Starting phenix.real_space_refine (version: 1.21rc1) on Tue Jul 18 14:42:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpd_3534/07_2023/5mpd_3534.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpd_3534/07_2023/5mpd_3534.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpd_3534/07_2023/5mpd_3534.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpd_3534/07_2023/5mpd_3534.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpd_3534/07_2023/5mpd_3534.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5mpd_3534/07_2023/5mpd_3534.pdb" } resolution = 4.1 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= 0.006 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: 4 Type Number sf(0) Gaussians S 151 5.16 5 C 26021 2.51 5 N 6810 2.21 5 O 7992 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "W GLU 34": "OE1" <-> "OE2" Residue "W GLU 46": "OE1" <-> "OE2" Residue "W GLU 146": "OE1" <-> "OE2" Residue "W GLU 167": "OE1" <-> "OE2" Residue "V PHE 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 61": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 81": "OE1" <-> "OE2" Residue "V TYR 108": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V TYR 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "V GLU 209": "OE1" <-> "OE2" Residue "V GLU 219": "OE1" <-> "OE2" Residue "V GLU 232": "OE1" <-> "OE2" Residue "V GLU 234": "OE1" <-> "OE2" Residue "V GLU 249": "OE1" <-> "OE2" Residue "V GLU 256": "OE1" <-> "OE2" Residue "V GLU 258": "OE1" <-> "OE2" Residue "V GLU 286": "OE1" <-> "OE2" Residue "T GLU 16": "OE1" <-> "OE2" Residue "T GLU 33": "OE1" <-> "OE2" Residue "T GLU 79": "OE1" <-> "OE2" Residue "T GLU 125": "OE1" <-> "OE2" Residue "T GLU 188": "OE1" <-> "OE2" Residue "T GLU 214": "OE1" <-> "OE2" Residue "T GLU 241": "OE1" <-> "OE2" Residue "T GLU 261": "OE1" <-> "OE2" Residue "X GLU 32": "OE1" <-> "OE2" Residue "X GLU 34": "OE1" <-> "OE2" Residue "X GLU 40": "OE1" <-> "OE2" Residue "X GLU 41": "OE1" <-> "OE2" Residue "X GLU 49": "OE1" <-> "OE2" Residue "X GLU 54": "OE1" <-> "OE2" Residue "X GLU 60": "OE1" <-> "OE2" Residue "X ASP 62": "OD1" <-> "OD2" Residue "X PHE 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 95": "OE1" <-> "OE2" Residue "X PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "X GLU 103": "OE1" <-> "OE2" Residue "X ASP 118": "OD1" <-> "OD2" Residue "Y GLU 22": "OE1" <-> "OE2" Residue "Y GLU 23": "OE1" <-> "OE2" Residue "Y GLU 31": "OE1" <-> "OE2" Residue "Y GLU 68": "OE1" <-> "OE2" Residue "Y GLU 80": "OE1" <-> "OE2" Residue "Y GLU 87": "OE1" <-> "OE2" Residue "Z GLU 14": "OE1" <-> "OE2" Residue "Z GLU 21": "OE1" <-> "OE2" Residue "Z GLU 35": "OE1" <-> "OE2" Residue "Z GLU 58": "OE1" <-> "OE2" Residue "Z GLU 73": "OE1" <-> "OE2" Residue "Z GLU 128": "OE1" <-> "OE2" Residue "Z GLU 147": "OE1" <-> "OE2" Residue "Z GLU 152": "OE1" <-> "OE2" Residue "Z GLU 160": "OE1" <-> "OE2" Residue "Z GLU 174": "OE1" <-> "OE2" Residue "Z GLU 194": "OE1" <-> "OE2" Residue "Z GLU 226": "OE1" <-> "OE2" Residue "Z GLU 228": "OE1" <-> "OE2" Residue "Z ASP 238": "OD1" <-> "OD2" Residue "Z GLU 260": "OE1" <-> "OE2" Residue "Z GLU 277": "OE1" <-> "OE2" Residue "Z GLU 291": "OE1" <-> "OE2" Residue "Z TYR 323": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 324": "OE1" <-> "OE2" Residue "Z GLU 337": "OE1" <-> "OE2" Residue "Z GLU 345": "OE1" <-> "OE2" Residue "Z GLU 521": "OE1" <-> "OE2" Residue "Z GLU 557": "OE1" <-> "OE2" Residue "Z GLU 704": "OE1" <-> "OE2" Residue "Z GLU 724": "OE1" <-> "OE2" Residue "Z GLU 726": "OE1" <-> "OE2" Residue "Z GLU 735": "OE1" <-> "OE2" Residue "Z GLU 755": "OE1" <-> "OE2" Residue "Z GLU 770": "OE1" <-> "OE2" Residue "Z GLU 806": "OE1" <-> "OE2" Residue "Z TYR 838": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Z GLU 841": "OE1" <-> "OE2" Residue "Z ASP 843": "OD1" <-> "OD2" Residue "Z GLU 966": "OE1" <-> "OE2" Residue "Z GLU 969": "OE1" <-> "OE2" Residue "N GLU 15": "OE1" <-> "OE2" Residue "N ASP 45": "OD1" <-> "OD2" Residue "N GLU 59": "OE1" <-> "OE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N GLU 107": "OE1" <-> "OE2" Residue "N GLU 112": "OE1" <-> "OE2" Residue "N GLU 121": "OE1" <-> "OE2" Residue "N ASP 127": "OD1" <-> "OD2" Residue "N GLU 138": "OE1" <-> "OE2" Residue "N GLU 149": "OE1" <-> "OE2" Residue "N GLU 167": "OE1" <-> "OE2" Residue "N GLU 251": "OE1" <-> "OE2" Residue "N GLU 271": "OE1" <-> "OE2" Residue "N PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 394": "NH1" <-> "NH2" Residue "N ARG 417": "NH1" <-> "NH2" Residue "N GLU 429": "OE1" <-> "OE2" Residue "N ASP 438": "OD1" <-> "OD2" Residue "N GLU 464": "OE1" <-> "OE2" Residue "N GLU 468": "OE1" <-> "OE2" Residue "N GLU 479": "OE1" <-> "OE2" Residue "N GLU 544": "OE1" <-> "OE2" Residue "N PHE 553": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 593": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 697": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 718": "OE1" <-> "OE2" Residue "N PHE 743": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 748": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N ARG 786": "NH1" <-> "NH2" Residue "N GLU 790": "OE1" <-> "OE2" Residue "N GLU 795": "OE1" <-> "OE2" Residue "N GLU 820": "OE1" <-> "OE2" Residue "N PHE 856": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N TYR 881": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 909": "OE1" <-> "OE2" Residue "N GLU 912": "OE1" <-> "OE2" Residue "S GLU 22": "OE1" <-> "OE2" Residue "S TYR 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 28": "OE1" <-> "OE2" Residue "S GLU 33": "OE1" <-> "OE2" Residue "S GLU 67": "OE1" <-> "OE2" Residue "S PHE 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 109": "OE1" <-> "OE2" Residue "S GLU 151": "OE1" <-> "OE2" Residue "S GLU 153": "OE1" <-> "OE2" Residue "S GLU 157": "OE1" <-> "OE2" Residue "S PHE 158": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 171": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 200": "OE1" <-> "OE2" Residue "S GLU 258": "OE1" <-> "OE2" Residue "S GLU 269": "OE1" <-> "OE2" Residue "S GLU 291": "OE1" <-> "OE2" Residue "S PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 329": "OE1" <-> "OE2" Residue "S GLU 433": "OE1" <-> "OE2" Residue "S GLU 447": "OE1" <-> "OE2" Residue "P GLU 77": "OE1" <-> "OE2" Residue "P GLU 102": "OE1" <-> "OE2" Residue "P GLU 133": "OE1" <-> "OE2" Residue "P GLU 149": "OE1" <-> "OE2" Residue "P GLU 150": "OE1" <-> "OE2" Residue "P GLU 155": "OE1" <-> "OE2" Residue "P GLU 162": "OE1" <-> "OE2" Residue "P GLU 182": "OE1" <-> "OE2" Residue "P GLU 185": "OE1" <-> "OE2" Residue "P TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 214": "OE1" <-> "OE2" Residue "P GLU 219": "OE1" <-> "OE2" Residue "P GLU 236": "OE1" <-> "OE2" Residue "P GLU 243": "OE1" <-> "OE2" Residue "P GLU 297": "OE1" <-> "OE2" Residue "P ARG 310": "NH1" <-> "NH2" Residue "P GLU 332": "OE1" <-> "OE2" Residue "P GLU 355": "OE1" <-> "OE2" Residue "P GLU 427": "OE1" <-> "OE2" Residue "Q GLU 22": "OE1" <-> "OE2" Residue "Q GLU 24": "OE1" <-> "OE2" Residue "Q ASP 34": "OD1" <-> "OD2" Residue "Q TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q TYR 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 102": "OE1" <-> "OE2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "Q GLU 123": "OE1" <-> "OE2" Residue "Q PHE 132": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 164": "OE1" <-> "OE2" Residue "Q GLU 217": "OE1" <-> "OE2" Residue "Q GLU 304": "OE1" <-> "OE2" Residue "Q GLU 322": "OE1" <-> "OE2" Residue "Q GLU 329": "OE1" <-> "OE2" Residue "Q GLU 352": "OE1" <-> "OE2" Residue "Q GLU 355": "OE1" <-> "OE2" Residue "Q GLU 374": "OE1" <-> "OE2" Residue "Q ASP 383": "OD1" <-> "OD2" Residue "Q GLU 414": "OE1" <-> "OE2" Residue "Q GLU 428": "OE1" <-> "OE2" Residue "R TYR 24": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 25": "OE1" <-> "OE2" Residue "R GLU 28": "OE1" <-> "OE2" Residue "R GLU 48": "OE1" <-> "OE2" Residue "R GLU 57": "OE1" <-> "OE2" Residue "R GLU 58": "OE1" <-> "OE2" Residue "R GLU 68": "OE1" <-> "OE2" Residue "R TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 112": "OE1" <-> "OE2" Residue "R GLU 121": "OE1" <-> "OE2" Residue "R GLU 127": "OE1" <-> "OE2" Residue "R GLU 139": "OE1" <-> "OE2" Residue "R TYR 141": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 169": "OD1" <-> "OD2" Residue "R TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 189": "OE1" <-> "OE2" Residue "R GLU 192": "OE1" <-> "OE2" Residue "R GLU 226": "OE1" <-> "OE2" Residue "R GLU 242": "OE1" <-> "OE2" Residue "R GLU 247": "OE1" <-> "OE2" Residue "R GLU 332": "OE1" <-> "OE2" Residue "U GLU 57": "OE1" <-> "OE2" Residue "U GLU 60": "OE1" <-> "OE2" Residue "U GLU 87": "OE1" <-> "OE2" Residue "U GLU 108": "OE1" <-> "OE2" Residue "U PHE 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U TYR 137": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "U GLU 141": "OE1" <-> "OE2" Residue "U GLU 162": "OE1" <-> "OE2" Residue "U GLU 165": "OE1" <-> "OE2" Residue "U GLU 167": "OE1" <-> "OE2" Residue "U GLU 172": "OE1" <-> "OE2" Residue "U GLU 209": "OE1" <-> "OE2" Residue "U GLU 246": "OE1" <-> "OE2" Residue "U GLU 250": "OE1" <-> "OE2" Residue "U GLU 293": "OE1" <-> "OE2" Residue "O GLU 17": "OE1" <-> "OE2" Residue "O GLU 30": "OE1" <-> "OE2" Residue "O ARG 58": "NH1" <-> "NH2" Residue "O ARG 60": "NH1" <-> "NH2" Residue "O GLU 94": "OE1" <-> "OE2" Residue "O GLU 108": "OE1" <-> "OE2" Residue "O GLU 154": "OE1" <-> "OE2" Residue "O TYR 195": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O GLU 209": "OE1" <-> "OE2" Residue "O GLU 240": "OE1" <-> "OE2" Residue "O GLU 284": "OE1" <-> "OE2" Residue "O GLU 298": "OE1" <-> "OE2" Residue "O GLU 346": "OE1" <-> "OE2" Residue "O GLU 378": "OE1" <-> "OE2" Residue "O GLU 385": "OE1" <-> "OE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 40974 Number of models: 1 Model: "" Number of chains: 13 Chain: "W" Number of atoms: 1534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1534 Classifications: {'peptide': 197} Link IDs: {'CIS': 1, 'PTRANS': 8, 'TRANS': 187} Chain: "V" Number of atoms: 2274 Number of conformers: 1 Conformer: "" Number of residues, atoms: 289, 2274 Classifications: {'peptide': 289} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 282} Chain: "T" Number of atoms: 2192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 266, 2192 Classifications: {'peptide': 266} Link IDs: {'PTRANS': 7, 'TRANS': 258} Chain: "X" Number of atoms: 1032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1032 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 9, 'TRANS': 117} Chain: "Y" Number of atoms: 435 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 435 Classifications: {'peptide': 51} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 49} Chain breaks: 1 Chain: "Z" Number of atoms: 7005 Number of conformers: 1 Conformer: "" Number of residues, atoms: 906, 7005 Classifications: {'peptide': 906} Link IDs: {'PTRANS': 30, 'TRANS': 875} Chain breaks: 1 Chain: "N" Number of atoms: 6882 Number of conformers: 1 Conformer: "" Number of residues, atoms: 890, 6882 Classifications: {'peptide': 890} Link IDs: {'PTRANS': 23, 'TRANS': 866} Chain breaks: 1 Chain: "S" Number of atoms: 3894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 475, 3894 Classifications: {'peptide': 475} Link IDs: {'PTRANS': 11, 'TRANS': 463} Chain: "P" Number of atoms: 3608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 440, 3608 Classifications: {'peptide': 440} Link IDs: {'PTRANS': 9, 'TRANS': 430} Chain: "Q" Number of atoms: 3499 Number of conformers: 1 Conformer: "" Number of residues, atoms: 434, 3499 Classifications: {'peptide': 434} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 426} Chain: "R" Number of atoms: 3060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 381, 3060 Classifications: {'peptide': 381} Link IDs: {'PTRANS': 7, 'TRANS': 373} Chain breaks: 1 Chain: "U" Number of atoms: 2373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 298, 2373 Classifications: {'peptide': 298} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 288} Chain: "O" Number of atoms: 3186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 388, 3186 Classifications: {'peptide': 388} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 378} Time building chain proxies: 18.33, per 1000 atoms: 0.45 Number of scatterers: 40974 At special positions: 0 Unit cell: (238.74, 211.14, 227.7, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 151 16.00 O 7992 8.00 N 6810 7.00 C 26021 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 15.30 Conformation dependent library (CDL) restraints added in 5.6 seconds 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 9824 Finding SS restraints... Secondary structure from input PDB file: 256 helices and 16 sheets defined 71.8% alpha, 4.