing sheet with id= Q, first strand: chain 'W' and resid 237 through 243 removed outlier: 6.602A pdb=" N VAL W 229 " --> pdb=" O MET W 238 " (cutoff:3.500A) removed outlier: 4.420A pdb=" N ILE W 240 " --> pdb=" O THR W 227 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N THR W 227 " --> pdb=" O ILE W 240 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N LEU W 242 " --> pdb=" O TRP W 225 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N TRP W 225 " --> pdb=" O LEU W 242 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ASP W 205 " --> pdb=" O THR W 228 " (cutoff:3.500A) removed outlier: 6.470A pdb=" N HIS W 283 " --> pdb=" O TRP W 202 " (cutoff:3.500A) removed outlier: 8.190A pdb=" N CYS W 204 " --> pdb=" O HIS W 283 " (cutoff:3.500A) removed outlier: 6.893A pdb=" N TYR W 285 " --> pdb=" O CYS W 204 " (cutoff:3.500A) removed outlier: 9.491A pdb=" N HIS W 206 " --> pdb=" O TYR W 285 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N VAL W 307 " --> pdb=" O PHE W 284 " (cutoff:3.500A) removed outlier: 8.182A pdb=" N THR W 286 " --> pdb=" O VAL W 307 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N HIS W 309 " --> pdb=" O THR W 286 " (cutoff:3.500A) Processing sheet with id= R, first strand: chain 'W' and resid 411 through 413 removed outlier: 3.561A pdb=" N LEU W 446 " --> pdb=" O GLN W 413 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N ARG W 460 " --> pdb=" O PHE W 468 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N PHE W 468 " --> pdb=" O ARG W 460 " (cutoff:3.500A) removed outlier: 6.165A pdb=" N GLU W 462 " --> pdb=" O GLU W 466 " (cutoff:3.500A) removed outlier: 4.910A pdb=" N GLU W 466 " --> pdb=" O GLU W 462 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG W 432 " --> pdb=" O HIS W 473 " (cutoff:3.500A) Processing sheet with id= S, first strand: chain 'X' and resid 184 through 186 Processing sheet with id= T, first strand: chain 'X' and resid 237 through 243 removed outlier: 6.517A pdb=" N VAL X 229 " --> pdb=" O MET X 238 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N ILE X 240 " --> pdb=" O THR X 227 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N THR X 227 " --> pdb=" O ILE X 240 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N LEU X 242 " --> pdb=" O TRP X 225 " (cutoff:3.500A) removed outlier: 6.722A pdb=" N TRP X 225 " --> pdb=" O LEU X 242 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N THR X 228 " --> pdb=" O ASP X 205 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASP X 205 " --> pdb=" O THR X 228 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N HIS X 283 " --> pdb=" O TRP X 202 " (cutoff:3.500A) removed outlier: 8.072A pdb=" N CYS X 204 " --> pdb=" O HIS X 283 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N TYR X 285 " --> pdb=" O CYS X 204 " (cutoff:3.500A) removed outlier: 9.489A pdb=" N HIS X 206 " --> pdb=" O TYR X 285 " (cutoff:3.500A) removed outlier: 6.248A pdb=" N VAL X 307 " --> pdb=" O PHE X 284 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N THR X 286 " --> pdb=" O VAL X 307 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N HIS X 309 " --> pdb=" O THR X 286 " (cutoff:3.500A) Processing sheet with id= U, first strand: chain 'X' and resid 411 through 413 removed outlier: 6.011A pdb=" N ARG X 460 " --> pdb=" O PHE X 468 " (cutoff:3.500A) removed outlier: 5.595A pdb=" N PHE X 468 " --> pdb=" O ARG X 460 " (cutoff:3.500A) removed outlier: 5.976A pdb=" N GLU X 462 " --> pdb=" O GLU X 466 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N GLU X 466 " --> pdb=" O GLU X 462 " (cutoff:3.500A) Processing sheet with id= V, first strand: chain 'X' and resid 423 through 426 Processing sheet with id= W, first strand: chain 'Y' and resid 236 through 243 removed outlier: 3.511A pdb=" N CYS Y 236 " --> pdb=" O ASP Y 231 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N VAL Y 229 " --> pdb=" O MET Y 238 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ILE Y 240 " --> pdb=" O THR Y 227 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N