Starting phenix.real_space_refine on Tue Apr 16 20:30:47 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tb4_10438/04_2024/6tb4_10438.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tb4_10438/04_2024/6tb4_10438.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tb4_10438/04_2024/6tb4_10438.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tb4_10438/04_2024/6tb4_10438.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tb4_10438/04_2024/6tb4_10438.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6tb4_10438/04_2024/6tb4_10438.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.059 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 153 5.16 5 C 25996 2.51 5 N 7082 2.21 5 O 7509 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M GLU 173": "OE1" <-> "OE2" Residue "M GLU 188": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 210": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 255": "NH1" <-> "NH2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A GLU 333": "OE1" <-> "OE2" Residue "C GLU 252": "OE1" <-> "OE2" Residue "C ARG 308": "NH1" <-> "NH2" Residue "F ARG 93": "NH1" <-> "NH2" Residue "F GLU 113": "OE1" <-> "OE2" Residue "F GLU 137": "OE1" <-> "OE2" Residue "F ARG 143": "NH1" <-> "NH2" Residue "F ARG 211": "NH1" <-> "NH2" Residue "F GLU 250": "OE1" <-> "OE2" Residue "D ARG 60": "NH1" <-> "NH2" Residue "D ARG 75": "NH1" <-> "NH2" Residue "D ARG 83": "NH1" <-> "NH2" Residue "D GLU 209": "OE1" <-> "OE2" Residue "D ARG 224": "NH1" <-> "NH2" Residue "D GLU 234": "OE1" <-> "OE2" Residue "D PHE 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 314": "NH1" <-> "NH2" Residue "D ARG 319": "NH1" <-> "NH2" Residue "D GLU 322": "OE1" <-> "OE2" Residue "D ARG 335": "NH1" <-> "NH2" Residue "D ARG 337": "NH1" <-> "NH2" Residue "E GLU 904": "OE1" <-> "OE2" Residue "E GLU 966": "OE1" <-> "OE2" Residue "J ARG 122": "NH1" <-> "NH2" Residue "J ARG 200": "NH1" <-> "NH2" Residue "K ARG 449": "NH1" <-> "NH2" Residue "K ARG 582": "NH1" <-> "NH2" Residue "G ARG 48": "NH1" <-> "NH2" Residue "G ARG 90": "NH1" <-> "NH2" Residue "G ARG 109": "NH1" <-> "NH2" Residue "G ARG 126": "NH1" <-> "NH2" Residue "G GLU 128": "OE1" <-> "OE2" Residue "G ARG 147": "NH1" <-> "NH2" Residue "G ARG 154": "NH1" <-> "NH2" Residue "G ARG 194": "NH1" <-> "NH2" Residue "G ARG 227": "NH1" <-> "NH2" Residue "G ARG 425": "NH1" <-> "NH2" Residue "G ARG 447": "NH1" <-> "NH2" Residue "G ARG 448": "NH1" <-> "NH2" Residue "G ARG 466": "NH1" <-> "NH2" Residue "G ARG 520": "NH1" <-> "NH2" Residue "G GLU 544": "OE1" <-> "OE2" Residue "G ARG 568": "NH1" <-> "NH2" Residue "G ARG 613": "NH1" <-> "NH2" Residue "G ARG 618": "NH1" <-> "NH2" Residue "G ARG 632": "NH1" <-> "NH2" Residue "H GLU 144": "OE1" <-> "OE2" Residue "H ARG 167": "NH1" <-> "NH2" Residue "H ARG 219": "NH1" <-> "NH2" Residue "H ARG 245": "NH1" <-> "NH2" Residue "H PHE 268": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 327": "OE1" <-> "OE2" Residue "H ARG 337": "NH1" <-> "NH2" Residue "H ARG 346": "NH1" <-> "NH2" Residue "H ARG 361": "NH1" <-> "NH2" Residue "H ARG 364": "NH1" <-> "NH2" Residue "H ARG 368": "NH1" <-> "NH2" Residue "H ARG 389": "NH1" <-> "NH2" Residue "H ARG 397": "NH1" <-> "NH2" Residue "H ARG 432": "NH1" <-> "NH2" Residue "I ARG 13": "NH1" <-> "NH2" Residue "I ARG 124": "NH1" <-> "NH2" Residue "L ARG 336": "NH1" <-> "NH2" Residue "L ARG 445": "NH1" <-> "NH2" Residue "L ARG 562": "NH1" <-> "NH2" Residue "L ARG 616": "NH1" <-> "NH2" Residue "L ARG 623": "NH1" <-> "NH2" Residue "L GLU 655": "OE1" <-> "OE2" Residue "L GLU 661": "OE1" <-> "OE2" Residue "L ARG 680": "NH1" <-> "NH2" Residue "L ARG 790": "NH1" <-> "NH2" Residue "L ARG 794": "NH1" <-> "NH2" Residue "L ARG 800": "NH1" <-> "NH2" Residue "L GLU 817": "OE1" <-> "OE2" Residue "L GLU 825": "OE1" <-> "OE2" Residue "L ARG 828": "NH1" <-> "NH2" Residue "L ARG 845": "NH1" <-> "NH2" Residue "L GLU 879": "OE1" <-> "OE2" Residue "L ARG 985": "NH1" <-> "NH2" Residue "L ARG 987": "NH1" <-> "NH2" Residue "L ARG 1075": "NH1" <-> "NH2" Residue "L GLU 1077": "OE1" <-> "OE2" Residue "L ARG 1083": "NH1" <-> "NH2" Residue "L GLU 1145": "OE1" <-> "OE2" Residue "L GLU 1184": "OE1" <-> "OE2" Residue "L ARG 1213": "NH1" <-> "NH2" Residue "L ARG 1219": "NH1" <-> "NH2" Residue "L ARG 1226": "NH1" <-> "NH2" Residue "L GLU 1235": "OE1" <-> "OE2" Residue "L ARG 1242": "NH1" <-> "NH2" Residue "L GLU 1250": "OE1" <-> "OE2" Residue "L ARG 1257": "NH1" <-> "NH2" Residue "L ARG 1284": "NH1" <-> "NH2" Residue "L ARG 1292": "NH1" <-> "NH2" Residue "L ARG 1389": "NH1" <-> "NH2" Residue "L ARG 1413": "NH1" <-> "NH2" Residue "L ARG 1417": "NH1" <-> "NH2" Residue "L ARG 1431": "NH1" <-> "NH2" Residue "L GLU 1434": "OE1" <-> "OE2" Residue "L ARG 1437": "NH1" <-> "NH2" Residue "L ARG 1513": "NH1" <-> "NH2" Residue "L GLU 1561": "OE1" <-> "OE2" Residue "L ARG 1566": "NH1" <-> "NH2" Residue "L ARG 1582": "NH1" <-> "NH2" Residue "L ARG 1603": "NH1" <-> "NH2" Residue "L ARG 1617": "NH1" <-> "NH2" Residue "L GLU 1622": "OE1" <-> "OE2" Residue "L ARG 1626": "NH1" <-> "NH2" Residue "L ARG 1628": "NH1" <-> "NH2" Residue "L GLU 1639": "OE1" <-> "OE2" Residue "L ARG 1643": "NH1" <-> "NH2" Residue "L GLU 1660": "OE1" <-> "OE2" Residue "L GLU 1671": "OE1" <-> "OE2" Residue "L ARG 1684": "NH1" <-> "NH2" Residue "L ARG 1765": "NH1" <-> "NH2" Residue "L ARG 1800": "NH1" <-> "NH2" Residue "L ARG 1838": "NH1" <-> "NH2" Residue "L ARG 1862": "NH1" <-> "NH2" Residue "L ARG 1894": "NH1" <-> "NH2" Residue "L ARG 1904": "NH1" <-> "NH2" Residue "L GLU 1934": "OE1" <-> "OE2" Residue "L ARG 1947": "NH1" <-> "NH2" Residue "L GLU 1952": "OE1" <-> "OE2" Residue "L GLU 2405": "OE1" <-> "OE2" Residue "L ARG 2434": "NH1" <-> "NH2" Residue "L TYR 2464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 2489": "NH1" <-> "NH2" Residue "L ARG 2536": "NH1" <-> "NH2" Residue "L GLU 2556": "OE1" <-> "OE2" Residue "L ARG 2576": "NH1" <-> "NH2" Residue "L ARG 2683": "NH1" <-> "NH2" Residue "L ARG 2717": "NH1" <-> "NH2" Residue "L ARG 2767": "NH1" <-> "NH2" Residue "L ARG 2817": "NH1" <-> "NH2" Residue "L GLU 2821": "OE1" <-> "OE2" Residue "L ARG 2828": "NH1" <-> "NH2" Residue "L ARG 2839": "NH1" <-> "NH2" Residue "L ARG 2889": "NH1" <-> "NH2" Residue "L ARG 2916": "NH1" <-> "NH2" Residue "L ARG 3174": "NH1" <-> "NH2" Residue "L GLU 3287": "OE1" <-> "OE2" Residue "L ARG 3414": "NH1" <-> "NH2" Residue "L GLU 3428": "OE1" <-> "OE2" Residue "L ARG 3451": "NH1" <-> "NH2" Residue "L ARG 3460": "NH1" <-> "NH2" Residue "L ARG 3502": "NH1" <-> "NH2" Residue "L ARG 3510": "NH1" <-> "NH2" Residue "L ARG 3516": "NH1" <-> "NH2" Residue "L ARG 3541": "NH1" <-> "NH2" Residue "L ARG 3554": "NH1" <-> "NH2" Residue "L ARG 3555": "NH1" <-> "NH2" Residue "L ARG 3623": "NH1" <-> "NH2" Residue "L ARG 3770": "NH1" <-> "NH2" Residue "L ARG 3774": "NH1" <-> "NH2" Residue "L ARG 3783": "NH1" <-> "NH2" Residue "L TYR 3824": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.12s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 40740 Number of models: 1 Model: "" Number of chains: 13 Chain: "M" Number of atoms: 1415 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 1415 Classifications: {'peptide': 180} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 171} Chain: "A" Number of atoms: 1300 Number of conformers: 1 Conformer: "" Number of residues, atoms: 173, 1300 Classifications: {'peptide': 173} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 9, 'TRANS': 163} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 86 Unresolved non-hydrogen angles: 106 Unresolved non-hydrogen dihedrals: 70 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 48 Chain: "C" Number of atoms: 518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 65, 518 Classifications: {'peptide': 65} Link IDs: {'PTRANS': 4, 'TRANS': 60} Chain breaks: 1 Chain: "F" Number of atoms: 1682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 210, 1682 Classifications: {'peptide': 210} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 12, 'TRANS': 197} Chain breaks: 3 Unresolved non-hydrogen bonds: 58 Unresolved non-hydrogen angles: 72 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 4, 'TYR:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 34 Chain: "D" Number of atoms: 1616 Number of conformers: 1 Conformer: "" Number of residues, atoms: 209, 1616 Classifications: {'peptide': 209} Incomplete info: {'truncation_to_alanine': 27} Link IDs: {'PTRANS': 6, 'TRANS': 202} Chain breaks: 2 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 93 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 75 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 3, 'ASN:plan1': 2, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 46 Chain: "E" Number of atoms: 1232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1232 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 2, 'TRANS': 151} Chain breaks: 1 Chain: "J" Number of atoms: 768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 768 Classifications: {'peptide': 96} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain breaks: 1 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "K" Number of atoms: 1192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 154, 1192 Classifications: {'peptide': 154} Link IDs: {'PTRANS': 13, 'TRANS': 140} Chain breaks: 1 Chain: "G" Number of atoms: 4075 Number of conformers: 1 Conformer: "" Number of residues, atoms: 522, 4075 Classifications: {'peptide': 522} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 16} Link IDs: {'PTRANS': 23, 'TRANS': 498} Chain breaks: 4 Unresolved non-hydrogen bonds: 54 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 42 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 30 Chain: "H" Number of atoms: 3263 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3263 Classifications: {'peptide': 421} Incomplete info: {'truncation_to_alanine': 28} Link IDs: {'PTRANS': 18, 'TRANS': 402} Chain breaks: 3 Unresolved non-hydrogen bonds: 116 Unresolved non-hydrogen angles: 150 Unresolved non-hydrogen dihedrals: 96 Unresolved non-hydrogen chiralities: 8 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 6, 'PHE:plan': 2, 'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 80 Chain: "I" Number of atoms: 981 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 981 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 9, 'TRANS': 113} Chain breaks: 1 Chain: "L" Number of atoms: 22318 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2968, 22318 Classifications: {'peptide': 2968} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 525} Link IDs: {'PTRANS': 114, 'TRANS': 2853} Chain breaks: 