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.95 Creating SS restraints... Processing helix chain 'W' and resid 24 through 44 removed outlier: 3.573A pdb=" N ASP W 31 " --> pdb=" O GLU W 27 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER W 32 " --> pdb=" O ALA W 28 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE W 37 " --> pdb=" O VAL W 33 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N ASN W 44 " --> pdb=" O LYS W 40 " (cutoff:3.500A) Processing helix chain 'W' and resid 68 through 78 removed outlier: 4.042A pdb=" N ILE W 72 " --> pdb=" O GLU W 68 " (cutoff:3.500A) Processing helix chain 'W' and resid 86 through 99 removed outlier: 3.895A pdb=" N ALA W 90 " --> pdb=" O HIS W 86 " (cutoff:3.500A) Processing helix chain 'W' and resid 121 through 132 removed outlier: 3.776A pdb=" N LEU W 125 " --> pdb=" O SER W 121 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LYS W 130 " --> pdb=" O ILE W 126 " (cutoff:3.500A) Processing helix chain 'W' and resid 154 through 162 Processing helix chain 'W' and resid 180 through 188 Processing helix chain 'V' and resid 31 through 44 removed outlier: 3.626A pdb=" N ALA V 43 " --> pdb=" O LYS V 39 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLY V 44 " --> pdb=" O HIS V 40 " (cutoff:3.500A) Processing helix chain 'V' and resid 84 through 98 removed outlier: 3.821A pdb=" N GLN V 97 " --> pdb=" O ASP V 93 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N THR V 98 " --> pdb=" O MET V 94 " (cutoff:3.500A) Processing helix chain 'V' and resid 119 through 133 Processing helix chain 'V' and resid 160 through 166 Processing helix chain 'V' and resid 168 through 173 Processing helix chain 'V' and resid 184 through 196 Processing helix chain 'V' and resid 206 through 215 removed outlier: 3.563A pdb=" N LYS V 211 " --> pdb=" O ALA V 207 " (cutoff:3.500A) Processing helix chain 'V' and resid 219 through 224 removed outlier: 3.504A pdb=" N GLY V 224 " --> pdb=" O GLN V 220 " (cutoff:3.500A) Processing helix chain 'V' and resid 230 through 255 removed outlier: 3.641A pdb=" N LEU V 238 " --> pdb=" O GLU V 234 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS V 246 " --> pdb=" O LYS V 242 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLN V 250 " --> pdb=" O LYS V 246 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ILE V 255 " --> pdb=" O TYR V 251 " (cutoff:3.500A) Processing helix chain 'V' and resid 262 through 270 Processing helix chain 'V' and resid 275 through 306 Processing helix chain 'T' and resid 8 through 18 removed outlier: 3.521A pdb=" N ALA T 14 " --> pdb=" O SER T 10 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N PHE T 15 " --> pdb=" O LEU T 11 " (cutoff:3.500A) removed outlier: 4.030A pdb=" N GLU T 16 " --> pdb=" O SER T 12 " (cutoff:3.500A) removed outlier: 3.738A pdb=" N GLY T 18 " --> pdb=" O ALA T 14 " (cutoff:3.500A) Processing helix chain 'T' and resid 19 through 41 Proline residue: T 28 - end of helix removed outlier: 3.869A pdb=" N ILE T 32 " --> pdb=" O PRO T 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU T 33 " --> pdb=" O PRO T 29 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE T 35 " --> pdb=" O LYS T 31 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N LYS T 36 " --> pdb=" O ILE T 32 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ILE T 41 " --> pdb=" O ASN T 37 " (cutoff:3.500A) Processing helix chain 'T' and resid 49 through 72 removed outlier: 3.527A pdb=" N ASN T 53 " --> pdb=" O ASP T 49 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE T 57 " --> pdb=" O ASN T 53 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR T 58 " --> pdb=" O ASP T 54 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE T 70 " --> pdb=" O ALA T 66 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN T 71 " --> pdb=" O LEU T 67 " (cutoff:3.500A) Processing helix chain 'T' and resid 74 through 91 removed outlier: 3.638A pdb=" N PHE T 78 " --> pdb=" O ASN T 74 " (cutoff:3.500A) Proline residue: T 87 - end of helix removed outlier: 3.616A pdb=" N SER T 91 " --> pdb=" O PRO T 87 " (cutoff:3.500A) Processing helix chain 'T' and resid 99 through 116 removed outlier: 3.914A pdb=" N SER T 103 " --> pdb=" O SER T 99 " (cutoff:3.500A) Processing helix chain 'T' and resid 118 through 130 removed outlier: 3.607A pdb=" N PHE T 122 " --> pdb=" O ASN T 118 " (cutoff:3.500A) Processing helix chain 'T' and resid 131 through 138 Processing helix chain 'T' and resid 142 through 155 Processing helix chain 'T' and resid 156 through 167 removed outlier: 3.560A pdb=" N LEU T 163 " --> pdb=" O LYS T 159 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N LEU T 164 " --> pdb=" O ALA T 160 " (cutoff:3.500A) Processing helix chain 'T' and resid 168 through 171 removed outlier: 3.866A pdb=" N ILE T 171 " --> pdb=" O SER T 168 " (cutoff:3.500A) No H-bonds generated for 'chain 'T' and resid 168 through 171' Processing helix chain 'T' and resid 174 through 197 removed outlier: 4.662A pdb=" N ILE T 180 " --> pdb=" O SER T 176 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N SER T 183 " --> pdb=" O ASP T 179 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA T 184 " --> pdb=" O ILE T 180 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LEU T 195 " --> pdb=" O LYS T 191 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N SER T 196 " --> pdb=" O ASN T 192 " (cutoff:3.500A) Processing helix chain 'T' and resid 201 through 209 Processing helix chain 'T' and resid 213 through 224 removed outlier: 3.608A pdb=" N THR T 217 " --> pdb=" O ASN T 213 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N GLU T 218 " --> pdb=" O GLU T 214 " (cutoff:3.500A) Processing helix chain 'T' and resid 236 through 247 removed outlier: 3.608A pdb=" N LYS T 240 " --> pdb=" O ASN T 236 " (cutoff:3.500A) Processing helix chain 'T' and resid 258 through 271 removed outlier: 3.847A pdb=" N ILE T 270 " --> pdb=" O TYR T 266 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N GLU T 271 " --> pdb=" O ALA T 267 " (cutoff:3.500A) Processing helix chain 'X' and resid 118 through 131 removed outlier: 3.635A pdb=" N ILE X 126 " --> pdb=" O TYR X 122 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N ASN X 131 " --> pdb=" O GLY X 127 " (cutoff:3.500A) Processing helix chain 'Y' and resid 18 through 31 removed outlier: 3.507A pdb=" N GLU Y 22 " --> pdb=" O LYS Y 18 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER Y 28 " --> pdb=" O ILE Y 24 " (cutoff:3.500A) removed outlier: 4.928A pdb=" N LEU Y 29 " --> pdb=" O ASN Y 25 " (cutoff:3.500A) Processing helix chain 'Y' and resid 36 through 42 Processing helix chain 'Y' and resid 71 through 88 removed outlier: 3.890A pdb=" N LYS Y 85 " --> pdb=" O LEU Y 81 " (cutoff:3.500A) Processing helix chain 'Z' and resid 8 through 19 removed outlier: 3.541A pdb=" N GLU Z 14 " --> pdb=" O GLN Z 10 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ILE Z 18 " --> pdb=" O GLU Z 14 " (cutoff:3.500A) Processing helix chain 'Z' and resid 24 through 33 Processing helix chain 'Z' and resid 37 through 55 removed outlier: 3.863A pdb=" N ALA Z 43 " --> pdb=" O SER Z 39 " (cutoff:3.500A) removed outlier: 4.551A pdb=" N LYS Z 46 " --> pdb=" O ASP Z 42 " (cutoff:3.500A) removed outlier: 4.123A pdb=" N THR Z 47 " --> pdb=" O ALA Z 43 " (cutoff:3.500A) Processing helix chain 'Z' and resid 61 through 66 Processing helix chain 'Z' and resid 68 through 78 removed outlier: 3.651A pdb=" N GLU Z 73 " --> pdb=" O ASN Z 69 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ILE Z 75 " --> pdb=" O LEU Z 71 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N LYS Z 76 " --> pdb=" O LYS Z 72 " (cutoff:3.500A) Processing helix chain 'Z' and resid 85 through 91 removed outlier: 3.548A pdb=" N LEU Z 89 " --> pdb=" O VAL Z 85 " (cutoff:3.500A) Processing helix chain 'Z' and resid 91 through 104 removed outlier: 4.270A pdb=" N THR Z 95 " --> pdb=" O PHE Z 91 " (cutoff:3.500A) Proline residue: Z 97 - end of helix removed outlier: 3.865A pdb=" N ILE Z 102 " --> pdb=" O ASP Z 98 " (cutoff:3.500A) Processing helix chain 'Z' and resid 108 through 126 removed outlier: 3.640A pdb=" N ALA Z 116 " --> pdb=" O LYS Z 112 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N ASP Z 117 " --> pdb=" O SER Z 113 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N VAL Z 118 " --> pdb=" O SER Z 114 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ILE Z 121 " --> pdb=" O ASP Z 117 " (cutoff:3.500A) Processing helix chain 'Z' and resid 131 through 141 removed outlier: 3.769A pdb=" N LEU Z 139 " --> pdb=" O LEU Z 135 " (cutoff:3.500A) Processing helix chain 'Z' and resid 148 through 170 removed outlier: 5.610A pdb=" N ILE Z 154 " --> pdb=" O GLY Z 150 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N ARG Z 155 " --> pdb=" O HIS Z 151 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N HIS Z 156 " --> pdb=" O GLU Z 152 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU Z 160 " --> pdb=" O HIS Z 156 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE Z 161 " --> pdb=" O LEU Z 157 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLU Z 163 " --> pdb=" O LEU Z 159 " (cutoff:3.500A) removed outlier: 4.191A pdb=" N GLN Z 168 " --> pdb=" O VAL Z 164 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N VAL Z 169 " --> pdb=" O TYR Z 165 " (cutoff:3.500A) Processing helix chain 'Z' and resid 189 through 204 removed outlier: 3.560A pdb=" N ASP Z 199 " --> pdb=" O PHE Z 195 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ARG Z 202 " --> pdb=" O GLU Z 198 " (cutoff:3.500A) Processing helix chain 'Z' and resid 207 through 216 removed outlier: 3.950A pdb=" N LEU Z 212 " --> pdb=" O VAL Z 208 " (cutoff:3.500A) Processing helix chain 'Z' and resid 217 through 232 removed outlier: 3.962A pdb=" N VAL Z 221 " --> pdb=" O GLU Z 217 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N LEU Z 224 " --> pdb=" O ALA Z 220 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N GLU Z 226 " --> pdb=" O ASP Z 222 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N ILE Z 227 " --> pdb=" O LEU Z 223 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ILE Z 230 " --> pdb=" O GLU Z 226 " (cutoff:3.500A) Processing helix chain 'Z' and resid 237 through 252 removed outlier: 3.608A pdb=" N THR Z 241 " --> pdb=" O VAL Z 237 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N CYS Z 246 " --> pdb=" O PHE Z 242 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N CYS Z 252 " --> pdb=" O TYR Z 248 " (cutoff:3.500A) Processing helix chain 'Z' and resid 253 through 256 removed outlier: 3.588A pdb=" N LEU Z 256 " --> pdb=" O VAL Z 253 " (cutoff:3.500A) No H-bonds generated for 'chain 'Z' and resid 253 through 256' Processing helix chain 'Z' and resid 257 through 275 removed outlier: 3.516A pdb=" N ALA Z 263 " --> pdb=" O PRO Z 259 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N THR Z 267 " --> pdb=" O ALA Z 263 " (cutoff:3.500A) Processing helix chain 'Z' and resid 278 through 289 removed outlier: 3.816A pdb=" N ALA Z 283 " --> pdb=" O THR Z 279 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU Z 284 " --> pdb=" O ASP Z 280 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG Z 287 " --> pdb=" O ALA Z 283 " (cutoff:3.500A) Processing helix chain 'Z' and resid 290 through 303 removed outlier: 3.685A pdb=" N ILE Z 294 " --> pdb=" O GLU Z 290 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER Z 296 " --> pdb=" O ASP Z 292 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N VAL Z 297 " --> pdb=" O MET Z 293 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N THR Z 301 " --> pdb=" O VAL Z 297 " (cutoff:3.500A) Processing helix chain 'Z' and resid 310 through 321 Processing helix chain 'Z' and resid 325 through 332 removed outlier: 3.560A pdb=" N ILE Z 329 " --> pdb=" O GLY Z 325 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE Z 330 " --> pdb=" O VAL Z 326 " (cutoff:3.500A) Processing helix chain 'Z' and resid 333 through 339 Processing helix chain 'Z' and resid 342 through 350 removed outlier: 3.740A pdb=" N ASN Z 347 " --> pdb=" O ALA Z 343 " (cutoff:3.500A) Processing helix chain 'Z' and resid 351 through 366 removed outlier: 3.508A pdb=" N GLU Z 355 " --> pdb=" O PRO Z 351 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP Z 356 " --> pdb=" O LYS Z 352 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LYS Z 359 " --> pdb=" O GLU Z 355 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N SER Z 360 " --> pdb=" O ASP Z 356 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N ASN Z 364 " --> pdb=" O SER Z 360 " (cutoff:3.500A) Processing helix chain 'Z' and resid 376 through 391 removed outlier: 3.944A pdb=" N LEU Z 381 " --> pdb=" O ALA Z 377 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE Z 385 " --> pdb=" O LEU Z 381 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N GLY Z 388 " --> pdb=" O SER Z 384 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ASN Z 391 " --> pdb=" O ASN Z 387 " (cutoff:3.500A) Processing helix chain 'Z' and resid 397 through 403 removed outlier: 3.732A pdb=" N VAL Z 401 " --> pdb=" O ASP Z 397 " (cutoff:3.500A) Processing helix chain 'Z' and resid 403 through 409 removed outlier: 4.247A pdb=" N VAL Z 407 " --> pdb=" O ASN Z 403 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS Z 409 " --> pdb=" O ASN Z 405 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 424 removed outlier: 4.011A pdb=" N THR Z 416 " --> pdb=" O GLY Z 412 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N SER Z 424 " --> pdb=" O ALA Z 420 " (cutoff:3.500A) Processing helix chain 'Z' and resid 432 through 441 removed outlier: 4.118A pdb=" N LEU Z 436 " --> pdb=" O GLY Z 432 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS Z 438 " --> pdb=" O GLN Z 434 " (cutoff:3.500A) removed outlier: 4.301A pdb=" N TYR Z 439 " --> pdb=" O GLN Z 435 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N TYR Z 441 " --> pdb=" O ASP Z 437 " (cutoff:3.500A) Processing helix chain 'Z' and resid 444 through 459 removed outlier: 4.150A pdb=" N LYS Z 448 " --> pdb=" O GLU Z 444 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU Z 452 " --> pdb=" O LYS Z 448 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU Z 453 " --> pdb=" O ALA Z 449 " (cutoff:3.500A) Processing helix chain 'Z' and resid 460 through 462 No H-bonds generated for 'chain 'Z' and resid 460 through 462' Processing helix chain 'Z' and resid 469 through 480 removed outlier: 3.852A pdb=" N LEU Z 473 " --> pdb=" O PRO Z 469 " (cutoff:3.500A) removed outlier: 5.291A pdb=" N ASP Z 476 " --> pdb=" O LEU Z 472 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N TYR Z 477 " --> pdb=" O LEU Z 473 " (cutoff:3.500A) Processing helix chain 'Z' and resid 482 through 498 Processing helix chain 'Z' and resid 502 through 509 Processing helix chain 'Z' and resid 520 through 522 No H-bonds generated for 'chain 'Z' and resid 520 through 522' Processing helix chain 'Z' and resid 523 through 535 removed outlier: 4.313A pdb=" N SER Z 527 " --> pdb=" O ALA Z 523 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N LEU Z 530 " --> pdb=" O ALA Z 526 " (cutoff:3.500A) Processing helix chain 'Z' and resid 542 through 556 removed outlier: 3.648A pdb=" N ILE Z 546 " --> pdb=" O ILE Z 542 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N PHE Z 550 " --> pdb=" O ILE Z 546 " (cutoff:3.500A) Processing helix chain 'Z' and resid 559 through 574 removed outlier: 3.608A pdb=" N VAL