THR Y 227 " --> pdb=" O ILE Y 240 " (cutoff:3.500A) removed outlier: 4.650A pdb=" N LEU Y 242 " --> pdb=" O TRP Y 225 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N TRP Y 225 " --> pdb=" O LEU Y 242 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N HIS Y 283 " --> pdb=" O TRP Y 202 " (cutoff:3.500A) removed outlier: 8.229A pdb=" N CYS Y 204 " --> pdb=" O HIS Y 283 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N TYR Y 285 " --> pdb=" O CYS Y 204 " (cutoff:3.500A) removed outlier: 8.553A pdb=" N HIS Y 206 " --> pdb=" O TYR Y 285 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N VAL Y 307 " --> pdb=" O PHE Y 284 " (cutoff:3.500A) Processing sheet with id= X, first strand: chain 'Y' and resid 411 through 413 removed outlier: 3.597A pdb=" N MET Y 411 " --> pdb=" O PHE Y 448 " (cutoff:3.500A) removed outlier: 5.834A pdb=" N ARG Y 460 " --> pdb=" O PHE Y 468 " (cutoff:3.500A) removed outlier: 5.509A pdb=" N PHE Y 468 " --> pdb=" O ARG Y 460 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N GLU Y 462 " --> pdb=" O GLU Y 466 " (cutoff:3.500A) removed outlier: 5.188A pdb=" N GLU Y 466 " --> pdb=" O GLU Y 462 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N MET Y 430 " --> pdb=" O GLN Y 475 " (cutoff:3.500A) Processing sheet with id= Y, first strand: chain 'Z' and resid 236 through 243 removed outlier: 7.025A pdb=" N VAL Z 229 " --> pdb=" O MET Z 238 " (cutoff:3.500A) removed outlier: 4.564A pdb=" N ILE Z 240 " --> pdb=" O THR Z 227 " (cutoff:3.500A) removed outlier: 6.719A pdb=" N THR Z 227 " --> pdb=" O ILE Z 240 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N LEU Z 242 " --> pdb=" O TRP Z 225 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TRP Z 225 " --> pdb=" O LEU Z 242 " (cutoff:3.500A) removed outlier: 6.400A pdb=" N HIS Z 283 " --> pdb=" O TRP Z 202 " (cutoff:3.500A) removed outlier: 7.641A pdb=" N CYS Z 204 " --> pdb=" O HIS Z 283 " (cutoff:3.500A) removed outlier: 6.661A pdb=" N TYR Z 285 " --> pdb=" O CYS Z 204 " (cutoff:3.500A) removed outlier: 8.580A pdb=" N HIS Z 206 " --> pdb=" O TYR Z 285 " (cutoff:3.500A) removed outlier: 6.456A pdb=" N VAL Z 307 " --> pdb=" O PHE Z 284 " (cutoff:3.500A) Processing sheet with id= Z, first strand: chain 'Z' and resid 411 through 413 removed outlier: 3.502A pdb=" N THR Z 470 " --> pdb=" O VAL Z 458 " (cutoff:3.500A) removed outlier: 6.030A pdb=" N ARG Z 460 " --> pdb=" O PHE Z 468 " (cutoff:3.500A) removed outlier: 5.719A pdb=" N PHE Z 468 " --> pdb=" O ARG Z 460 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N MET Z 430 " --> pdb=" O GLN Z 475 " (cutoff:3.500A) 1917 hydrogen bonds defined for protein. 5229 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 434 hydrogen bonds 840 hydrogen bond angles 0 basepair planarities 181 basepair parallelities 326 stacking parallelities Total time for adding SS restraints: 18.41 Time building geometry restraints manager: 20.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.15 - 1.29: 8148 1.29 - 1.42: 16959 1.42 - 1.56: 31542 1.56 - 1.69: 1043 1.69 - 1.83: 250 Bond restraints: 57942 Sorted by residual: bond pdb=" C ASN Z 463 " pdb=" N ASN Z 464 " ideal model delta sigma weight residual 1.332 1.220 0.112 1.40e-02 5.10e+03 6.44e+01 bond pdb=" C VAL B 186 " pdb=" O VAL B 186 " ideal model delta sigma weight residual 1.236 1.154 0.083 1.10e-02 8.26e+03 5.63e+01 bond pdb=" C ARG X 355 " pdb=" N LEU X 356 " ideal model delta sigma weight residual 1.330 1.228 0.103 1.38e-02 5.25e+03 5.52e+01 bond pdb=" C GLN A 38 " pdb=" O GLN A 38 " ideal model delta sigma weight residual 1.237 1.151 0.086 1.19e-02 7.06e+03 5.23e+01 bond pdb=" C GLU B 184 " pdb=" O GLU B 184 " ideal model delta sigma weight residual 1.236 1.152 0.084 1.18e-02 7.18e+03 5.11e+01 ... (remaining 57937 not shown) Histogram of bond angle deviations from ideal: 95.22 - 103.24: 1227 103.24 - 111.26: 23243 111.26 - 119.27: 27071 119.27 - 127.29: 27450 127.29 - 135.31: 1443 Bond angle restraints: 80434 Sorted by residual: angle pdb=" PB ATP B 302 " pdb=" O3B ATP B 302 " pdb=" PG ATP B 302 " ideal model delta sigma weight residual 139.87 113.42 26.45 1.00e+00 1.00e+00 7.00e+02 angle pdb=" PB ATP E 302 " pdb=" O3B ATP E 302 " pdb=" PG ATP E 302 " ideal model delta sigma weight residual 139.87 114.76 25.11 1.00e+00 1.00e+00 6.30e+02 angle pdb=" PB ATP F 302 " pdb=" O3B ATP F 302 " pdb=" PG ATP F 302 " ideal model delta sigma weight residual 139.87 115.25 24.62 1.00e+00 1.00e+00 6.06e+02 angle pdb=" PB ATP C 302 " pdb=" O3B ATP C 302 " pdb=" PG ATP C 302 " ideal model delta sigma weight residual 139.87 118.58 21.29 1.00e+00 1.00e+00 4.53e+02 angle pdb=" PB ATP I 302 " pdb=" O3B ATP I 302 " pdb=" PG ATP I 302 " ideal model delta sigma weight residual 139.87 119.92 19.95 1.00e+00 1.00e+00 3.98e+02 ... (remaining 80429 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.60: 32251 35.60 - 71.21: 1456 71.21 - 106.81: 92 106.81 - 142.41: 2 142.41 - 178.01: 11 Dihedral angle restraints: 33812 sinusoidal: 17518 harmonic: 16294 Sorted by residual: dihedral pdb=" O4' U 7 49 " pdb=" C2' U 7 49 " pdb=" C1' U 7 49 " pdb=" C3' U 7 49 " ideal model delta sinusoidal sigma weight residual -35.00 33.96 -68.96 1 8.00e+00 1.56e-02 9.62e+01 dihedral pdb=" CD ARG W 367 " pdb=" NE ARG W 367 " pdb=" CZ ARG W 367 " pdb=" NH1 ARG W 367 " ideal model delta sinusoidal sigma weight residual 0.00 89.17 -89.17 1 1.00e+01 1.00e-02 9.46e+01 dihedral pdb=" C4' U 7 49 " pdb=" C3' U 7 49 " pdb=" C2' U 7 49 " pdb=" C1' U 7 49 " ideal model delta sinusoidal sigma weight residual -35.00 29.48 -64.48 1 8.00e+00 1.56e-02 8.54e+01 ... (remaining 33809 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.216: 8947 0.216 - 0.431: 190 0.431 - 0.647: 14 0.647 - 0.862: 1 0.862 - 1.078: 1 Chirality restraints: 9153 Sorted by residual: chirality pdb=" CA GLU K 24 " pdb=" N GLU K 24 " pdb=" C GLU K 24 " pdb=" CB GLU K 24 " both_signs ideal model delta sigma weight residual False 2.51 1.43 1.08 2.00e-01 2.50e+01 2.90e+01 chirality pdb=" CA GLN K 22 " pdb=" N GLN K 22 " pdb=" C GLN K 22 " pdb=" CB GLN K 22 " both_signs ideal model delta sigma weight residual False 2.51 1.79 0.72 2.00e-01 2.50e+01 1.29e+01 chirality pdb=" P DT 1 35 " pdb=" OP1 DT 1 35 " pdb=" OP2 DT 1 35 " pdb=" O5' DT 1 35 " both_signs ideal model delta sigma weight residual True 2.35 -2.89 -0.55 2.00e-01 2.50e+01 7.47e+00 ... (remaining 9150 not shown) Planarity restraints: 8462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP G 20 " -0.216 2.00e-02 2.50e+03 1.07e-01 2.86e+02 pdb=" CG TRP G 20 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 TRP G 20 " 0.070 2.00e-02 2.50e+03 pdb=" CD2 TRP G 20 " 0.091 2.00e-02 2.50e+03 pdb=" NE1 TRP G 20 " 0.057 2.00e-02 2.50e+03 pdb=" CE2 TRP G 20 " -0.004 2.00e-02 2.50e+03 pdb=" CE3 TRP G 20 " 0.137 2.00e-02 2.50e+03 pdb=" CZ2 TRP G 20 " -0.130 2.00e-02 2.50e+03 pdb=" CZ3 TRP G 20 " 0.049 2.00e-02 2.50e+03 pdb=" CH2 TRP G 20 " -0.105 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG W 367 " -1.100 9.50e-02 1.11e+02 4.93e-01 1.46e+02 pdb=" NE ARG W 367 " 0.066 2.00e-02 2.50e+03 pdb=" CZ ARG W 367 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG W 367 " -0.014 2.00e-02 2.50e+03 pdb=" NH2 ARG W 367 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG Y 526 " -1.087 9.50e-02 1.11e+02 4.87e-01 1.43e+02 pdb=" NE ARG Y 526 " 0.065 2.00e-02 2.50e+03 pdb=" CZ ARG Y 526 " 0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG Y 526 " -0.011 2.00e-02 2.50e+03 pdb=" NH2 ARG Y 526 " -0.018 2.00e-02 2.50e+03 ... (remaining 8459 not shown) Histogram of nonbonded interaction distances: 1.16 - 1.91: 65 1.91 - 2.66: 1479 2.66 - 3.40: 73457 3.40 - 4.15: 143944 4.15 - 4.90: 237264 Nonbonded interactions: 456209 Sorted by model distance: nonbonded pdb=" OE2 GLU B 162 " pdb=" NH1 ARG B 189 " model vdw 1.162 2.520 nonbonded pdb=" NH1 ARG X 322 " pdb=" N3 DA 2 4 " model vdw 1.188 2.600 nonbonded pdb=" CZ ARG K 191 " pdb=" NH2 ARG L 243 " model vdw 1.222 3.350 nonbonded pdb=" NH2 ARG W 380 " pdb=" O5' DT 5 