46 Unresolved chain link angles: 19 Unresolved non-hydrogen bonds: 1901 Unresolved non-hydrogen angles: 2429 Unresolved non-hydrogen dihedrals: 1563 Unresolved non-hydrogen chiralities: 196 Planarities with less than four sites: {'GLN:plan1': 28, 'ASP:plan': 25, 'TYR:plan': 18, 'ASN:plan1': 31, 'TRP:plan': 5, 'HIS:plan': 9, 'PHE:plan': 32, 'GLU:plan': 47, 'ARG:plan': 21} Unresolved non-hydrogen planarities: 981 Chain: "B" Number of atoms: 380 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 380 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 76} Link IDs: {'TRANS': 75} Chain breaks: 2 Unresolved non-hydrogen bonds: 152 Unresolved non-hydrogen angles: 228 Unresolved non-hydrogen dihedrals: 76 Planarities with less than four sites: {'UNK:plan-1': 76} Unresolved non-hydrogen planarities: 76 Time building chain proxies: 18.72, per 1000 atoms: 0.46 Number of scatterers: 40740 At special positions: 0 Unit cell: (202.74, 265.96, 119.9, 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 153 16.00 O 7509 8.00 N 7082 7.00 C 25996 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: 15.70 Conformation dependent library (CDL) restraints added in 7.3 seconds 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 10282 Finding SS restraints... Secondary structure from input PDB file: 255 helices and 15 sheets defined 60.0% alpha, 3.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.42 Creating SS restraints... Processing helix chain 'M' and resid 81 through 90 Processing helix chain 'M' and resid 128 through 143 removed outlier: 3.960A pdb=" N ALA M 140 " --> pdb=" O SER M 136 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ARG M 141 " --> pdb=" O ARG M 137 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE M 142 " --> pdb=" O LYS M 138 " (cutoff:3.500A) Processing helix chain 'M' and resid 171 through 177 Processing helix chain 'M' and resid 220 through 237 removed outlier: 3.885A pdb=" N TYR M 224 " --> pdb=" O ARG M 220 " (cutoff:3.500A) Proline residue: M 232 - end of helix Processing helix chain 'A' and resid 160 through 169 Processing helix chain 'A' and resid 172 through 179 removed outlier: 3.641A pdb=" N ALA A 179 " --> pdb=" O ARG A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 200 Processing helix chain 'A' and resid 222 through 230 removed outlier: 3.695A pdb=" N ILE A 226 " --> pdb=" O ALA A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 258 removed outlier: 3.735A pdb=" N LEU A 246 " --> pdb=" O GLU A 242 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N GLY A 252 " --> pdb=" O THR A 248 " (cutoff:3.500A) Processing helix chain 'A' and resid 266 through 291 removed outlier: 3.607A pdb=" N LYS A 291 " --> pdb=" O ILE A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 342 removed outlier: 4.070A pdb=" N MET A 335 " --> pdb=" O THR A 331 " (cutoff:3.500A) Processing helix chain 'A' and resid 350 through 356 removed outlier: 3.603A pdb=" N ARG A 354 " --> pdb=" O GLY A 350 " (cutoff:3.500A) Processing helix chain 'C' and resid 238 through 244 Processing helix chain 'C' and resid 258 through 277 removed outlier: 4.009A pdb=" N ARG C 262 " --> pdb=" O PRO C 258 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LEU C 277 " --> pdb=" O ALA C 273 " (cutoff:3.500A) Processing helix chain 'F' and resid 69 through 75 removed outlier: 3.715A pdb=" N LEU F 73 " --> pdb=" O SER F 69 " (cutoff:3.500A) Processing helix chain 'F' and resid 107 through 117 removed outlier: 3.538A pdb=" N TYR F 114 " --> pdb=" O ALA F 110 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ARG F 117 " --> pdb=" O GLU F 113 " (cutoff:3.500A) Processing helix chain 'F' and resid 124 through 132 Processing helix chain 'F' and resid 194 through 203 Processing helix chain 'F' and resid 213 through 230 removed outlier: 3.878A pdb=" N ASN F 219 " --> pdb=" O SER F 215 " (cutoff:3.500A) removed outlier: 4.299A pdb=" N THR F 222 " --> pdb=" O LEU F 218 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N GLU F 223 " --> pdb=" O ASN F 219 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE F 224 " --> pdb=" O ILE F 220 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ALA F 227 " --> pdb=" O GLU F 223 " (cutoff:3.500A) Processing helix chain 'F' and resid 296 through 301 Processing helix chain 'F' and resid 325 through 336 removed outlier: 3.871A pdb=" N VAL F 330 " --> pdb=" O ARG F 326 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA F 332 " --> pdb=" O ARG F 328 " (cutoff:3.500A) removed outlier: 4.336A pdb=" N TRP F 333 " --> pdb=" O PHE F 329 " (cutoff:3.500A) Processing helix chain 'D' and resid 16 through 26 removed outlier: 3.634A pdb=" N GLU D 26 " --> pdb=" O PHE D 22 " (cutoff:3.500A) Processing helix chain 'D' and resid 31 through 61 removed outlier: 3.617A pdb=" N THR D 35 " --> pdb=" O PRO D 31 " (cutoff:3.500A) Processing helix chain 'D' and resid 66 through 75 removed outlier: 4.180A pdb=" N VAL D 70 " --> pdb=" O VAL D 66 " (cutoff:3.500A) Processing helix chain 'D' and resid 78 through 89 removed outlier: 3.864A pdb=" N ASN D 82 " --> pdb=" O LYS D 78 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 197 Processing helix chain 'D' and resid 202 through 212 removed outlier: 4.082A pdb=" N TRP D 207 " --> pdb=" O GLU D 203 " (cutoff:3.500A) removed outlier: 3.706A pdb=" N