Z 563 " --> pdb=" O LYS Z 559 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU Z 568 " --> pdb=" O ARG Z 564 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N GLY Z 571 " --> pdb=" O ALA Z 567 " (cutoff:3.500A) Processing helix chain 'Z' and resid 580 through 591 removed outlier: 3.770A pdb=" N VAL Z 584 " --> pdb=" O GLN Z 580 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N GLU Z 586 " --> pdb=" O ASP Z 582 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR Z 587 " --> pdb=" O ASP Z 583 " (cutoff:3.500A) removed outlier: 4.439A pdb=" N ILE Z 591 " --> pdb=" O THR Z 587 " (cutoff:3.500A) Processing helix chain 'Z' and resid 593 through 609 removed outlier: 3.691A pdb=" N ALA Z 598 " --> pdb=" O PRO Z 594 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N ILE Z 599 " --> pdb=" O MET Z 595 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N VAL Z 601 " --> pdb=" O SER Z 597 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N LEU Z 602 " --> pdb=" O ALA Z 598 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N SER Z 605 " --> pdb=" O VAL Z 601 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N CYS Z 606 " --> pdb=" O LEU Z 602 " (cutoff:3.500A) Processing helix chain 'Z' and resid 613 through 635 removed outlier: 4.153A pdb=" N ILE Z 617 " --> pdb=" O ASP Z 613 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N LEU Z 620 " --> pdb=" O LEU Z 616 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N ARG Z 623 " --> pdb=" O ASP Z 619 " (cutoff:3.500A) Proline residue: Z 626 - end of helix removed outlier: 3.914A pdb=" N LYS Z 630 " --> pdb=" O PRO Z 626 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N GLU Z 633 " --> pdb=" O VAL Z 629 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N ALA Z 635 " --> pdb=" O GLY Z 631 " (cutoff:3.500A) Processing helix chain 'Z' and resid 701 through 727 removed outlier: 3.689A pdb=" N ASP Z 712 " --> pdb=" O GLY Z 708 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LYS Z 713 " --> pdb=" O LYS Z 709 " (cutoff:3.500A) Processing helix chain 'Z' and resid 730 through 750 removed outlier: 4.158A pdb=" N ASP Z 734 " --> pdb=" O ALA Z 730 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU Z 736 " --> pdb=" O ILE Z 732 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ALA Z 737 " --> pdb=" O VAL Z 733 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU Z 748 " --> pdb=" O ALA Z 744 " (cutoff:3.500A) Processing helix chain 'Z' and resid 750 through 769 removed outlier: 3.718A pdb=" N LYS Z 754 " --> pdb=" O GLU Z 750 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU Z 755 " --> pdb=" O ASP Z 751 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N MET Z 756 " --> pdb=" O ILE Z 752 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ARG Z 759 " --> pdb=" O GLU Z 755 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N GLY Z 762 " --> pdb=" O LEU Z 758 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N HIS Z 763 " --> pdb=" O ARG Z 759 " (cutoff:3.500A) Processing helix chain 'Z' and resid 774 through 787 removed outlier: 4.249A pdb=" N LEU Z 778 " --> pdb=" O ARG Z 774 " (cutoff:3.500A) removed outlier: 3.795A pdb=" N ILE Z 782 " --> pdb=" O LEU Z 778 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N VAL Z 783 " --> pdb=" O ALA Z 779 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N SER Z 786 " --> pdb=" O ILE Z 782 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ASP Z 787 " --> pdb=" O VAL Z 783 " (cutoff:3.500A) Processing helix chain 'Z' and resid 790 through 801 removed outlier: 4.363A pdb=" N ASP Z 794 " --> pdb=" O MET Z 790 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N THR Z 795 " --> pdb=" O LYS Z 791 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ARG Z 798 " --> pdb=" O ASP Z 794 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N PHE Z 799 " --> pdb=" O THR Z 795 " (cutoff:3.500A) Processing helix chain 'Z' and resid 807 through 822 removed outlier: 3.527A pdb=" N SER Z 811 " --> pdb=" O VAL Z 807 " (cutoff:3.500A) removed outlier: 3.979A pdb=" N PHE Z 813 " --> pdb=" O MET Z 809 " (cutoff:3.500A) removed outlier: 4.163A pdb=" N CYS Z 818 " --> pdb=" O ALA Z 814 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY Z 819 " --> pdb=" O MET Z 815 " (cutoff:3.500A) Processing helix chain 'Z' and resid 825 through 839 removed outlier: 3.969A pdb=" N LEU Z 831 " --> pdb=" O LEU Z 827 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ARG Z 832 " --> pdb=" O ALA Z 828 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N TYR Z 837 " --> pdb=" O GLN Z 833 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N SER Z 839 " --> pdb=" O ALA Z 835 " (cutoff:3.500A) Processing helix chain 'Z' and resid 863 through 869 removed outlier: 3.691A pdb=" N ASP Z 869 " --> pdb=" O ASP Z 865 " (cutoff:3.500A) Processing helix chain 'Z' and resid 875 through 882 removed outlier: 3.766A pdb=" N SER Z 880 " --> pdb=" O VAL Z 876 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ILE Z 881 " --> pdb=" O THR Z 877 " (cutoff:3.500A) Processing helix chain 'Z' and resid 947 through 950 Processing helix chain 'N' and resid 6 through 13 removed outlier: 3.560A pdb=" N LEU N 13 " --> pdb=" O LEU N 9 " (cutoff:3.500A) Processing helix chain 'N' and resid 17 through 29 removed outlier: 3.516A pdb=" N GLU N 26 " --> pdb=" O THR N 22 " (cutoff:3.500A) Processing helix chain 'N' and resid 31 through 36 Processing helix chain 'N' and resid 37 through 52 removed outlier: 4.089A pdb=" N ASN N 41 " --> pdb=" O SER N 37 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N GLU N 42 " --> pdb=" O GLU N 38 " (cutoff:3.500A) Proline residue: N 44 - end of helix Processing helix chain 'N' and resid 57 through 73 Processing helix chain 'N' and resid 74 through 86 removed outlier: 3.629A pdb=" N ALA N 78 " --> pdb=" O GLU N 74 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N LYS N 86 " --> pdb=" O ALA N 82 " (cutoff:3.500A) Processing helix chain 'N' and resid 88 through 94 removed outlier: 4.069A pdb=" N ASP N 92 " --> pdb=" O ARG N 88 " (cutoff:3.500A) Processing helix chain 'N' and resid 99 through 118 removed outlier: 3.666A pdb=" N GLN N 111 " --> pdb=" O GLU N 107 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU N 112 " --> pdb=" O MET N 108 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N THR N 118 " --> pdb=" O SER N 114 " (cutoff:3.500A) Processing helix chain 'N' and resid 130 through 147 removed outlier: 3.577A pdb=" N GLU N 138 " --> pdb=" O THR N 134 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE N 141 " --> pdb=" O PHE N 137 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N CYS N 144 " --> pdb=" O MET N 140 " (cutoff:3.500A) Processing helix chain 'N' and resid 149 through 160 removed outlier: 4.041A pdb=" N ALA N 153 " --> pdb=" O GLU N 149 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA N 157 " --> pdb=" O ALA N 153 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLU N 159 " --> pdb=" O GLY N 155 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N GLY N 160 " --> pdb=" O ILE N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 162 through 173 removed outlier: 3.764A pdb=" N ILE N 166 " --> pdb=" O ARG N 162 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LYS N 173 " --> pdb=" O ALA N 169 " (cutoff:3.500A) Processing helix chain 'N' and resid 178 through 196 removed outlier: 3.548A pdb=" N LYS N 184 " --> pdb=" O SER N 180 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N LEU N 189 " --> pdb=" O ILE N 185 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N THR N 196 " --> pdb=" O LEU N 192 " (cutoff:3.500A) Processing helix chain 'N' and resid 199 through 216 removed outlier: 3.689A pdb=" N LEU N 214 " --> pdb=" O SER N 210 " (cutoff:3.500A) Processing helix chain 'N' and resid 222 through 233 removed outlier: 3.693A pdb=" N LYS N 227 " --> pdb=" O LEU N 223 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N VAL N 228 " --> pdb=" O THR N 224 " (cutoff:3.500A) Processing helix chain 'N' and resid 234 through 245 removed outlier: 3.954A pdb=" N ALA N 238 " --> pdb=" O ASP N 234 " (cutoff:3.500A) Processing helix chain 'N' and resid 250 through 265 removed outlier: 3.794A pdb=" N SER N 263 " --> pdb=" O PHE N 259 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N SER N 264 " --> pdb=" O ASP N 260 " (cutoff:3.500A) Processing helix chain 'N' and resid 266 through 281 removed outlier: 3.910A pdb=" N THR N 275 " --> pdb=" O GLU N 271 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ALA N 279 " --> pdb=" O THR N 275 " (cutoff:3.500A) Processing helix chain 'N' and resid 283 through 291 removed outlier: 3.982A pdb=" N LEU N 287 " --> pdb=" O ASP N 283 " (cutoff:3.500A) Processing helix chain 'N' and resid 292 through 306 Processing helix chain 'N' and resid 311 through 321 Processing helix chain 'N' and resid 325 through 340 removed outlier: 3.814A pdb=" N VAL N 332 " --> pdb=" O PHE N 328 " (cutoff:3.500A) Processing helix chain 'N' and resid 346 through 352 Processing helix chain 'N' and resid 352 through 358 removed outlier: 3.633A pdb=" N LEU N 356 " --> pdb=" O ASN N 352 " (cutoff:3.500A) Processing helix chain 'N' and resid 360 through 370 removed outlier: 3.504A pdb=" N LYS N 364 " --> pdb=" O GLN N 360 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N PHE N 365 " --> pdb=" O ASN N 361 " (cutoff:3.500A) Processing helix chain 'N' and resid 370 through 375 Processing helix chain 'N' and resid 381 through 387 removed outlier: 4.053A pdb=" N MET N 386 " --> pdb=" O GLY N 382 " (cutoff:3.500A) Processing helix chain 'N' and resid 388 through 390 No H-bonds generated for 'chain 'N' and resid 388 through 390' Processing helix chain 'N' and resid 397 through 412 removed outlier: 3.784A pdb=" N LYS N 401 " --> pdb=" O SER N 397 " (cutoff:3.500A) removed outlier: 4.276A pdb=" N LEU N 405 " --> pdb=" O LYS N 401 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TYR N 406 " --> pdb=" O GLY N 402 " (cutoff:3.500A) Processing helix chain 'N' and resid 416 through 431 removed outlier: 3.661A pdb=" N ASP N 421 " --> pdb=" O ARG N 417 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TYR N 422 " --> pdb=" O ASP N 418 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ASN N 425 " --> pdb=" O ASP N 421 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ILE N 426 " --> pdb=" O TYR N 422 " (cutoff:3.500A) Processing helix chain 'N' and resid 436 through 454 removed outlier: 3.709A pdb=" N ASP N 440 " --> pdb=" O ASP N 436 " (cutoff:3.500A) Processing helix chain 'N' and resid 459 through 473 removed outlier: 3.515A pdb=" N VAL N 469 " --> pdb=" O ALA N 465 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU N 470 " --> pdb=" O LEU N 466 " (cutoff:3.500A) Processing helix chain 'N' and resid 474 through 490 removed outlier: 4.002A pdb=" N GLU N 479 " --> pdb=" O ALA N 475 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ALA N 480 " --> pdb=" O THR N 476 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU N 483 " --> pdb=" O GLU N 479 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N GLY N 486 " --> pdb=" O ALA N 482 " (cutoff:3.500A) Processing helix chain 'N' and resid 494 through 508 removed outlier: 3.514A pdb=" N HIS N 499 " --> pdb=" O PRO N 495 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N GLN N 506 " --> pdb=" O PHE N 502 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N GLU N 507 " --> pdb=" O THR N 503 " (cutoff:3.500A) Processing helix chain 'N' and resid 510 through 525 removed outlier: 3.650A pdb=" N VAL N 519 " --> pdb=" O ARG N 515 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA N 522 " --> pdb=" O ALA N 518 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ASN N 525 " --> pdb=" O LEU N 521 " (cutoff:3.500A) Processing helix chain 'N' and resid 528 through 531 Processing helix chain 'N' and resid 532 through 542 removed outlier: 3.612A pdb=" N THR N 537 " --> pdb=" O ASP N 533 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS N 538 " --> pdb=" O ASP N 534 " (cutoff:3.500A) Processing helix chain 'N' and resid 544 through 559 removed outlier: 4.009A pdb=" N PHE N 553 " --> pdb=" O TYR N 549 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ILE N 555 " --> pdb=" O GLY N 551 " (cutoff:3.500A) Processing helix chain 'N' and resid 564 through 578 removed outlier: 3.616A pdb=" N VAL N 568 " --> pdb=" O ASN N 564 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU N 571 " --> pdb=" O ALA N 567 " (cutoff:3.500A) Processing helix chain 'N' and resid 580 through 595 removed outlier: 3.779A pdb=" N VAL N 588 " --> pdb=" O ARG N 584 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N LEU N 591 " --> pdb=" O ALA N 587 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N GLY N 592 " --> pdb=" O VAL N 588 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE N 593 " --> pdb=" O ILE N 589 " (cutoff:3.500A) removed outlier: 3.871A pdb=" N VAL N 594 " --> pdb=" O ALA N 590 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N LEU N 595 " --> pdb=" O LEU N 591 " (cutoff:3.500A) Processing helix chain 'N' and resid 601 through 610 removed outlier: 3.566A pdb=" N GLN N 607 " --> pdb=" O PRO N 603 " (cutoff:3.500A) removed outlier: 4.438A pdb=" N LEU N 608 " --> pdb=" O ARG N 604 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N LEU N 609 " --> pdb=" O ILE N 605 " (cutoff:3.500A) Processing helix chain 'N' and resid 614 through 629 removed outlier: 3.773A pdb=" N ALA N 622 " --> pdb=" O ARG N 618 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N PHE N 623 " --> pdb=" O CYS N 619 " (cutoff:3.500A) Processing helix chain 'N' and resid 634 through 646 removed outlier: 3.672A pdb=" N ILE N 638 " --> pdb=" O LEU N 634 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP N 639 " --> pdb=" O GLN N 635 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N VAL N 640 " --> pdb=" O SER N 636 " (cutoff:3.500A) Proline residue: N 643 - end of helix removed outlier: 4.091A pdb=" N LYS N 646 " --> pdb=" O ASP N 642 " (cutoff:3.500A) Processing helix chain 'N' and resid 649 through 665 removed outlier: 3.569A pdb=" N MET