3 " model vdw 1.232 2.520 nonbonded pdb=" OP2 DG 1 36 " pdb=" CE LYS I 119 " model vdw 1.236 3.440 ... (remaining 456204 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 '2' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27 or resid 29)) selection = (chain '5' and (resid 1 through 11 or resid 13 through 18 or resid 20 through 25 \ or resid 27 through 28)) } ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'W' and (resid 29 through 516 or resid 524 through 542 or resid 600)) selection = chain 'X' } ncs_group { reference = (chain 'Y' and (resid 196 through 287 or resid 295 through 340 or resid 354 thro \ ugh 525 or (resid 526 and (name N or name CA or name C or name O or name CB )) o \ r resid 527)) selection = chain 'Z' } ncs_group { reference = chain 'w' selection = chain 'x' selection = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 6.700 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: 0.050 Extract box with map and model: 33.400 Check model and map are aligned: 0.610 Set scattering table: 0.380 Process input model: 117.890 Find NCS groups from input model: 2.410 Set up NCS constraints: 0.440 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 164.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6840 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 : 0.013 0.112 57942 Z= 0.842 Angle : 1.649 26.449 80434 Z= 1.166 Chirality : 0.086 1.078 9153 Planarity : 0.020 0.493 8462 Dihedral : 16.879 178.015 23276 Min Nonbonded Distance : 1.162 Molprobity Statistics. All-atom Clashscore : 11.38 Ramachandran Plot: Outliers : 0.16 % Allowed : 2.45 % Favored : 97.39 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.23 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.04 (0.10), residues: 5554 helix: -1.16 (0.08), residues: 2863 sheet: 0.26 (0.21), residues: 559 loop : 0.06 (0.13), residues: 2132 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1337 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 1323 time to evaluate : 5.559 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 2 residues processed: 1335 average time/residue: 0.6287 time to fit residues: 1316.1468 Evaluate side-chains 539 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 537 time to evaluate : 4.603 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3773 time to fit residues: 7.4711 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 502 optimal weight: 0.7980 chunk 450 optimal weight: 0.9980 chunk 250 optimal weight: 0.9990 chunk 154 optimal weight: 0.9990 chunk 304 optimal weight: 0.9990 chunk 240 optimal weight: 1.9990 chunk 466 optimal weight: 0.9990 chunk 180 optimal weight: 0.9990 chunk 283 optimal weight: 0.9980 chunk 347 optimal weight: 2.9990 chunk 540 optimal weight: 2.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 HIS B 38 GLN D 38 GLN F 38 GLN G 77 HIS G 269 GLN H 38 GLN I 80 GLN I 213 GLN J 98 GLN J 185 GLN K 213 GLN K 269 GLN L 213 GLN O 42 HIS O 61 GLN O 269 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 369 HIS O 370 HIS O 420 GLN O 603 GLN O 613 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 135 ASN S 28 GLN S 37 ASN y 577 GLN W 88 GLN W 217 HIS W 272 HIS W 463 ASN X 217 HIS X 272 HIS X 303 GLN X 363 GLN Y 296 HIS Y 309 HIS ** Y 375 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 463 ASN Z 203 GLN ** Z 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 283 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 428 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7052 moved from start: 0.3199 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 57942 Z= 0.219 Angle : 0.639 11.632 80434 Z= 0.344 Chirality : 0.040 0.218 9153 Planarity : 0.005 0.071 8462 Dihedral : 18.126 177.729 11671 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 2.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.02 % 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: 0.73 (0.11), residues: 5554 helix: 0.73 (0.09), residues: 2878 sheet: 0.27 (0.22), residues: 514 loop : 0.44 (0.14), residues: 2162 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 117 poor density : 589 time to evaluate : 4.