SER D 208 " --> pdb=" O TYR D 204 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 209 " --> pdb=" O VAL D 205 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N CYS D 210 " --> pdb=" O HIS D 206 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ARG D 211 " --> pdb=" O TRP D 207 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 218 removed outlier: 6.233A pdb=" N THR D 216 " --> pdb=" O ALA D 213 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ARG D 218 " --> pdb=" O PHE D 215 " (cutoff:3.500A) Processing helix chain 'D' and resid 219 through 227 removed outlier: 3.640A pdb=" N CYS D 227 " --> pdb=" O PHE D 223 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 268 removed outlier: 3.663A pdb=" N ILE D 242 " --> pdb=" O SER D 238 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 317 Processing helix chain 'E' and resid 818 through 845 Processing helix chain 'E' and resid 882 through 898 removed outlier: 3.502A pdb=" N SER E 886 " --> pdb=" O ASP E 882 " (cutoff:3.500A) Processing helix chain 'E' and resid 907 through 935 removed outlier: 3.722A pdb=" N SER E 911 " --> pdb=" O ALA E 907 " (cutoff:3.500A) Processing helix chain 'E' and resid 951 through 963 removed outlier: 3.796A pdb=" N ILE E 955 " --> pdb=" O SER E 951 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU E 956 " --> pdb=" O ASN E 952 " (cutoff:3.500A) Processing helix chain 'E' and resid 968 through 1000 removed outlier: 4.116A pdb=" N TYR E 972 " --> pdb=" O PRO E 968 " (cutoff:3.500A) Processing helix chain 'J' and resid 59 through 66 removed outlier: 3.615A pdb=" N LEU J 63 " --> pdb=" O LEU J 59 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N MET J 66 " --> pdb=" O ILE J 62 " (cutoff:3.500A) Processing helix chain 'J' and resid 76 through 87 Processing helix chain 'J' and resid 94 through 121 Processing helix chain 'J' and resid 195 through 206 Processing helix chain 'K' and resid 505 through 512 removed outlier: 3.646A pdb=" N ALA K 512 " --> pdb=" O ARG K 508 " (cutoff:3.500A) Processing helix chain 'K' and resid 525 through 550 Processing helix chain 'K' and resid 559 through 568 removed outlier: 3.614A pdb=" N LEU K 563 " --> pdb=" O ARG K 559 " (cutoff:3.500A) Processing helix chain 'K' and resid 592 through 606 Processing helix chain 'G' and resid 44 through 57 Processing helix chain 'G' and resid 61 through 69 removed outlier: 3.715A pdb=" N LEU G 66 " --> pdb=" O THR G 62 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ARG G 67 " --> pdb=" O GLU G 63 " (cutoff:3.500A) Processing helix chain 'G' and resid 105 through 120 removed outlier: 3.597A pdb=" N CYS G 118 " --> pdb=" O LEU G 114 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N GLU G 119 " --> pdb=" O LYS G 115 " (cutoff:3.500A) Processing helix chain 'G' and resid 125 through 130 removed outlier: 3.612A pdb=" N LEU G 129 " --> pdb=" O TYR G 125 " (cutoff:3.500A) Processing helix chain 'G' and resid 133 through 148 Processing helix chain 'G' and resid 149 through 161 Processing helix chain 'G' and resid 170 through 177 removed outlier: 3.625A pdb=" N GLY G 177 " --> pdb=" O SER G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 180 through 187 Processing helix chain 'G' and resid 188 through 196 removed outlier: 3.539A pdb=" N HIS G 196 " --> pdb=" O ILE G 192 " (cutoff:3.500A) Processing helix chain 'G' and resid 204 through 212 Processing helix chain 'G' and resid 222 through 233 Processing helix chain 'G' and resid 353 through 367 Processing helix chain 'H' and resid 21 through 31 Processing helix chain 'H' and resid 36 through 63 Processing helix chain 'H' and resid 71 through 81 removed outlier: 4.026A pdb=" N ILE H 75 " --> pdb=" O HIS H 71 " (cutoff:3.500A) Processing helix chain 'H' and resid 218 through 233 removed outlier: 3.815A pdb=" N GLN H 222 " --> pdb=" O SER H 218 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N LEU H 223 " --> pdb=" O ARG H 219 " (cutoff:3.500A) Processing helix chain 'H' and resid 240 through 254 removed outlier: 4.647A pdb=" N SER H 247 " --> pdb=" O LEU H 243 " (cutoff:3.500A) removed outlier: 5.217A pdb=" N ALA H 248 " --> pdb=" O LEU H 244 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA H 254 " --> pdb=" O GLN H 250 " (cutoff:3.500A) Processing helix chain 'H' and resid 257 through 260 removed outlier: 3.886A pdb=" N GLN H 260 " --> pdb=" O GLY H 257 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 257 through 260' Processing helix chain 'H' and resid 261 through 276 Processing helix chain 'H' and resid 279 through 296 Processing helix chain 'H' and resid 304 through 318 Proline residue: H 310 - end of helix Processing helix chain 'H' and resid 332 through 351 Processing helix chain 'H' and resid 357 through 372 removed outlier: 4.211A pdb=" N SER H 372 " --> pdb=" O ARG H 368 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 390 removed outlier: 4.282A pdb=" N GLN H 381 " --> pdb=" O THR H 377 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N GLY H 390 " --> pdb=" O LEU H 386 " (cutoff:3.500A) Processing helix chain 'H' and resid 394 through 411 removed outlier: 4.062A pdb=" N VAL H 399 " --> pdb=" O VAL H 395 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N LEU H 401 " --> pdb=" O ARG H 397 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N GLY