N 662 " --> pdb=" O ILE N 658 " (cutoff:3.500A) Processing helix chain 'N' and resid 672 through 688 removed outlier: 4.111A pdb=" N ALA N 676 " --> pdb=" O ASN N 672 " (cutoff:3.500A) Processing helix chain 'N' and resid 692 through 707 removed outlier: 3.734A pdb=" N GLY N 704 " --> pdb=" O CYS N 700 " (cutoff:3.500A) Processing helix chain 'N' and resid 726 through 737 removed outlier: 3.872A pdb=" N MET N 735 " --> pdb=" O VAL N 731 " (cutoff:3.500A) Processing helix chain 'N' and resid 742 through 751 removed outlier: 3.830A pdb=" N LEU N 745 " --> pdb=" O TRP N 742 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N ALA N 746 " --> pdb=" O PHE N 743 " (cutoff:3.500A) Processing helix chain 'N' and resid 789 through 819 removed outlier: 3.625A pdb=" N GLY N 793 " --> pdb=" O GLU N 789 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N GLU N 797 " --> pdb=" O GLY N 793 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU N 804 " --> pdb=" O ALA N 800 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N SER N 805 " --> pdb=" O THR N 801 " (cutoff:3.500A) removed outlier: 4.492A pdb=" N LYS N 811 " --> pdb=" O THR N 807 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N ARG N 813 " --> pdb=" O ARG N 809 " (cutoff:3.500A) removed outlier: 5.460A pdb=" N ALA N 814 " --> pdb=" O ALA N 810 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N LYS N 818 " --> pdb=" O ALA N 814 " (cutoff:3.500A) Processing helix chain 'N' and resid 820 through 822 No H-bonds generated for 'chain 'N' and resid 820 through 822' Processing helix chain 'N' and resid 875 through 880 removed outlier: 3.968A pdb=" N ARG N 880 " --> pdb=" O PRO N 876 " (cutoff:3.500A) Processing helix chain 'N' and resid 919 through 925 Processing helix chain 'S' and resid 19 through 42 removed outlier: 3.825A pdb=" N SER S 42 " --> pdb=" O LEU S 38 " (cutoff:3.500A) Processing helix chain 'S' and resid 47 through 65 Processing helix chain 'S' and resid 71 through 79 Processing helix chain 'S' and resid 84 through 96 Processing helix chain 'S' and resid 119 through 126 removed outlier: 3.590A pdb=" N GLU S 124 " --> pdb=" O SER S 120 " (cutoff:3.500A) Processing helix chain 'S' and resid 130 through 150 removed outlier: 4.496A pdb=" N ILE S 134 " --> pdb=" O VAL S 130 " (cutoff:3.500A) Processing helix chain 'S' and resid 152 through 170 removed outlier: 3.509A pdb=" N VAL S 156 " --> pdb=" O LEU S 152 " (cutoff:3.500A) Proline residue: S 165 - end of helix removed outlier: 3.633A pdb=" N TYR S 170 " --> pdb=" O ASN S 166 " (cutoff:3.500A) Processing helix chain 'S' and resid 173 through 198 removed outlier: 3.528A pdb=" N ILE S 179 " --> pdb=" O SER S 175 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ALA S 181 " --> pdb=" O ASN S 177 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS S 182 " --> pdb=" O LEU S 178 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LEU S 183 " --> pdb=" O ILE S 179 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N PHE S 185 " --> pdb=" O ALA S 181 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TYR S 186 " --> pdb=" O LYS S 182 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N HIS S 191 " --> pdb=" O ILE S 187 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N SER S 198 " --> pdb=" O LEU S 194 " (cutoff:3.500A) Processing helix chain 'S' and resid 200 through 225 removed outlier: 3.960A pdb=" N ASP S 204 " --> pdb=" O GLU S 200 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASN S 205 " --> pdb=" O ILE S 201 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N ILE S 208 " --> pdb=" O ASP S 204 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ILE S 209 " --> pdb=" O ASN S 205 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N MET S 214 " --> pdb=" O LEU S 210 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE S 220 " --> pdb=" O LYS S 216 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU S 223 " --> pdb=" O LYS S 219 " (cutoff:3.500A) Processing helix chain 'S' and resid 226 through 244 removed outlier: 3.595A pdb=" N ASN S 244 " --> pdb=" O ASP S 240 " (cutoff:3.500A) Processing helix chain 'S' and resid 246 through 255 removed outlier: 3.550A pdb=" N ASP S 252 " --> pdb=" O ASP S 248 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N SER S 255 " --> pdb=" O SER S 251 " (cutoff:3.500A) Processing helix chain 'S' and resid 265 through 283 removed outlier: 3.694A pdb=" N GLU S 269 " --> pdb=" O SER S 265 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLN S 283 " --> pdb=" O ILE S 279 " (cutoff:3.500A) Processing helix chain 'S' and resid 286 through 300 removed outlier: 4.144A pdb=" N GLU S 291 " --> pdb=" O SER S 287 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N TYR S 292 " --> pdb=" O THR S 288 " (cutoff:3.500A) Processing helix chain 'S' and resid 306 through 325 removed outlier: 3.786A pdb=" N GLN S 312 " --> pdb=" O GLY S 308 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N CYS S 319 " --> pdb=" O LYS S 315 " (cutoff:3.500A) Processing helix chain 'S' and resid 329 through 335 removed outlier: 4.178A pdb=" N PHE S 333 " --> pdb=" O GLU S 329 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N GLN S 335 " --> pdb=" O SER S 331 " (cutoff:3.500A) Processing helix chain 'S' and resid 342 through 355 removed outlier: 3.511A pdb=" N LEU S 348 " --> pdb=" O PRO S 344 " (cutoff:3.500A) Processing helix chain 'S' and resid 356 through 367 removed outlier: 3.669A pdb=" N PHE S 360 " --> pdb=" O ASP S 356 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR S 361 " --> pdb=" O LEU S 357 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N SER S 362 " --> pdb=" O LYS S 358 " (cutoff:3.500A) Processing helix chain 'S' and resid 367 through 374 removed outlier: 3.915A pdb=" N ASP S 374 " --> pdb=" O LEU S 370 " (cutoff:3.500A) Processing helix chain 'S' and resid 376 through 399 removed outlier: 3.748A pdb=" N ARG S 382 " --> pdb=" O GLN S 378 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU S 383 " --> pdb=" O LEU S 379 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N ARG S 384 " --> pdb=" O CYS S 380 " (cutoff:3.500A) removed outlier: 4.929A pdb=" N SER S 385 " --> pdb=" O VAL S 381 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N ASN S 386 " --> pdb=" O ARG S 382 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N ILE S 388 " --> pdb=" O ARG S 384 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE S 395 " --> pdb=" O GLY S 391 " (cutoff:3.500A) Processing helix chain 'S' and resid 404 through 411 Processing helix chain 'S' and resid 415 through 427 removed outlier: 3.668A pdb=" N VAL S 423 " --> pdb=" O VAL S 419 " (cutoff:3.500A) Processing helix chain 'S' and resid 455 through 489 removed outlier: 4.168A pdb=" N GLN S 459 " --> pdb=" O GLU S 455 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N GLU S 463 " --> pdb=" O GLN S 459 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ARG S 464 " --> pdb=" O VAL S 460 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASP S 473 " --> pdb=" O ASN S 469 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ARG S 480 " --> pdb=" O LEU S 476 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N TYR S 481 " --> pdb=" O VAL S 477 " (cutoff:3.500A) Proline residue: S 482 - end of helix removed outlier: 3.707A pdb=" N LYS S 485 " --> pdb=" O TYR S 481 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS S 486 " --> pdb=" O PRO S 482 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 20 Processing helix chain 'P' and resid 20 through 31 removed outlier: 3.951A pdb=" N GLN P 29 " --> pdb=" O ASP P 25 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N ASN P 30 " --> pdb=" O SER P 26 " (cutoff:3.500A) Processing helix chain 'P' and resid 31 through 43 removed outlier: 3.701A pdb=" N ALA P 35 " --> pdb=" O ASP P 31 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N GLU P 43 " --> pdb=" O LEU P 39 " (cutoff:3.500A) Processing helix chain 'P' and resid 47 through 68 removed outlier: 3.528A pdb=" N ALA P 53 " --> pdb=" O ALA P 49 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N GLU P 57 " --> pdb=" O ALA P 53 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP P 64 " --> pdb=" O ALA P 60 " (cutoff:3.500A) Processing helix chain 'P' and resid 71 through 86 removed outlier: 3.987A pdb=" N LEU P 75 " --> pdb=" O LYS P 71 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN P 76 " --> pdb=" O TRP P 72 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N GLU P 77 " --> pdb=" O ASP P 73 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N SER P 83 " --> pdb=" O LEU P 79 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N HIS P 86 " --> pdb=" O LEU P 82 " (cutoff:3.500A) Processing helix chain 'P' and resid 91 through 108 removed outlier: 3.983A pdb=" N TYR P 95 " --> pdb=" O LEU P 91 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N MET P 96 " --> pdb=" O SER P 92 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N GLN P 98 " --> pdb=" O GLN P 94 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU P 104 " --> pdb=" O VAL P 100 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LYS P 105 " --> pdb=" O MET P 101 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N SER P 106 " --> pdb=" O GLU P 102 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS P 108 " --> pdb=" O LEU P 104 " (cutoff:3.500A) Processing helix chain 'P' and resid 110 through 126 Processing helix chain 'P' and resid 131 through 150 removed outlier: 3.781A pdb=" N GLU P 135 " --> pdb=" O PHE P 131 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N ASP P 142 " --> pdb=" O ARG P 138 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLU P 149 " --> pdb=" O GLU P 145 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N GLU P 150 " --> pdb=" O ILE P 146 " (cutoff:3.500A) Processing helix chain 'P' and resid 152 through 164 removed outlier: 3.891A pdb=" N GLN P 164 " --> pdb=" O LEU P 160 " (cutoff:3.500A) Processing helix chain 'P' and resid 172 through 191 removed outlier: 3.530A pdb=" N SER P 187 " --> pdb=" O GLN P 183 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU P 189 " --> pdb=" O GLU P 185 " (cutoff:3.500A) Processing helix chain 'P' and resid 192 through 201 removed outlier: 3.617A pdb=" N ALA P 196 " --> pdb=" O ASP P 192 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N VAL P 198 " --> pdb=" O SER P 194 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ARG P 201 " --> pdb=" O THR P 197 " (cutoff:3.500A) Processing helix chain 'P' and resid 204 through 209 removed outlier: 3.827A pdb=" N PHE P 208 " --> pdb=" O LEU P 204 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N LYS P 209 " --> pdb=" O LYS P 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 204 through 209' Processing helix chain 'P' and resid 210 through 212 No H-bonds generated for 'chain 'P' and resid 210 through 212' Processing helix chain 'P' and resid 213 through 231 removed outlier: 3.652A pdb=" N LEU P 218 " --> pdb=" O GLU P 214 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLU P 219 " --> pdb=" O SER P 215 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS P 231 " --> pdb=" O ILE P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 233 through 246 removed outlier: 3.612A pdb=" N GLU P 243 " --> pdb=" O GLN P 239 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE P 244 " --> pdb=" O TYR P 240 " (cutoff:3.500A) Processing helix chain 'P' and resid 247 through 253 removed outlier: 3.533A pdb=" N ASP P 253 " --> pdb=" O ALA P 249 " (cutoff:3.500A) Processing helix chain 'P' and resid 253 through 271 Proline residue: P 259 - end of helix removed outlier: 3.633A pdb=" N SER P 262 " --> pdb=" O LYS P 258 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N LEU P 270 " --> pdb=" O TYR P 266 " (cutoff:3.500A) Processing helix chain 'P' and resid 274 through 287 removed outlier: 3.558A pdb=" N ASP P 279 " --> pdb=" O ASN P 275 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LYS P 283 " --> pdb=" O ASP P 279 " (cutoff:3.500A) Processing helix chain 'P' and resid 287 through 293 removed outlier: 3.856A pdb=" N LYS P 291 " --> pdb=" O ASP P 287 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N LYS P 292 " --> pdb=" O ASN P 288 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N LEU P 293 " --> pdb=" O ASN P 289 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 287 through 293' Processing helix chain 'P' and resid 294 through 305 removed outlier: 3.799A pdb=" N LEU P 299 " --> pdb=" O SER P 295 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LEU P 302 " --> pdb=" O SER P 298 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N PHE P 303 " --> pdb=" O LEU P 299 " (cutoff:3.500A) Processing helix chain 'P' and resid 310 through 323 removed outlier: 3.672A pdb=" N VAL P 314 " --> pdb=" O ARG P 310 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS P 316 " --> pdb=" O PRO P 312 " (cutoff:3.500A) Proline residue: P 320 - end of helix Processing helix chain 'P' and resid 334 through 339 removed outlier: 3.515A pdb=" N GLU P 339 " --> pdb=" O LYS P 335 " (cutoff:3.500A) Processing helix chain 'P' and resid 340 through 356 removed outlier: 3.569A pdb=" N ARG P 351 " --> pdb=" O GLU P 347 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N GLU P 355 " --> pdb=" O ARG P 351 " (cutoff:3.500A) Processing helix chain 'P' and resid 362 through 370 Processing helix chain 'P' and resid 372 through 387 removed outlier: 3.509A pdb=" N SER P 381 " --> pdb=" O GLU P 377 " (cutoff:3.500A) Processing helix chain 'P' and resid 407 through 440 removed outlier: 3.715A pdb=" N LEU P 411 " --> pdb=" O ASN P 407 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TRP P 415 " --> pdb=" O LEU P 411 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASP P 420 " --> pdb=" O SER P 416 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N GLU P 427 " --> pdb=" O LEU P 423 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR P 434 " --> pdb=" O GLY P 430 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LYS P 435 " --> pdb=" O HIS P 431 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLU P 436 " --> pdb=" O LEU P 432 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N GLU P 437 " --> pdb=" O ILE P 433 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE P 438 " --> pdb=" O THR P 434 " (cutoff:3.500A) Processing helix chain 'Q' and resid 2 through 16 Processing helix chain 'Q' and resid 19 through 39 removed outlier: 3.885A pdb=" N ALA Q 23 " --> pdb=" O GLN Q 19 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLN Q 25 " --> pdb=" O ASN Q 21 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N VAL Q 26 " --> pdb=" O GLU Q 22 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N SER Q 29 " --> pdb=" O GLN Q 25 " (cutoff:3.500A) Processing helix chain 'Q' and resid 50 through 65 removed outlier: 3.856A pdb=" N TYR Q 65 " --> pdb=" O LEU Q 61 " (cutoff:3.500A) Processing helix chain 'Q' and resid 71 through 89 removed outlier: 3.652A pdb=" N GLU Q 76 " --> pdb=" O ASP Q 72 " (cutoff:3.500A) Proline residue: Q 79 - end of helix removed outlier: 3.556A pdb=" N THR Q 82 " --> pdb=" O ILE Q 78 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N GLU Q 83 " --> pdb=" O PRO Q 79 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N ALA Q 89 " --> pdb=" O MET Q 85 " (cutoff:3.500A) Processing helix chain 'Q' and resid 92 through 107 Processing helix chain 'Q' and resid 109 through 127 removed outlier: 4.166A pdb=" N ASP Q 113 " --> pdb=" O ASP Q 109 " (cutoff:3.500A) Processing helix chain 'Q' and resid 130 through 149 removed outlier: 3.647A pdb=" N SER Q 136 " --> pdb=" O PHE Q 132 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N LYS Q 149 " --> pdb=" O HIS Q 145 " (cutoff:3.500A) Processing helix chain 'Q' and resid 150 through 165 removed outlier: 3.611A pdb=" N ASP Q 160 " --> pdb=" O ALA Q 156 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU Q 162 " --> pdb=" O ILE Q 158 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLU Q 164 " --> pdb=" O ASP Q 160 " (cutoff:3.500A) Processing helix chain 'Q' and resid 171 through 173 No H-bonds generated for 'chain 'Q' and resid 171 through 173' Processing helix chain 'Q' and resid 174 through 188 removed outlier: 3.721A pdb=" N LYS Q 187 " --> pdb=" O LYS Q 183 " (cutoff:3.500A) Processing helix chain 'Q' and resid 191 through 204 Processing helix chain 'Q' and resid 211 through 229 removed outlier: 3.582A pdb=" N LEU Q 225 " --> pdb=" O MET Q 221 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N GLU Q 228 " --> pdb=" O ILE Q 224 " (cutoff:3.500A) Processing helix chain 'Q' and resid 231 through 249 removed outlier: 3.862A pdb=" N ALA Q 235 " --> pdb=" O ASP Q 231 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N PHE Q 236 " --> pdb=" O TYR Q 232 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N SER Q 237 " --> pdb=" O LYS Q 233 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN Q 248 " --> pdb=" O GLU Q 244 " (cutoff:3.500A) Processing helix chain 'Q' and resid 254 through 273 removed outlier: 3.615A pdb=" N SER Q 268 " --> pdb=" O TYR Q 264 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N LYS Q 269 " --> pdb=" O MET Q 265 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE Q 270 " --> pdb=" O LEU Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 275 through 282 removed outlier: 3.716A pdb=" N LYS Q 279 " --> pdb=" O ILE Q 275 " (cutoff:3.500A) Processing helix chain 'Q' and resid 293 through 309 removed outlier: 3.524A pdb=" N ASP Q 297 " --> pdb=" O SER Q 293 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N ALA Q 301 " --> pdb=" O ASP Q 297 " (cutoff:3.500A) Processing helix chain 'Q' and resid 310 through 321 removed outlier: 3.757A pdb=" N PHE Q 314 " --> pdb=" O SER Q 310 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLN Q 320 " --> pdb=" O THR Q 316 " (cutoff:3.500A) Processing helix chain 'Q' and resid 321 through 328 removed outlier: 3.558A pdb=" N ASP Q 328 " --> pdb=" O GLU Q 324 " (cutoff:3.500A) Processing helix chain 'Q' and resid 328 through 352 removed outlier: 3.562A pdb=" N HIS Q 334 " --> pdb=" O LEU Q 330 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ALA Q 337 " --> pdb=" O SER Q 333 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLU Q 344 " --> pdb=" O ASP Q 340 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N SER Q 345 " --> pdb=" O THR Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 359 through 367 removed outlier: 3.680A pdb=" N ILE Q 365 " --> pdb=" O HIS Q 361 " (cutoff:3.500A) Processing helix chain 'Q' and resid 369 through 384 removed outlier: 3.755A pdb=" N LEU Q 382 " --> pdb=" O SER Q 378 " (cutoff:3.500A) Processing helix chain 'Q' and resid 406 through 430 removed outlier: 3.535A pdb=" N ASP Q 410 " --> pdb=" O ASP Q 406 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N GLU Q 414 " --> pdb=" O ASP Q 410 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N LYS Q 421 " --> pdb=" O GLY Q 417 " (cutoff:3.500A) Processing helix chain 'Q' and resid 431 through 433 No H-bonds generated for 'chain 'Q' and resid 431 through 433' Processing helix chain 'R' and resid 21 through 35 removed outlier: 5.193A pdb=" N SER R 27 " --> pdb=" O ASN R 23 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N LEU R 32 " --> pdb=" O GLU R 28 " (cutoff:3.500A) Processing helix chain 'R' and resid 39 through 58 removed outlier: 3.786A pdb=" N GLU R 48 " --> pdb=" O LYS R 44 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N PHE R 49 " --> pdb=" O GLU R 45 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LYS R 53 " --> pdb=" O PHE R 49 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS R 55 " --> pdb=" O LEU R 51 " (cutoff:3.500A) Processing helix chain 'R' and resid 59 through 70 removed outlier: 3.515A pdb=" N LYS R 64 " --> pdb=" O ALA R 60 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N TYR R 65 " --> pdb=" O PRO R 61 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N GLU R 68 " --> pdb=" O LYS R 64 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N GLU R 69 " --> pdb=" O TYR R 65 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 123 Processing helix chain 'R' and resid 128 through 145 removed outlier: 3.664A pdb=" N ILE R 144 " --> pdb=" O TYR R 140 " (cutoff:3.500A) Processing helix chain 'R' and resid 146 through 160 removed outlier: 3.971A pdb=" N ALA R 150 " --> pdb=" O ASP R 146 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N LYS R 152 " --> pdb=" O ASP R 148 " (cutoff:3.500A) Processing helix chain 'R' and resid 163 through 182 removed outlier: 4.035A pdb=" N THR R 173 " --> pdb=" O ASP R 169 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE R 174 " --> pdb=" O VAL R 170 " (cutoff:3.500A) Processing helix chain 'R' and resid 184 through 202 removed outlier: 3.921A pdb=" N LYS R 190 " --> pdb=" O TYR R 186 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA R 193 " --> pdb=" O GLU R 189 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N SER R 196 " --> pdb=" O GLU R 192 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N GLU R 199 " --> pdb=" O ASN R 195 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS R 200 " --> pdb=" O SER R 196 " (cutoff:3.500A) Processing helix chain 'R' and resid 203 through 221 removed outlier: 3.527A pdb=" N ARG R 207 " --> pdb=" O ASP R 203 " (cutoff:3.500A) Processing helix chain 'R' and resid 224 through 237 removed outlier: 3.855A pdb=" N LYS R 229 " --> pdb=" O LYS R 225 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ASP R 233 " --> pdb=" O LYS R 229 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N ALA R 236 " --> pdb=" O VAL R 232 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N THR R 237 " --> pdb=" O ASP R 233 " (cutoff:3.500A) Processing helix chain 'R' and resid 245 through 261 removed outlier: 3.710A pdb=" N PHE R 259 " --> pdb=" O VAL R 255 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 270 Processing helix chain 'R' and resid 273 through 280 removed outlier: 3.645A pdb=" N LEU R 277 " --> pdb=" O SER R 273 " (cutoff:3.500A) Processing helix chain 'R' and resid 283 through 298 Processing helix chain 'R' and resid 303 through 315 removed outlier: 3.701A pdb=" N TYR R 312 " --> pdb=" O LEU R 308 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ALA R 313 " --> pdb=" O LEU R 309 " (cutoff:3.500A) Processing helix chain 'R' and resid 320 through 324 removed outlier: 4.071A pdb=" N ARG R 324 " --> pdb=" O TYR R 321 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 345 removed outlier: 3.560A pdb=" N TYR R 338 " --> pdb=" O ARG R 334 " (cutoff:3.500A) removed outlier: 3.880A pdb=" N SER R 344 " --> pdb=" O GLN R 340 " (cutoff:3.500A) Processing helix chain 'R' and resid 350 through 358 Processing helix chain 'R' and resid 360 through 372 removed outlier: 3.505A pdb=" N ASN R 366 " --> pdb=" O ALA R 362 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ASP R 367 " --> pdb=" O PHE R 363 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N LYS R 370 " --> pdb=" O ASN R 366 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N PHE R 371 " --> pdb=" O ASP R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 395 through 424 removed outlier: 3.832A pdb=" N GLN R 399 " --> pdb=" O ASN R 395 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N LEU R 402 " --> pdb=" O ALA R 398 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N GLY R 409 " --> pdb=" O LYS R 405 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU R 410 " --> pdb=" O GLN R 406 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS R 416 " --> pdb=" O THR R 412 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N VAL R 421 " --> pdb=" O TYR R 417 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N LEU R 423 " --> pdb=" O ALA R 419 " (cutoff:3.500A) Processing helix chain 'U' and resid 11 through 25 removed outlier: 3.697A pdb=" N LEU U 15 " --> pdb=" O ALA U 11 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LEU U 19 " --> pdb=" O LEU U 15 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N GLU U 23 " --> pdb=" O LEU U 19 " (cutoff:3.500A) Processing helix chain 'U' and resid 69 through 84 removed outlier: 4.007A pdb=" N ILE U 73 " --> pdb=" O ASP U 69 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLU U 74 " --> pdb=" O HIS U 70 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N MET U 79 " --> pdb=" O ASN U 75 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N CYS U 80 " --> pdb=" O MET U 76 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS U 82 " --> pdb=" O GLU U 78 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE U 83 " --> pdb=" O MET U 79 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 112 removed outlier: 4.272A pdb=" N ILE U 106 " --> pdb=" O SER U 102 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N LEU U 109 " --> pdb=" O LYS U 105 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LYS U 112 " --> pdb=" O GLU U 108 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 Processing helix chain 'U' and resid 185 through 215 removed outlier: 3.504A pdb=" N VAL U 207 " --> pdb=" O LYS U 203 " (cutoff:3.500A) Processing helix chain 'U' and resid 222 through 235 removed outlier: 3.904A pdb=" N LEU U 226 " --> pdb=" O ASN U 222 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N LYS U 228 " --> pdb=" O THR U 224 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N PHE U 233 " --> pdb=" O LEU U 229 " (cutoff:3.500A) Processing helix chain 'U' and resid 242 through 298 removed outlier: 3.588A pdb=" N ASP U 253 " --> pdb=" O VAL U 249 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE U 285 " --> pdb=" O LEU U 281 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU U 291 " --> pdb=" O ALA U 287 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ILE U 292 " --> pdb=" O PHE U 288 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ILE U 296 " --> pdb=" O ILE U 292 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 18 removed outlier: 3.586A pdb=" N THR O 13 " --> pdb=" O THR O 9 " (cutoff:3.500A) Processing helix chain 'O' and resid 22 through 36 removed outlier: 3.734A pdb=" N PHE O 26 " --> pdb=" O LEU O 22 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU O 30 " --> pdb=" O PHE O 26 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LYS O 31 " --> pdb=" O GLU O 27 " (cutoff:3.500A) Processing helix chain 'O' and resid 37 through 52 removed outlier: 3.516A pdb=" N LEU O 41 " --> pdb=" O LEU O 37 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N LEU O 45 " --> pdb=" O LEU O 41 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N ASP O 51 " --> pdb=" O LYS O 47 " (cutoff:3.500A) Processing helix chain 'O' and resid 57 through 69 Processing helix chain 'O' and resid 74 through 89 removed outlier: 3.616A pdb=" N TYR O 81 " --> pdb=" O SER O 77 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU O 82 " --> pdb=" O VAL O 78 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ALA O 84 " --> pdb=" O LYS O 80 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N SER O 85 " --> pdb=" O TYR O 81 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N ASP O 88 " --> pdb=" O ALA O 84 " (cutoff:3.500A) Processing helix chain 'O' and resid 91 through 118 removed outlier: 3.913A pdb=" N SER O 111 " --> pdb=" O GLN O 107 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LYS O 112 " --> pdb=" O GLU O 108 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ARG O 115 " --> pdb=" O SER O 111 " (cutoff:3.500A) Processing helix chain 'O' and resid 122 through 140 removed outlier: 4.176A pdb=" N ILE O 126 " --> pdb=" O HIS O 122 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU O 139 " --> pdb=" O ARG O 135 " (cutoff:3.500A) Processing helix chain 'O' and resid 142 through 160 removed outlier: 3.520A pdb=" N ALA O 146 " --> pdb=" O ASP O 142 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ASP O 148 " --> pdb=" O VAL O 144 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N LEU O 149 " --> pdb=" O LYS O 145 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LYS O 160 " --> pdb=" O THR O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 183 removed outlier: 3.944A pdb=" N THR O 168 " --> pdb=" O PRO O 