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 117 outliers final: 77 residues processed: 684 average time/residue: 0.6157 time to fit residues: 698.5369 Evaluate side-chains 477 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 400 time to evaluate : 4.587 Switching outliers to nearest non-outliers outliers start: 77 outliers final: 0 residues processed: 77 average time/residue: 0.4142 time to fit residues: 66.8535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 300 optimal weight: 0.5980 chunk 167 optimal weight: 4.9990 chunk 449 optimal weight: 0.0070 chunk 367 optimal weight: 6.9990 chunk 149 optimal weight: 1.9990 chunk 541 optimal weight: 2.9990 chunk 584 optimal weight: 0.7980 chunk 482 optimal weight: 8.9990 chunk 536 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 434 optimal weight: 7.9990 overall best weight: 1.2802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN E 269 GLN F 38 GLN K 22 GLN K 269 GLN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN W 217 HIS W 272 HIS ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 463 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.3964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 57942 Z= 0.215 Angle : 0.561 8.196 80434 Z= 0.302 Chirality : 0.038 0.240 9153 Planarity : 0.004 0.092 8462 Dihedral : 18.179 176.667 11671 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 1.78 % Favored : 98.20 % Rotamer Outliers : 1.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.19 (0.11), residues: 5554 helix: 1.26 (0.10), residues: 2892 sheet: 0.31 (0.22), residues: 509 loop : 0.46 (0.14), residues: 2153 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 461 time to evaluate : 4.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 66 outliers final: 33 residues processed: 502 average time/residue: 0.5782 time to fit residues: 482.1529 Evaluate side-chains 395 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 362 time to evaluate : 4.639 Switching outliers to nearest non-outliers outliers start: 33 outliers final: 0 residues processed: 33 average time/residue: 0.4075 time to fit residues: 31.3385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 534 optimal weight: 0.9990 chunk 406 optimal weight: 5.9990 chunk 280 optimal weight: 0.9990 chunk 59 optimal weight: 10.0000 chunk 258 optimal weight: 2.9990 chunk 363 optimal weight: 10.0000 chunk 543 optimal weight: 0.9990 chunk 575 optimal weight: 5.9990 chunk 283 optimal weight: 4.9990 chunk 514 optimal weight: 9.9990 chunk 154 optimal weight: 2.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 37 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN I 22 GLN K 193 HIS O 521 GLN ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 309 HIS Y 375 GLN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7223 moved from start: 0.4556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 57942 Z= 0.262 Angle : 0.565 7.976 80434 Z= 0.302 Chirality : 0.038 0.252 9153 Planarity : 0.004 0.061 8462 Dihedral : 18.309 176.625 11671 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.14 % Favored : 97.84 % Rotamer Outliers : 1.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.27 (0.11), residues: 5554 helix: 1.39 (0.10), residues: 2889 sheet: 0.42 (0.22), residues: 501 loop : 0.37 (0.14), residues: 2164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 476 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 73 poor density : 403 time to evaluate : 4.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 73 outliers final: 36 residues processed: 461 average time/residue: 0.5831 time to fit residues: 446.6714 Evaluate side-chains 381 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 345 time to evaluate : 4.674 Switching outliers to nearest non-outliers outliers start: 36 outliers final: 0 residues processed: 36 average time/residue: 0.4001 time to fit residues: 33.4071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 478 optimal weight: 10.0000 chunk 326 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 428 optimal weight: 6.9990 chunk 237 optimal weight: 4.9990 chunk 490 optimal weight: 0.0980 chunk 397 optimal weight: 0.0970 chunk 0 optimal weight: 10.0000 chunk 293 optimal weight: 2.9990 chunk 516 optimal weight: 2.9990 chunk 145 optimal weight: 0.