H 402 " --> pdb=" O ILE H 398 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N ASN H 403 " --> pdb=" O VAL H 399 " (cutoff:3.500A) Processing helix chain 'H' and resid 415 through 431 Processing helix chain 'H' and resid 451 through 458 Processing helix chain 'H' and resid 464 through 469 Processing helix chain 'H' and resid 473 through 481 Processing helix chain 'I' and resid 13 through 20 Processing helix chain 'I' and resid 21 through 23 No H-bonds generated for 'chain 'I' and resid 21 through 23' Processing helix chain 'I' and resid 30 through 58 removed outlier: 3.536A pdb=" N THR I 51 " --> pdb=" O LEU I 47 " (cutoff:3.500A) Processing helix chain 'I' and resid 77 through 89 removed outlier: 3.814A pdb=" N ILE I 81 " --> pdb=" O THR I 77 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ARG I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) Processing helix chain 'I' and resid 98 through 110 Processing helix chain 'L' and resid 5 through 13 removed outlier: 3.736A pdb=" N THR L 12 " --> pdb=" O ASP L 8 " (cutoff:3.500A) Processing helix chain 'L' and resid 21 through 36 Processing helix chain 'L' and resid 44 through 60 Proline residue: L 52 - end of helix removed outlier: 3.684A pdb=" N GLU L 60 " --> pdb=" O ASP L 56 " (cutoff:3.500A) Processing helix chain 'L' and resid 69 through 85 removed outlier: 3.667A pdb=" N LYS L 73 " --> pdb=" O SER L 69 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ILE L 85 " --> pdb=" O ILE L 81 " (cutoff:3.500A) Processing helix chain 'L' and resid 90 through 102 Processing helix chain 'L' and resid 112 through 127 removed outlier: 3.893A pdb=" N THR L 127 " --> pdb=" O THR L 123 " (cutoff:3.500A) Processing helix chain 'L' and resid 135 through 157 Proline residue: L 151 - end of helix Processing helix chain 'L' and resid 188 through 203 removed outlier: 3.507A pdb=" N LYS L 198 " --> pdb=" O MET L 194 " (cutoff:3.500A) Processing helix chain 'L' and resid 208 through 219 removed outlier: 3.619A pdb=" N GLU L 216 " --> pdb=" O SER L 212 " (cutoff:3.500A) Processing helix chain 'L' and resid 264 through 290 removed outlier: 3.587A pdb=" N TYR L 283 " --> pdb=" O SER L 279 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N ARG L 288 " --> pdb=" O LEU L 284 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN L 289 " --> pdb=" O PHE L 285 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ALA L 290 " --> pdb=" O ILE L 286 " (cutoff:3.500A) Processing helix chain 'L' and resid 302 through 307 removed outlier: 3.712A pdb=" N ARG L 307 " --> pdb=" O ASP L 303 " (cutoff:3.500A) Processing helix chain 'L' and resid 316 through 331 removed outlier: 3.835A pdb=" N ARG L 320 " --> pdb=" O LEU L 316 " (cutoff:3.500A) Processing helix chain 'L' and resid 333 through 338 removed outlier: 3.704A pdb=" N MET L 338 " --> pdb=" O ASP L 334 " (cutoff:3.500A) Processing helix chain 'L' and resid 356 through 361 Processing helix chain 'L' and resid 363 through 379 removed outlier: 3.738A pdb=" N SER L 369 " --> pdb=" O PRO L 365 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL L 371 " --> pdb=" O ALA L 367 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ASP L 373 " --> pdb=" O SER L 369 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N PHE L 374 " --> pdb=" O THR L 370 " (cutoff:3.500A) Processing helix chain 'L' and resid 383 through 394 removed outlier: 3.636A pdb=" N ILE L 393 " --> pdb=" O LYS L 389 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N TYR L 394 " --> pdb=" O SER L 390 " (cutoff:3.500A) Processing helix chain 'L' and resid 405 through 418 removed outlier: 4.201A pdb=" N LEU L 415 " --> pdb=" O SER L 411 " (cutoff:3.500A) Processing helix chain 'L' and resid 418 through 423 Processing helix chain 'L' and resid 429 through 434 Processing helix chain 'L' and resid 434 through 452 removed outlier: 3.536A pdb=" N ILE L 438 " --> pdb=" O LEU L 434 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ARG L 445 " --> pdb=" O ALA L 441 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N MET L 448 " --> pdb=" O LYS L 444 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ARG L 452 " --> pdb=" O MET L 448 " (cutoff:3.500A) Processing helix chain 'L' and resid 452 through 457 Processing helix chain 'L' and resid 557 through 579 removed outlier: 3.597A pdb=" N LYS L 573 " --> pdb=" O MET L 569 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N THR L 574 " --> pdb=" O THR L 570 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ILE L 575 " --> pdb=" O PHE L 571 " (cutoff:3.500A) Processing helix chain 'L' and resid 604 through 609 removed outlier: 3.714A pdb=" N ASN L 609 " --> pdb=" O ASN L 605 " (cutoff:3.500A) Processing helix chain 'L' and resid 611 through 621 Processing helix chain 'L' and resid 622 through 625 removed outlier: 3.640A pdb=" N PHE L 625 " --> pdb=" O LEU L 622 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 622 through 625' Processing helix chain 'L' and resid 654 through 669 removed outlier: 3.739A pdb=" N LEU L 659 " --> pdb=" O GLU L 655 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N GLU L 661 " --> pdb=" O LYS L 657 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N MET L 666 " --> pdb=" O ILE L 662 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N PHE L 667 " --> pdb=" O PHE L 663 