164 " (cutoff:3.500A) Processing helix chain 'O' and resid 184 through 198 removed outlier: 3.563A pdb=" N PHE O 188 " --> pdb=" O ASP O 184 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N TYR O 190 " --> pdb=" O ASN O 186 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N LEU O 194 " --> pdb=" O TYR O 190 " (cutoff:3.500A) Processing helix chain 'O' and resid 206 through 224 removed outlier: 3.564A pdb=" N LEU O 223 " --> pdb=" O ILE O 219 " (cutoff:3.500A) Processing helix chain 'O' and resid 229 through 235 Processing helix chain 'O' and resid 236 through 241 Processing helix chain 'O' and resid 245 through 248 Processing helix chain 'O' and resid 249 through 261 removed outlier: 3.635A pdb=" N VAL O 260 " --> pdb=" O ASN O 256 " (cutoff:3.500A) Processing helix chain 'O' and resid 262 through 277 removed outlier: 3.645A pdb=" N PHE O 266 " --> pdb=" O ASP O 262 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N SER O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N VAL O 272 " --> pdb=" O SER O 268 " (cutoff:3.500A) removed outlier: 4.594A pdb=" N SER O 275 " --> pdb=" O LYS O 271 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS O 276 " --> pdb=" O VAL O 272 " (cutoff:3.500A) Processing helix chain 'O' and resid 277 through 283 removed outlier: 3.786A pdb=" N ALA O 281 " --> pdb=" O ILE O 277 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N GLN O 282 " --> pdb=" O PRO O 278 " (cutoff:3.500A) Processing helix chain 'O' and resid 283 through 303 removed outlier: 3.661A pdb=" N ILE O 291 " --> pdb=" O LEU O 287 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N CYS O 292 " --> pdb=" O ARG O 288 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS O 303 " --> pdb=" O THR O 299 " (cutoff:3.500A) Processing helix chain 'O' and resid 310 through 318 Processing helix chain 'O' and resid 320 through 334 removed outlier: 3.560A pdb=" N VAL O 324 " --> pdb=" O PRO O 320 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLU O 325 " --> pdb=" O LYS O 321 " (cutoff:3.500A) removed outlier: 4.248A pdb=" N HIS O 326 " --> pdb=" O ASP O 322 " (cutoff:3.500A) Processing helix chain 'O' and resid 360 through 387 removed outlier: 3.815A pdb=" N THR O 364 " --> pdb=" O GLY O 360 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ARG O 369 " --> pdb=" O LYS O 365 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N GLU O 372 " --> pdb=" O ASP O 368 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL O 377 " --> pdb=" O TRP O 373 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N ALA O 386 " --> pdb=" O LYS O 382 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'W' and resid 61 through 66 removed outlier: 6.711A pdb=" N VAL W 61 " --> pdb=" O SER W 53 " (cutoff:3.500A) removed outlier: 7.212A pdb=" N SER W 53 " --> pdb=" O VAL W 61 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N PHE W 65 " --> pdb=" O VAL W 49 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N VAL W 49 " --> pdb=" O PHE W 65 " (cutoff:3.500A) removed outlier: 5.832A pdb=" N GLU W 4 " --> pdb=" O THR W 48 " (cutoff:3.500A) removed outlier: 7.660A pdb=" N GLY W 50 " --> pdb=" O GLU W 4 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N THR W 6 " --> pdb=" O GLY W 50 " (cutoff:3.500A) removed outlier: 7.393A pdb=" N ILE W 52 " --> pdb=" O THR W 6 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N LEU W 8 " --> pdb=" O ILE W 52 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ALA W 5 " --> pdb=" O ARG W 109 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N VAL W 111 " --> pdb=" O ALA W 5 " (cutoff:3.500A) removed outlier: 5.848A pdb=" N VAL W 7 " --> pdb=" O VAL W 111 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N PHE W 113 " --> pdb=" O VAL W 7 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N VAL W 9 " --> pdb=" O PHE W 113 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLN W 108 " --> pdb=" O ALA W 138 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N ASP W 140 " --> pdb=" O GLN W 108 " (cutoff:3.500A) removed outlier: 6.246A pdb=" N ILE W 110 " --> pdb=" O ASP W 140 " (cutoff:3.500A) removed outlier: 7.593A pdb=" N ILE W 142 " --> pdb=" O ILE W 110 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ALA W 112 " --> pdb=" O ILE W 142 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N VAL W 139 " --> pdb=" O HIS W 170 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N LEU W 172 " --> pdb=" O VAL W 139 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ILE W 141 " --> pdb=" O LEU W 172 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'V' and resid 153 through 156 removed outlier: 3.533A pdb=" N ASP V 154 " --> pdb=" O VAL V 140 " (cutoff:3.500A) removed outlier: 10.255A pdb=" N VAL V 137 " --> pdb=" O MET V 103 " (cutoff:3.500A) removed outlier: 7.449A pdb=" N VAL V 105 " --> pdb=" O VAL V 137 " (cutoff:3.500A) removed outlier: 8.446A pdb=" N VAL V 139 " --> pdb=" O VAL V 105 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N TRP V 107 " --> pdb=" O VAL V 139 " (cutoff:3.500A) removed outlier: 8.279A pdb=" N VAL V 141 " --> pdb=" O TRP V 107 " (cutoff:3.500A) removed outlier: 6.827A pdb=" N HIS V 109 " --> pdb=" O VAL V 141 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N VAL V 104 " --> pdb=" O GLY V 55 " (cutoff:3.500A) removed outlier: 6.700A pdb=" N GLY V 55 " --> pdb=" O VAL V 104 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY V 106 " --> pdb=" O MET V 53 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLY V 51 " --> pdb=" O TYR V 108 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N MET V 50 " --> pdb=" O ALA V 70 " (cutoff:3.500A) removed outlier: 5.567A pdb=" N ALA V 70 " --> pdb=" O MET V 50 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N LEU V 52 " --> pdb=" O VAL V 68 " (cutoff:3.500A) removed outlier: 4.561A pdb=" N VAL V 68 " --> pdb=" O LEU V 52 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LEU V 54 " --> pdb=" O VAL V 66 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ASP V 67 " --> pdb=" O SER V 30 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N HIS V 204 " --> pdb=" O ILE V 29 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'X' and resid 8 through 10 removed outlier: 3.642A pdb=" N LEU X 66 " --> pdb=" O PHE X 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'X' and resid 13 through 15 removed outlier: 4.618A pdb=" N PHE X 98 " --> pdb=" O CYS X 15 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N TYR X 97 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N ALA X 88 " --> pdb=" O VAL X 76 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N VAL X 76 " --> pdb=" O ALA X 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'Z' and resid 927 through 929 removed outlier: 3.557A pdb=" N ALA Z 906 " --> pdb=" O VAL Z 929 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N ASN Z 905 " --> pdb=" O THR Z 946 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N THR Z 946 " --> pdb=" O ASN Z 905 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'Z' and resid 952 through 956 removed outlier: 7.018A pdb=" N GLU Z 966 " --> pdb=" O VAL Z 955 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'N' and resid 713 through 715 Processing sheet with id=AA8, first strand: chain 'N' and resid 758 through 762 removed outlier: 3.517A pdb=" N ILE N 759 " --> pdb=" O GLY N 901 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'N' and resid 768 through 769 Processing sheet with id=AB1, first strand: chain 'N' and resid 866 through 869 removed outlier: 3.583A pdb=" N TYR N 866 " --> pdb=" O CYS N 775 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'S' and resid 401 through 403 removed outlier: 3.505A pdb=" N ILE S 402 " --> pdb=" O ILE S 443 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'P' and resid 399 through 401 removed outlier: 6.841A pdb=" N LYS O 338 " --> pdb=" O SER O 351 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'Q' and resid 357 through 358 Processing sheet with id=AB5, first strand: chain 'R' and resid 347 through 349 Processing sheet with id=AB6, first strand: chain 'U' and resid 7 through 10 removed outlier: 5.060A pdb=" N VAL U 48 " --> pdb=" O ASP U 40 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N ASP U 40 " --> pdb=" O VAL U 48 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLY U 91 " --> pdb=" O ILE U 37 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N GLY U 39 " --> pdb=" O LEU U 89 " (cutoff:3.500A) removed outlier: 5.259A pdb=" N LEU U 89 " --> pdb=" O GLY U 39 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N ALA U 136 " --> pdb=" O LEU U 157 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL U 138 " --> pdb=" O LEU U 155 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU U 155 " --> pdb=" O VAL U 138 " (cutoff:3.500A) removed outlier: 6.160A pdb=" N LYS U 144 " --> pdb=" O SER U 149 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N SER U 149 " --> pdb=" O LYS U 144 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'U' and resid 56 through 58 removed outlier: 3.505A pdb=" N GLU U 57 " --> pdb=" O PHE U 67 " (cutoff:3.500A) 2220 hydrogen bonds defined for protein. 6594 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 14.03 Time building geometry restraints manager: 16.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.00 - 1.23: 3355 1.23 - 1.47: 19219 1.47 - 1.70: 18829 1.70 - 1.94: 258 1.94 - 2.17: 1 Bond restraints: 41662 Sorted by residual: bond pdb=" CA PRO N 8 " pdb=" CB PRO N 8 " ideal model delta sigma weight residual 1.534 2.174 -0.640 1.49e-02 4.50e+03 1.85e+03 bond pdb=" CA THR S 127 " pdb=" CB THR S 127 " ideal model delta sigma weight residual 1.528 1.801 -0.273 1.66e-02 3.63e+03 2.70e+02 bond pdb=" CA GLN N 738 " pdb=" C GLN N 738 " ideal model delta sigma weight residual 1.521 1.369 0.152 1.17e-02 7.31e+03 1.70e+02 bond pdb=" CA TYR V 196 " pdb=" CB TYR V 196 " ideal model delta sigma weight residual 1.530 1.738 -0.207 1.69e-02 3.50e+03 1.50e+02 bond pdb=" C GLN Y 89 " pdb=" OXT GLN Y 89 " ideal model delta sigma weight residual 1.231 1.000 0.231 2.00e-02 2.50e+03 1.34e+02 ... (remaining 41657 not shown) Histogram of bond angle deviations from ideal: 60.37 - 76.73: 2 76.73 - 93.08: 16 93.08 - 109.44: 8775 109.44 - 125.80: 44871 125.80 - 142.16: 2615 Bond angle restraints: 56279 Sorted by residual: angle pdb=" N PRO N 8 " pdb=" CA PRO N 8 " pdb=" CB PRO N 8 " ideal model delta sigma weight residual 103.33 68.21 35.12 1.10e+00 8.26e-01 1.02e+03 angle pdb=" C TYR V 196 " pdb=" CA TYR V 196 " pdb=" CB TYR V 196 " ideal model delta sigma weight residual 110.42 60.37 50.05 1.99e+00 2.53e-01 6.33e+02 angle pdb=" C ASP Y 65 " pdb=" CA ASP Y 65 " pdb=" CB ASP Y 65 " ideal model delta sigma weight residual 110.10 80.67 29.43 1.90e+00 2.77e-01 2.40e+02 angle pdb=" CA SER S 197 " pdb=" C SER S 197 " pdb=" O SER S 197 " ideal model delta sigma weight residual 120.70 105.28 15.42 1.03e+00 9.43e-01 2.24e+02 angle pdb=" N HIS S 20 " pdb=" CA HIS S 20 " pdb=" C HIS S 20 " ideal model delta sigma weight residual 111.07 126.40 -15.33 1.07e+00 8.73e-01 2.05e+02 ... (remaining 56274 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.99: 23108 18.99 - 37.99: 1632 37.99 - 56.98: 350 56.98 - 75.97: 267 75.97 - 94.96: 144 Dihedral angle restraints: 25501 sinusoidal: 10350 harmonic: 15151 Sorted by residual: dihedral pdb=" C TYR V 196 " pdb=" N TYR V 196 " pdb=" CA TYR V 196 " pdb=" CB TYR V 196 " ideal model delta harmonic sigma weight residual -122.60 -75.03 -47.57 0 2.50e+00 1.60e-01 3.62e+02 dihedral pdb=" N PRO N 8 " pdb=" C PRO N 8 " pdb=" CA PRO N 8 " pdb=" CB PRO N 8 " ideal model delta harmonic sigma weight residual 115.10 74.32 40.78 0 2.50e+00 1.60e-01 2.66e+02 dihedral pdb=" N LYS S 126 " pdb=" C LYS S 126 " pdb=" CA LYS S 126 " pdb=" CB LYS S 126 " ideal model delta harmonic sigma weight residual 122.80 161.39 -38.59 0 2.50e+00 1.60e-01 2.38e+02 ... (remaining 25498 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.317: 5754 0.317 - 0.634: 663 0.634 - 0.950: 25 0.950 - 1.267: 4 1.267 - 1.584: 1 Chirality restraints: 6447 Sorted by residual: chirality pdb=" CA LYS S 126 " pdb=" N LYS S 126 " pdb=" C LYS S 126 " pdb=" CB LYS S 126 " both_signs ideal model delta sigma weight residual False 2.51 0.93 1.58 2.00e-01 2.50e+01 6.27e+01 chirality pdb=" CA ASP Z 142 " pdb=" N ASP Z 142 " pdb=" C ASP Z 142 " pdb=" CB ASP Z 142 " both_signs ideal model delta sigma weight residual False 2.51 1.42 1.09 2.00e-01 2.50e+01 2.99e+01 chirality pdb=" CA PRO N 8 " pdb=" N PRO N 8 " pdb=" C PRO N 8 " pdb=" CB PRO N 8 " both_signs ideal model delta sigma weight residual False 2.72 3.78 -1.06 2.00e-01 2.50e+01 2.82e+01 ... (remaining 6444 not shown) Planarity restraints: 7202 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR O 62 " -0.332 2.00e-02 2.50e+03 1.86e-01 6.91e+02 pdb=" CG TYR O 62 " 0.051 2.00e-02 2.50e+03 pdb=" CD1 TYR O 62 " 0.151 2.00e-02 2.50e+03 pdb=" CD2 TYR O 62 " 0.218 2.00e-02 2.50e+03 pdb=" CE1 TYR O 62 " 0.115 2.00e-02 2.50e+03 pdb=" CE2 TYR O 62 " 0.081 2.00e-02 2.50e+03 pdb=" CZ TYR O 62 " -0.013 2.00e-02 2.50e+03 pdb=" OH TYR O 62 " -0.271 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 471 " 0.257 2.00e-02 2.50e+03 1.47e-01 4.31e+02 pdb=" CG TYR N 471 " -0.059 2.00e-02 2.50e+03 pdb=" CD1 TYR N 471 " -0.166 2.00e-02 2.50e+03 pdb=" CD2 TYR N 471 " -0.089 2.00e-02 2.50e+03 pdb=" CE1 TYR N 471 " -0.043 2.00e-02 2.50e+03 pdb=" CE2 TYR N 471 " -0.120 2.00e-02 2.50e+03 pdb=" CZ TYR N 471 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR N 471 " 0.225 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR Q 306 " 0.283 2.00e-02 2.50e+03 1.46e-01 4.24e+02 pdb=" CG TYR Q 306 " -0.103 2.00e-02 2.50e+03 pdb=" CD1 TYR Q 306 " -0.135 2.00e-02 2.50e+03 pdb=" CD2 TYR Q 306 " -0.127 2.00e-02 2.50e+03 pdb=" CE1 TYR Q 306 " -0.077 2.00e-02 2.50e+03 pdb=" CE2 TYR Q 306 " -0.054 2.00e-02 2.50e+03 pdb=" CZ TYR Q 306 " 0.025 2.00e-02 2.50e+03 pdb=" OH TYR Q 306 " 0.187 2.00e-02 2.50e+03 ... (remaining 7199 not shown) Histogram of nonbonded interaction distances: 0.66 - 1.50: 7 1.50 - 2.35: 40 2.35 - 3.20: 37378 3.20 - 