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 GLN E 185 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS I 269 GLN O 33 ASN ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 283 HIS Y 463 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 moved from start: 0.4823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 57942 Z= 0.186 Angle : 0.512 12.304 80434 Z= 0.276 Chirality : 0.037 0.188 9153 Planarity : 0.004 0.061 8462 Dihedral : 18.307 178.265 11671 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.21 % Favored : 97.77 % Rotamer Outliers : 0.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.44 (0.11), residues: 5554 helix: 1.58 (0.10), residues: 2887 sheet: 0.42 (0.22), residues: 517 loop : 0.39 (0.14), residues: 2150 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 431 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 388 time to evaluate : 4.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 11 residues processed: 420 average time/residue: 0.5859 time to fit residues: 410.0596 Evaluate side-chains 350 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 339 time to evaluate : 4.578 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4184 time to fit residues: 14.6036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 193 optimal weight: 0.9980 chunk 517 optimal weight: 7.9990 chunk 113 optimal weight: 7.9990 chunk 337 optimal weight: 20.0000 chunk 141 optimal weight: 3.9990 chunk 575 optimal weight: 4.9990 chunk 477 optimal weight: 0.2980 chunk 266 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 chunk 190 optimal weight: 4.9990 chunk 302 optimal weight: 0.7980 overall best weight: 2.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 223 ASN D 38 GLN E 185 GLN ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS F 80 GLN O 50 GLN O 342 HIS ** O 353 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 125 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 413 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 206 HIS Y 463 ASN Y 504 GLN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7285 moved from start: 0.5245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.111 57942 Z= 0.292 Angle : 0.569 11.016 80434 Z= 0.303 Chirality : 0.039 0.184 9153 Planarity : 0.004 0.062 8462 Dihedral : 18.528 176.479 11671 Min Nonbonded Distance : 1.810 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.11), residues: 5554 helix: 1.53 (0.10), residues: 2880 sheet: 0.20 (0.22), residues: 524 loop : 0.31 (0.14), residues: 2150 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 434 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 373 time to evaluate : 4.583 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 61 outliers final: 38 residues processed: 418 average time/residue: 0.5579 time to fit residues: 391.9308 Evaluate side-chains 363 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 325 time to evaluate : 4.666 Switching outliers to nearest non-outliers outliers start: 38 outliers final: 0 residues processed: 38 average time/residue: 0.4187 time to fit residues: 36.0187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 555 optimal weight: 8.9990 chunk 64 optimal weight: 0.8980 chunk 328 optimal weight: 0.9990 chunk 420 optimal weight: 7.9990 chunk 325 optimal weight: 5.9990 chunk 484 optimal weight: 0.8980 chunk 321 optimal weight: 0.6980 chunk 573 optimal weight: 7.9990 chunk 358 optimal weight: 8.9990 chunk 349 optimal weight: 10.0000 chunk 264 optimal weight: 0.7980 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 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS ** Q 