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N HIS L 669 " --> pdb=" O THR L 665 " (cutoff:3.500A) Processing helix chain 'L' and resid 677 through 682 removed outlier: 3.543A pdb=" N GLU L 681 " --> pdb=" O GLU L 677 " (cutoff:3.500A) Processing helix chain 'L' and resid 682 through 693 removed outlier: 3.591A pdb=" N LYS L 688 " --> pdb=" O PRO L 684 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N LEU L 691 " --> pdb=" O TYR L 687 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N ASP L 692 " --> pdb=" O LYS L 688 " (cutoff:3.500A) Processing helix chain 'L' and resid 694 through 696 No H-bonds generated for 'chain 'L' and resid 694 through 696' Processing helix chain 'L' and resid 697 through 704 removed outlier: 3.647A pdb=" N LEU L 704 " --> pdb=" O PRO L 700 " (cutoff:3.500A) Processing helix chain 'L' and resid 709 through 724 removed outlier: 3.570A pdb=" N SER L 714 " --> pdb=" O SER L 710 " (cutoff:3.500A) removed outlier: 4.756A pdb=" N GLY L 715 " --> pdb=" O SER L 711 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LYS L 722 " --> pdb=" O ILE L 718 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N SER L 723 " --> pdb=" O THR L 719 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LYS L 724 " --> pdb=" O PHE L 720 " (cutoff:3.500A) Processing helix chain 'L' and resid 725 through 729 removed outlier: 4.115A pdb=" N GLY L 729 " --> pdb=" O VAL L 726 " (cutoff:3.500A) Processing helix chain 'L' and resid 732 through 751 removed outlier: 3.513A pdb=" N ILE L 740 " --> pdb=" O SER L 736 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N PHE L 743 " --> pdb=" O LEU L 739 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N SER L 749 " --> pdb=" O LEU L 745 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N VAL L 750 " --> pdb=" O CYS L 746 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N SER L 751 " --> pdb=" O PHE L 747 " (cutoff:3.500A) Processing helix chain 'L' and resid 764 through 777 removed outlier: 3.511A pdb=" N LEU L 770 " --> pdb=" O ASN L 766 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N SER L 772 " --> pdb=" O LEU L 768 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N THR L 777 " --> pdb=" O LEU L 773 " (cutoff:3.500A) Processing helix chain 'L' and resid 783 through 796 removed outlier: 4.015A pdb=" N ILE L 789 " --> pdb=" O TYR L 785 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N SER L 795 " --> pdb=" O THR L 791 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N ILE L 796 " --> pdb=" O LEU L 792 " (cutoff:3.500A) Processing helix chain 'L' and resid 802 through 806 removed outlier: 3.563A pdb=" N TYR L 805 " --> pdb=" O GLU L 802 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N LYS L 806 " --> pdb=" O ASN L 803 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 802 through 806' Processing helix chain 'L' and resid 808 through 817 removed outlier: 4.030A pdb=" N VAL L 814 " --> pdb=" O PRO L 810 " (cutoff:3.500A) Processing helix chain 'L' and resid 831 through 841 removed outlier: 3.850A pdb=" N TYR L 835 " --> pdb=" O GLU L 831 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL L 836 " --> pdb=" O ARG L 832 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLU L 837 " --> pdb=" O ASP L 833 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N THR L 841 " --> pdb=" O GLU L 837 " (cutoff:3.500A) Processing helix chain 'L' and resid 852 through 857 removed outlier: 4.151A pdb=" N TYR L 855 " --> pdb=" O HIS L 852 " (cutoff:3.500A) Processing helix chain 'L' and resid 859 through 866 removed outlier: 3.569A pdb=" N ALA L 863 " --> pdb=" O PRO L 859 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N GLY L 866 " --> pdb=" O TYR L 862 " (cutoff:3.500A) Processing helix chain 'L' and resid 870 through 884 removed outlier: 3.794A pdb=" N ASP L 883 " --> pdb=" O GLU L 879 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASN L 884 " --> pdb=" O LEU L 880 " (cutoff:3.500A) Processing helix chain 'L' and resid 886 through 895 removed outlier: 3.504A pdb=" N ASP L 891 " --> pdb=" O ALA L 887 " (cutoff:3.500A) Proline residue: L 892 - end of helix removed outlier: 3.647A pdb=" N GLU L 895 " --> pdb=" O ASP L 891 " (cutoff:3.500A) Processing helix chain 'L' and resid 897 through 906 removed outlier: 4.304A pdb=" N GLU L 903 " --> pdb=" O ASP L 899 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA L 904 " --> pdb=" O ASP L 900 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N SER L 906 " --> pdb=" O MET L 902 " (cutoff:3.500A) Processing helix chain 'L' and resid 917 through 929 removed outlier: 3.741A pdb=" N LEU L 923 " --> pdb=" O SER L 919 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU L 929 " --> pdb=" O ILE L 925 " (cutoff:3.500A) Processing helix chain 'L' and resid 973 through 982 removed outlier: 3.696A pdb=" N SER L 979 " --> pdb=" O SER L 975 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N THR L 982 " --> pdb=" O PHE L 978 " (cutoff:3.500A) Processing helix chain 'L' and resid 987 through 1007 removed outlier: 3.516A pdb=" N ARG L 991 " --> pdb=" O ARG L 987 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE L 995 " --> pdb=" O ARG L 991 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LEU L1004 " --> pdb=" O GLY L1000 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N