4.05: 100331 4.05 - 4.90: 180131 Warning: very small nonbonded interaction distances. Nonbonded interactions: 317887 Sorted by model distance: nonbonded pdb=" ND2 ASN Y 21 " pdb=" NH1 ARG S 55 " model vdw 0.656 3.200 nonbonded pdb=" NE2 GLN T 84 " pdb=" CA PRO N 8 " model vdw 1.301 3.550 nonbonded pdb=" O TYR V 196 " pdb=" CD2 TYR V 196 " model vdw 1.324 3.340 nonbonded pdb=" ND2 ASN T 80 " pdb=" CB ALA N 11 " model vdw 1.365 3.540 nonbonded pdb=" OE2 GLU V 169 " pdb=" ND2 ASN V 193 " model vdw 1.408 2.520 ... (remaining 317882 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.870 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.030 Extract box with map and model: 16.230 Check model and map are aligned: 0.610 Set scattering table: 0.310 Process input model: 91.890 Find NCS groups from input model: 1.420 Set up NCS constraints: 0.140 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:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 116.470 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3870 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 : 0.035 0.640 41662 Z= 2.227 Angle : 3.400 50.053 56279 Z= 2.343 Chirality : 0.201 1.584 6447 Planarity : 0.027 0.300 7202 Dihedral : 17.759 94.963 15677 Min Nonbonded Distance : 0.656 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 2.09 % Allowed : 5.60 % Favored : 92.31 % Rotamer Outliers : 2.78 % Cbeta Deviations : 6.72 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -2.14 (0.10), residues: 5108 helix: -0.73 (0.08), residues: 3138 sheet: -1.30 (0.32), residues: 188 loop : -2.58 (0.12), residues: 1782 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1753 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 127 poor density : 1626 time to evaluate : 4.542 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 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: 127 outliers final: 26 residues processed: 1716 average time/residue: 0.5451 time to fit residues: 1499.8919 Evaluate side-chains 879 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 853 time to evaluate : 4.776 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 0 residues processed: 26 average time/residue: 0.3746 time to fit residues: 25.6604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 428 optimal weight: 5.9990 chunk 385 optimal weight: 2.9990 chunk 213 optimal weight: 6.9990 chunk 131 optimal weight: 9.9990 chunk 259 optimal weight: 7.9990 chunk 205 optimal weight: 10.0000 chunk 398 optimal weight: 3.9990 chunk 154 optimal weight: 10.0000 chunk 242 optimal weight: 6.9990 chunk 296 optimal weight: 6.9990 chunk 461 optimal weight: 5.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 12 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 86 HIS W 108 GLN W 170 HIS V 102 GLN ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** V 215 ASN ** V 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 80 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 123 HIS Y 88 ASN Z 15 GLN Z 129 ASN Z 166 ASN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 215 ASN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 387 ASN Z 463 HIS Z 539 ASN Z 549 ASN ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 622 HIS Z 829 GLN ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 898 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 926 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN N 71 ASN N 182 ASN ** N 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 240 GLN N 300 ASN N 346 ASN ** N 361 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 444 HIS N 472 ASN N 510 HIS N 564 ASN N 654 GLN N 666 GLN N 667 GLN ** N 747 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 878 GLN S 20 HIS S 65 ASN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 154 GLN ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 206 GLN S 314 ASN S 334 HIS ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 437 ASN S 470 GLN ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 29 GLN ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 78 GLN P 113 ASN P 230 HIS P 289 ASN P 349 ASN P 385 ASN ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN Q 87 GLN Q 260 GLN ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 372 GLN Q 394 ASN ** Q 420 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 184 GLN R 195 ASN R 325 HIS ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN U 70 HIS ** U 156 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 252 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 294 ASN ** O 23 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** O 40 GLN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 273 GLN O 362 GLN O 389 GLN Total number of N/Q/H flips: 62 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4506 moved from start: 0.5267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.061 41662 Z= 0.328 Angle : 0.859 14.819 56279 Z= 0.460 Chirality : 0.045 0.221 6447 Planarity : 0.006 0.073 7202 Dihedral : 5.862 38.570 5504 Min Nonbonded Distance : 2.076 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.47 % Allowed : 4.40 % Favored : 95.13 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.58 (0.11), residues: 5108 helix: 0.44 (0.08), residues: 3284 sheet: -1.22 (0.32), residues: 227 loop : -1.88 (0.14), residues: 1597 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 1100 time to evaluate : 4.611 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 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: 12 outliers final: 4 residues processed: 1107 average time/residue: 0.5401 time to fit residues: 979.0284 Evaluate side-chains 753 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 749 time to evaluate : 4.602 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.4070 time to fit residues: 9.5559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 256 optimal weight: 8.9990 chunk 143 optimal weight: 30.0000 chunk 383 optimal weight: 6.9990 chunk 314 optimal weight: 0.8980 chunk 127 optimal weight: 10.0000 chunk 462 optimal weight: 9.9990 chunk 499 optimal weight: 0.7980 chunk 411 optimal weight: 9.9990 chunk 458 optimal weight: 5.9990 chunk 157 optimal weight: 20.0000 chunk 370 optimal weight: 9.9990 overall best weight: 4.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 170 HIS V 102 GLN V 109 HIS ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 220 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 ASN T 255 GLN X 131 ASN Y 25 ASN Z 129 ASN Z 380 ASN Z 391 ASN Z 618 GLN ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 926 ASN Z 959 HIS N 29 ASN N 34 GLN N 233 ASN N 346 ASN N 430 ASN N 529 GLN N 679 ASN N 747 HIS ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 334 HIS S 335 GLN ** S 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 472 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 48 GLN P 337 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 106 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 361 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 130 GLN R 143 GLN R 385 ASN ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 HIS U 173 HIS U 223 HIS U 251 ASN O 23 HIS O 122 HIS O 169 ASN ** O 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS O 389 GLN Total number of N/Q/H flips: 37 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4720 moved from start: 0.6540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.094 41662 Z= 0.272 Angle : 0.744 13.081 56279 Z= 0.395 Chirality : 0.042 0.251 6447 Planarity : 0.005 0.078 7202 Dihedral : 5.432 36.612 5504 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.95 Ramachandran Plot: Outliers : 0.33 % Allowed : 4.91 % Favored : 94.75 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % 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: -0.39 (0.11), residues: 5108 helix: 0.54 (0.09), residues: 3303 sheet: -0.93 (0.33), residues: 218 loop : -1.77 (0.14), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 979 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 973 time to evaluate : 4.436 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 1 residues processed: 976 average time/residue: 0.5353 time to fit residues: 864.0220 Evaluate side-chains 710 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 709 time to evaluate : 4.653 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3553 time to fit residues: 7.3745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 456 optimal weight: 20.0000 chunk 347 optimal weight: 9.9990 chunk 239 optimal weight: 8.9990 chunk 51 optimal weight: 1.9990 chunk 220 optimal weight: 30.0000 chunk 310 optimal weight: 4.9990 chunk 463 optimal weight: 7.9990 chunk 491 optimal weight: 7.9990 chunk 242 optimal weight: 20.0000 chunk 439 optimal weight: 8.9990 chunk 132 optimal weight: 9.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 170 HIS ** V 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 167 ASN ** V 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 83 ASN ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 93 ASN T 116 GLN X 102 GLN Z 235 GLN ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 801 HIS ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 958 ASN N 17 GLN N 34 GLN ** N 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 360 GLN ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 614 ASN N 654 GLN ** N 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 235 ASN S 335 GLN ** S 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 282 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN Q 106 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 ASN Q 273 ASN Q 320 GLN Q 361 HIS ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 401 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 50 ASN U 70 HIS ** U 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN O 211 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4954 moved from start: 0.7604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.101 41662 Z= 0.320 Angle : 0.784 10.559 56279 Z= 0.415 Chirality : 0.044 0.308 6447 Planarity : 0.005 0.061 7202 Dihedral : 5.654 35.572 5504 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 16.75 Ramachandran Plot: Outliers : 0.29 % Allowed : 5.27 % Favored : 94.44 % Rotamer Outliers : 0.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % 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: -0.79 (0.11), residues: 5108 helix: 0.20 (0.09), residues: 3313 sheet: -1.19 (0.34), residues: 208 loop : -1.84 (0.14), residues: 1587 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 919 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 914 time to evaluate : 4.473 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 outliers start: 5 outliers final: 2 residues processed: 919 average time/residue: 0.5194 time to fit residues: 793.9349 Evaluate side-chains 690 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 688 time to evaluate : 4.822 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.3684 time to fit residues: 8.2094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 408 optimal weight: 8.9990 chunk 278 optimal weight: 20.0000 chunk 7 optimal weight: 8.9990 chunk 365 optimal weight: 5.9990 chunk 202 optimal weight: 9.9990 chunk 419 optimal weight: 3.9990 chunk 339 optimal weight: 6.9990 chunk 0 optimal weight: 50.0000 chunk 250 optimal weight: 8.9990 chunk 440 optimal weight: 7.9990 chunk 123 optimal weight: 20.0000 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 73 GLN V 145 GLN V 186 GLN ** V 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 771 HIS ** Z 871 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 34 GLN N 231 ASN ** N 256 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 679 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 283 GLN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS P 348 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 37 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 253 ASN Q 308 ASN R 217 HIS ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 401 HIS U 70 HIS U 107 ASN ** U 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 114 GLN ** O 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 175 ASN O 235 HIS O 345 ASN Total number of N/Q/H flips: 23 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5062 moved from start: 0.8291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 41662 Z= 0.314 Angle : 0.784 14.220 56279 Z= 0.412 Chirality : 0.044 0.273 6447 Planarity : 0.005 0.063 7202 Dihedral : 5.792 38.952 5504 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 18.45 Ramachandran Plot: Outliers : 0.23 % Allowed : 6.01 % Favored : 93.75 % Rotamer Outliers : 0.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % 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: -1.04 (0.11), residues: 5108 helix: -0.01 (0.09), residues: 3287 sheet: -1.21 (0.35), residues: 203 loop : -1.88 (0.15), residues: 1618 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 905 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 901 time to evaluate : 5.006 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 outliers start: 4 outliers final: 0 residues processed: 905 average time/residue: 0.5240 time to fit residues: 791.5865 Evaluate side-chains 677 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 677 time to evaluate : 4.943 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.9320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 165 optimal weight: 20.0000 chunk 442 optimal weight: 9.9990 chunk 97 optimal weight: 20.0000 chunk 288 optimal weight: 30.0000 chunk 121 optimal weight: 8.9990 chunk 491 optimal weight: 5.9990 chunk 408 optimal weight: 10.0000 chunk 227 optimal weight: 40.0000 chunk 40 optimal weight: 9.9990 chunk 162 optimal weight: 10.0000 chunk 258 optimal weight: 0.0040 overall best weight: 7.