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN W 463 ASN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 206 HIS Y 463 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7234 moved from start: 0.5365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 57942 Z= 0.168 Angle : 0.512 11.836 80434 Z= 0.273 Chirality : 0.036 0.190 9153 Planarity : 0.004 0.069 8462 Dihedral : 18.444 178.187 11671 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.16 % Favored : 97.82 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.55 (0.11), residues: 5554 helix: 1.77 (0.10), residues: 2874 sheet: 0.27 (0.22), residues: 524 loop : 0.35 (0.14), residues: 2156 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 404 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 379 time to evaluate : 4.653 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 12 residues processed: 399 average time/residue: 0.5787 time to fit residues: 386.7927 Evaluate side-chains 343 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 331 time to evaluate : 4.621 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.4332 time to fit residues: 15.5977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 354 optimal weight: 4.9990 chunk 229 optimal weight: 5.9990 chunk 342 optimal weight: 8.9990 chunk 172 optimal weight: 0.6980 chunk 112 optimal weight: 0.0980 chunk 111 optimal weight: 9.9990 chunk 364 optimal weight: 20.0000 chunk 390 optimal weight: 2.9990 chunk 283 optimal weight: 3.9990 chunk 53 optimal weight: 0.0870 chunk 450 optimal weight: 2.9990 overall best weight: 1.3762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS H 213 GLN ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 206 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.5546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.068 57942 Z= 0.215 Angle : 0.522 7.516 80434 Z= 0.279 Chirality : 0.037 0.188 9153 Planarity : 0.004 0.064 8462 Dihedral : 18.491 177.639 11671 Min Nonbonded Distance : 1.853 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.66 % Favored : 97.32 % Rotamer Outliers : 0.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.11), residues: 5554 helix: 1.72 (0.10), residues: 2890 sheet: 0.34 (0.22), residues: 519 loop : 0.34 (0.14), residues: 2145 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 348 time to evaluate : 4.617 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 16 residues processed: 368 average time/residue: 0.5770 time to fit residues: 357.7956 Evaluate side-chains 348 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 332 time to evaluate : 4.740 Switching outliers to nearest non-outliers outliers start: 16 outliers final: 0 residues processed: 16 average time/residue: 0.4815 time to fit residues: 19.7185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 521 optimal weight: 0.6980 chunk 549 optimal weight: 7.9990 chunk 501 optimal weight: 6.9990 chunk 534 optimal weight: 9.9990 chunk 321 optimal weight: 2.9990 chunk 232 optimal weight: 7.9990 chunk 419 optimal weight: 4.9990 chunk 164 optimal weight: 0.7980 chunk 482 optimal weight: 9.9990 chunk 505 optimal weight: 0.9980 chunk 532 optimal weight: 3.9990 overall best weight: 1.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 83 GLN y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 200 HIS Z 328 ASN ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.5753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 57942 Z= 0.268 Angle : 0.558 13.658 80434 Z= 0.295 Chirality : 0.038 0.225 9153 Planarity : 0.004 0.044 8462 Dihedral : 18.609 176.759 11671 Min Nonbonded Distance : 1.842 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.75 % Favored : 97.23 % Rotamer Outliers : 0.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.11), residues: 5554 helix: 1.64 (0.10), residues: 2892 sheet: 0.21 (0.22), residues: 522 loop : 0.24 (0.14), residues: 2140 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 353 time to evaluate : 4.