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 176 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** T 123 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 338 HIS ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN N 329 HIS ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 679 ASN N 681 ASN ** N 690 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 738 GLN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 283 GLN S 334 HIS ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 472 HIS ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 308 ASN Q 320 GLN ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 136 ASN ** R 323 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 325 HIS ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 HIS ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 211 GLN O 235 HIS ** O 283 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5147 moved from start: 0.8925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.082 41662 Z= 0.324 Angle : 0.801 12.288 56279 Z= 0.422 Chirality : 0.045 0.236 6447 Planarity : 0.005 0.061 7202 Dihedral : 6.000 39.213 5504 Min Nonbonded Distance : 2.070 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.70 % Favored : 93.09 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % 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: -1.26 (0.11), residues: 5108 helix: -0.20 (0.09), residues: 3281 sheet: -1.33 (0.35), residues: 188 loop : -1.92 (0.15), residues: 1639 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 873 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 871 time to evaluate : 5.179 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 outliers start: 2 outliers final: 0 residues processed: 873 average time/residue: 0.5282 time to fit residues: 770.8933 Evaluate side-chains 671 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 671 time to evaluate : 4.670 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.7037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 473 optimal weight: 4.9990 chunk 55 optimal weight: 7.9990 chunk 280 optimal weight: 10.0000 chunk 358 optimal weight: 6.9990 chunk 278 optimal weight: 20.0000 chunk 413 optimal weight: 0.9990 chunk 274 optimal weight: 2.9990 chunk 489 optimal weight: 8.9990 chunk 306 optimal weight: 5.9990 chunk 298 optimal weight: 5.9990 chunk 226 optimal weight: 5.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN Z 23 GLN Z 151 HIS ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 235 GLN ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 338 HIS Z 435 GLN ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN N 360 GLN ** N 430 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 444 HIS N 681 ASN N 690 HIS ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 225 HIS S 280 ASN S 347 HIS ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 437 ASN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 285 GLN P 337 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 114 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 273 ASN Q 308 ASN ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 94 HIS U 192 ASN U 260 ASN U 262 GLN ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS Total number of N/Q/H flips: 25 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5072 moved from start: 0.9089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.053 41662 Z= 0.239 Angle : 0.715 10.153 56279 Z= 0.375 Chirality : 0.042 0.192 6447 Planarity : 0.005 0.068 7202 Dihedral : 5.682 36.440 5504 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.22 % Allowed : 5.95 % Favored : 93.83 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.97 (0.11), residues: 5108 helix: 0.03 (0.09), residues: 3301 sheet: -1.28 (0.35), residues: 200 loop : -1.83 (0.15), residues: 1607 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 892 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 891 time to evaluate : 4.607 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 outliers start: 1 outliers final: 0 residues processed: 891 average time/residue: 0.5234 time to fit residues: 780.8360 Evaluate side-chains 690 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 690 time to evaluate : 4.540 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.5726 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 302 optimal weight: 9.9990 chunk 195 optimal weight: 20.0000 chunk 292 optimal weight: 4.9990 chunk 147 optimal weight: 20.0000 chunk 96 optimal weight: 10.0000 chunk 94 optimal weight: 20.0000 chunk 311 optimal weight: 6.9990 chunk 333 optimal weight: 0.8980 chunk 242 optimal weight: 30.0000 chunk 45 optimal weight: 9.9990 chunk 384 optimal weight: 8.9990 overall best weight: 6.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS W 165 GLN ** V 126 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 200 ASN ** V 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN Y 25 ASN ** Z 23 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN N 288 ASN ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 580 ASN N 607 GLN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN ** S 311 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** S 317 HIS S 334 HIS ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 438 HIS ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 48 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 54 GLN Q 247 HIS Q 308 ASN ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 397 ASN ** R 399 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 70 HIS U 94 HIS ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 192 ASN U 216 ASN U 252 HIS ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5180 moved from start: 0.9490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.059 41662 Z= 0.307 Angle : 0.788 12.649 56279 Z= 0.413 Chirality : 0.044 0.191 6447 Planarity : 0.005 0.104 7202 Dihedral : 5.885 43.264 5504 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 19.94 Ramachandran Plot: Outliers : 0.16 % Allowed : 7.15 % Favored : 92.70 % Rotamer Outliers : 0.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % 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: -1.25 (0.11), residues: 5108 helix: -0.20 (0.09), residues: 3292 sheet: -1.44 (0.35), residues: 184 loop : -1.89 (0.15), residues: 1632 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 859 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 858 time to evaluate : 4.915 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 outliers start: 1 outliers final: 0 residues processed: 859 average time/residue: 0.5230 time to fit residues: 754.0898 Evaluate side-chains 679 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 679 time to evaluate : 4.653 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.6292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 445 optimal weight: 0.4980 chunk 469 optimal weight: 20.0000 chunk 427 optimal weight: 0.9990 chunk 456 optimal weight: 20.0000 chunk 468 optimal weight: 0.9990 chunk 274 optimal weight: 10.0000 chunk 198 optimal weight: 9.9990 chunk 358 optimal weight: 10.0000 chunk 140 optimal weight: 30.0000 chunk 412 optimal weight: 20.0000 chunk 431 optimal weight: 1.9990 overall best weight: 2.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 217 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 112 ASN T 116 GLN ** T 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 502 ASN ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 280 GLN N 308 ASN ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 580 ASN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN ** S 386 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 458 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS ** P 386 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 HIS Q 308 ASN ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 399 GLN ** U 127 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS O 326 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5057 moved from start: 0.9559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.054 41662 Z= 0.207 Angle : 0.699 11.682 56279 Z= 0.367 Chirality : 0.042 0.251 6447 Planarity : 0.004 0.059 7202 Dihedral : 5.533 44.368 5504 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 16.27 Ramachandran Plot: Outliers : 0.20 % Allowed : 5.85 % Favored : 93.95 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.87 (0.12), residues: 5108 helix: 0.13 (0.09), residues: 3297 sheet: -1.53 (0.35), residues: 199 loop : -1.79 (0.15), residues: 1612 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 897 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 897 time to evaluate : 4.600 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 outliers start: 0 outliers final: 0 residues processed: 897 average time/residue: 0.5388 time to fit residues: 810.5300 Evaluate side-chains 691 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 691 time to evaluate : 4.903 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 6.8830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 454 optimal weight: 0.8980 chunk 299 optimal weight: 6.9990 chunk 482 optimal weight: 20.0000 chunk 294 optimal weight: 10.0000 chunk 228 optimal weight: 0.0020 chunk 335 optimal weight: 5.9990 chunk 506 optimal weight: 20.0000 chunk 465 optimal weight: 5.9990 chunk 403 optimal weight: 20.0000 chunk 41 optimal weight: 0.8980 chunk 311 optimal weight: 10.0000 overall best weight: 2.7592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 217 HIS ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** T 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 25 ASN ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 707 ASN ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 166 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** S 280 ASN S 334 HIS ** S 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 458 GLN ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS Q 247 HIS Q 273 ASN Q 308 ASN ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 252 HIS ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5053 moved from start: 0.9697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.053 41662 Z= 0.210 Angle : 0.702 10.852 56279 Z= 0.366 Chirality : 0.041 0.259 6447 Planarity : 0.004 0.056 7202 Dihedral : 5.407 43.900 5504 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 16.36 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.15 % Favored : 93.66 % Rotamer Outliers : 0.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.12), residues: 5108 helix: 0.22 (0.09), residues: 3288 sheet: -1.32 (0.35), residues: 207 loop : -1.69 (0.15), residues: 1613 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10216 Ramachandran restraints generated. 5108 Oldfield, 0 Emsley, 5108 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 874 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 872 time to evaluate : 4.533 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 outliers start: 2 outliers final: 1 residues processed: 873 average time/residue: 0.5180 time to fit residues: 757.1427 Evaluate side-chains 697 residues out of total 4574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 696 time to evaluate : 4.746 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.3697 time to fit residues: 7.4124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 508 random chunks: chunk 247 optimal weight: 0.7980 chunk 320 optimal weight: 10.0000 chunk 429 optimal weight: 10.0000 chunk 123 optimal weight: 20.0000 chunk 371 optimal weight: 0.9980 chunk 59 optimal weight: 7.9990 chunk 111 optimal weight: 6.9990 chunk 403 optimal weight: 0.7980 chunk 168 optimal weight: 20.0000 chunk 414 optimal weight: 10.0000 chunk 51 optimal weight: 20.0000 overall best weight: 3.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** W 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 HIS ** V 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 111 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 92 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** T 116 GLN ** T 192 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 243 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 618 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 760 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 226 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 329 HIS ** N 707 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 139 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 191 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** S 317 HIS ** S 438 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 15 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 337 HIS P 417 HIS ** P 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 247 HIS Q 308 ASN ** R 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 252 HIS ** U 260 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 169 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 235 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.199916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.184370 restraints weight = 130508.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.182018 restraints weight = 177062.511| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.180366 restraints weight = 155070.507| |-----------------------------------------------------------------------------| r_work (final): 0.4412 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6173 moved from start: 0.9855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.057 41662 Z= 0.223 Angle : 0.705 11.142 56279 Z= 0.369 Chirality : 0.042 0.252 6447 Planarity : 0.005 0.069 7202 Dihedral : 5.402 45.680 5504 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 17.29 Ramachandran Plot: Outliers : 0.22 % Allowed : 6.17 % Favored : 93.62 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.47 % Cis-general : 0.02 % Twisted Proline : 0.00 % Twisted General : 0.04 % 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: -0.71 (0.12), residues: 5108 helix: 0.22 (0.09), residues: 3290 sheet: -1.12 (0.35), residues: 205 loop : -1.71 (0.15), residues: 1613 =============================================================================== Job complete usr+sys time: 12483.90 seconds wall clock time: 224 minutes 56.21 seconds (13496.21 seconds total)