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 11 residues processed: 365 average time/residue: 0.5737 time to fit residues: 353.1363 Evaluate side-chains 334 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 323 time to evaluate : 4.586 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.4009 time to fit residues: 14.4930 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 350 optimal weight: 0.9980 chunk 565 optimal weight: 10.0000 chunk 344 optimal weight: 0.0370 chunk 268 optimal weight: 10.0000 chunk 392 optimal weight: 8.9990 chunk 592 optimal weight: 3.9990 chunk 545 optimal weight: 0.9990 chunk 472 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 364 optimal weight: 0.0570 chunk 289 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN ** F 43 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 223 ASN O 116 ASN ** O 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** y 577 GLN W 37 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 200 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 57942 Z= 0.167 Angle : 0.518 9.885 80434 Z= 0.275 Chirality : 0.036 0.307 9153 Planarity : 0.003 0.050 8462 Dihedral : 18.533 178.120 11671 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.30 % Favored : 97.68 % Rotamer Outliers : 0.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.11), residues: 5554 helix: 1.70 (0.10), residues: 2913 sheet: 0.28 (0.22), residues: 517 loop : 0.30 (0.14), residues: 2124 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11108 Ramachandran restraints generated. 5554 Oldfield, 0 Emsley, 5554 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 370 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 359 time to evaluate : 4.590 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 365 average time/residue: 0.5732 time to fit residues: 353.4222 Evaluate side-chains 333 residues out of total 4897 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 329 time to evaluate : 4.592 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4391 time to fit residues: 9.3473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 595 random chunks: chunk 374 optimal weight: 9.9990 chunk 502 optimal weight: 9.9990 chunk 144 optimal weight: 1.9990 chunk 435 optimal weight: 6.9990 chunk 69 optimal weight: 0.6980 chunk 131 optimal weight: 0.6980 chunk 472 optimal weight: 3.9990 chunk 197 optimal weight: 0.8980 chunk 485 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 chunk 87 optimal weight: 5.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 213 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 269 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 38 GLN F 43 HIS ** O 304 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 20 ASN y 577 GLN W 88 GLN ** W 475 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 241 ASN ** X 461 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 200 HIS ** Z 363 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.114976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.081222 restraints weight = 140019.760| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.082351 restraints weight = 85815.814| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.082527 restraints weight = 64768.475| |-----------------------------------------------------------------------------| r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.5910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 57942 Z= 0.159 Angle : 0.516 12.498 80434 Z= 0.273 Chirality : 0.036 0.252 9153 Planarity : 0.003 0.053 8462 Dihedral : 18.487 178.593 11671 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.02 % Allowed : 2.48 % Favored : 97.50 % Rotamer Outliers : 0.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.11), residues: 5554 helix: 1.74 (0.10), residues: 2924 sheet: 0.34 (0.22), residues: 520 loop : 0.31 (0.14), residues: 2110 =============================================================================== Job complete usr+sys time: 9262.20 seconds wall clock time: 166 minutes 6.03 seconds (9966.03 seconds total)