PHE L1005 " --> pdb=" O ILE L1001 " (cutoff:3.500A) Processing helix chain 'L' and resid 1014 through 1021 Processing helix chain 'L' and resid 1053 through 1055 No H-bonds generated for 'chain 'L' and resid 1053 through 1055' Processing helix chain 'L' and resid 1056 through 1068 removed outlier: 3.706A pdb=" N LYS L1060 " --> pdb=" O GLU L1056 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N SER L1064 " --> pdb=" O LYS L1060 " (cutoff:3.500A) Processing helix chain 'L' and resid 1069 through 1071 No H-bonds generated for 'chain 'L' and resid 1069 through 1071' Processing helix chain 'L' and resid 1074 through 1092 removed outlier: 4.080A pdb=" N ALA L1080 " --> pdb=" O GLU L1076 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU L1081 " --> pdb=" O GLU L1077 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLY L1084 " --> pdb=" O ALA L1080 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ASN L1087 " --> pdb=" O ARG L1083 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ILE L1090 " --> pdb=" O CYS L1086 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU L1091 " --> pdb=" O ASN L1087 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N LEU L1092 " --> pdb=" O HIS L1088 " (cutoff:3.500A) Processing helix chain 'L' and resid 1123 through 1133 removed outlier: 4.336A pdb=" N TYR L1130 " --> pdb=" O ASP L1126 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ALA L1131 " --> pdb=" O ALA L1127 " (cutoff:3.500A) Processing helix chain 'L' and resid 1136 through 1158 removed outlier: 3.660A pdb=" N GLN L1148 " --> pdb=" O LEU L1144 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N TYR L1151 " --> pdb=" O VAL L1147 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N CYS L1154 " --> pdb=" O ILE L1150 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU L1156 " --> pdb=" O ASP L1152 " (cutoff:3.500A) Processing helix chain 'L' and resid 1168 through 1180 removed outlier: 4.099A pdb=" N VAL L1172 " --> pdb=" O ALA L1168 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N CYS L1174 " --> pdb=" O LEU L1170 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N SER L1175 " --> pdb=" O ASN L1171 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE L1177 " --> pdb=" O MET L1173 " (cutoff:3.500A) Processing helix chain 'L' and resid 1185 through 1199 removed outlier: 3.564A pdb=" N LYS L1189 " --> pdb=" O PRO L1185 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N GLY L1192 " --> pdb=" O LYS L1188 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N GLU L1197 " --> pdb=" O CYS L1193 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N MET L1198 " --> pdb=" O ILE L1194 " (cutoff:3.500A) Processing helix chain 'L' and resid 1208 through 1213 removed outlier: 4.071A pdb=" N ALA L1212 " --> pdb=" O LYS L1208 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG L1213 " --> pdb=" O TYR L1209 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1208 through 1213' Processing helix chain 'L' and resid 1213 through 1227 removed outlier: 3.647A pdb=" N VAL L1224 " --> pdb=" O ALA L1220 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N LEU L1225 " --> pdb=" O LEU L1221 " (cutoff:3.500A) Processing helix chain 'L' and resid 1234 through 1249 removed outlier: 3.812A pdb=" N THR L1239 " --> pdb=" O GLU L1235 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ALA L1240 " --> pdb=" O VAL L1236 " (cutoff:3.500A) removed outlier: 3.779A pdb=" N LEU L1243 " --> pdb=" O THR L1239 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N ILE L1244 " --> pdb=" O ALA L1240 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU L1248 " --> pdb=" O ILE L1244 " (cutoff:3.500A) Processing helix chain 'L' and resid 1263 through 1270 removed outlier: 3.630A pdb=" N LEU L1268 " --> pdb=" O VAL L1264 " (cutoff:3.500A) Processing helix chain 'L' and resid 1281 through 1297 removed outlier: 3.559A pdb=" N THR L1286 " --> pdb=" O ILE L1282 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA L1287 " --> pdb=" O VAL L1283 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N GLN L1288 " --> pdb=" O ARG L1284 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU L1291 " --> pdb=" O ALA L1287 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR L1297 " --> pdb=" O THR L1293 " (cutoff:3.500A) Processing helix chain 'L' and resid 1301 through 1306 Processing helix chain 'L' and resid 1309 through 1320 removed outlier: 3.626A pdb=" N LEU L1313 " --> pdb=" O CYS L1309 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA L1315 " --> pdb=" O HIS L1311 " (cutoff:3.500A) Proline residue: L1316 - end of helix removed outlier: 4.063A pdb=" N LYS L1320 " --> pdb=" O PRO L1316 " (cutoff:3.500A) Processing helix chain 'L' and resid 1328 through 1341 removed outlier: 3.860A pdb=" N GLY L1332 " --> pdb=" O GLN L1328 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N ILE L1334 " --> pdb=" O GLN L1330 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N ALA L1336 " --> pdb=" O GLY L1332 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ILE L1337 " --> pdb=" O ASN L1333 " (cutoff:3.500A) Processing helix chain 'L' and resid 1351 through 1364 removed outlier: 3.862A pdb=" N ARG L1356 " --> pdb=" O GLU L1352 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N LEU L1357 " --> pdb=" O GLU L1353 " (cutoff:3.500A) Processing helix chain 'L' and resid 1383 through 1403 removed outlier: 3.856A pdb=" N VAL L1393 " --> pdb=" O ARG L1389 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N CYS L1394 " --> pdb=" O LEU L1390 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N ILE L1395 " --> pdb=" O ARG L1391 " (cutoff:3.500A) removed outlier: 4.173A pdb=" N GLN L1396 " --> pdb=" O VAL L1392 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ILE L1402 " --> pdb=" O LEU L1398 " (cutoff:3.500A) Processing helix chain 'L' and resid 1407 through 1412 Processing helix chain 'L' and resid 1416 through 1427 removed outlier: 3.639A pdb=" N LYS L1426 " --> pdb=" O VAL L1422 " (cutoff:3.500A) Processing helix chain 'L' and resid 1433 through 1444 removed outlier: 3.694A pdb=" N ALA L1438 " --> pdb=" O GLU L1434 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA L1439 " --> pdb=" O ILE L1435 " (cutoff:3.500A) Processing helix chain 'L' and resid 1455 through 1469 Proline residue: L1464 - end of helix Processing helix chain 'L' and resid 1476 through 1487 Processing helix chain 'L' and resid 1497 through 1510 removed outlier: 3.564A pdb=" N LEU L1503 " --> pdb=" O GLY L1499 " (cutoff:3.500A) removed outlier: 4.129A pdb=" N ASP L1504 " --> pdb=" O SER L1500 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N ALA L1508 " --> pdb=" O ASP L1504 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N TRP L1509 " --> pdb=" O HIS L1505 " (cutoff:3.500A) Processing helix chain 'L' and resid 1511 through 1515 Processing helix chain 'L' and resid 1527 through 1537 removed outlier: 3.652A pdb=" N ILE L1531 " --> pdb=" O SER L1527 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N ILE L1532 " --> pdb=" O THR L1528 " (cutoff:3.500A) Processing helix chain 'L' and resid 1538 through 1542 removed outlier: 3.985A pdb=" N LEU L1542 " --> pdb=" O PHE L1539 " (cutoff:3.500A) Processing helix chain 'L' and resid 1550 through 1563 removed outlier: 3.523A pdb=" N MET L1554 " --> pdb=" O MET L1550 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN L1563 " --> pdb=" O TYR L1559 " (cutoff:3.500A) Processing helix chain 'L' and resid 1570 through 1573 Processing helix chain 'L' and resid 1574 through 1583 removed outlier: 3.588A pdb=" N LYS L1578 " --> pdb=" O GLU L1574 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N PHE L1579 " --> pdb=" O PRO L1575 " (cutoff:3.500A) Processing helix chain 'L' and resid 1583 through 1592 removed outlier: 3.503A pdb=" N SER L1587 " --> pdb=" O PHE L1583 " (cutoff:3.500A) Processing helix chain 'L' and resid 1597 through 1610 removed outlier: 3.826A pdb=" N THR L1601 " --> pdb=" O LYS L1597 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N ARG L1603 " --> pdb=" O GLU L1599 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N PHE L1604 " --> pdb=" O ILE L1600 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N TYR L1606 " --> pdb=" O THR L1602 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY L1609 " --> pdb=" O VAL L1605 " (cutoff:3.500A) Processing helix chain 'L' and resid 1613 through 1623 removed outlier: 3.828A pdb=" N ALA L1618 " --> pdb=" O SER L1614 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS L1619 " --> pdb=" O SER L1615 " (cutoff:3.500A) Processing helix chain 'L' and resid 1624 through 1629 removed outlier: 3.778A pdb=" N ARG L1628 " --> pdb=" O LEU L1624 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLY L1629 " --> pdb=" O PRO L1625 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1624 through 1629' Processing helix chain 'L' and resid 1630 through 1633 Processing helix chain 'L' and resid 1643 through 1656 removed outlier: 3.678A pdb=" N LEU L1647 " --> pdb=" O ARG L1643 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASP L1649 " --> pdb=" O SER L1645 " (cutoff:3.500A) Processing helix chain 'L' and resid 1666 through 1683 removed outlier: 3.741A pdb=" N THR L1681 " --> pdb=" O SER L1677 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N LEU L1682 " --> pdb=" O VAL L1678 " (cutoff:3.500A) Processing helix chain 'L' and resid 1693 through 1708 removed outlier: 3.876A pdb=" N LEU L1705 " --> pdb=" O GLU L1701 " (cutoff:3.500A) Processing helix chain 'L' and resid 1710 through 1714 Processing helix chain 'L' and resid 1724 through 1728 removed outlier: 3.585A pdb=" N ILE L1728 " --> pdb=" O ILE L1725 " (cutoff:3.500A) Processing helix chain 'L' and resid 1742 through 1746 Processing helix chain 'L' and resid 1755 through 1767 removed outlier: 3.913A pdb=" N LEU L1760 " --> pdb=" O VAL L1756 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP L1761 " --> pdb=" O GLN L1757 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N ILE L1764 " --> pdb=" O LEU L1760 " (cutoff:3.500A) Processing helix chain 'L' and resid 1777 through 1783 removed outlier: 3.816A pdb=" N TYR L1780 " --> pdb=" O VAL L1777 " (cutoff:3.500A) Processing helix chain 'L' and resid 1784 through 1795 removed outlier: 3.641A pdb=" N CYS L1788 " --> pdb=" O PHE L1784 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU L1793 " --> pdb=" O ILE L1789 " (cutoff:3.500A) Processing helix chain 'L' and resid 1812 through 1820 removed outlier: 4.010A pdb=" N SER L1818 " --> pdb=" O LYS L1814 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ASP L1819 " --> pdb=" O SER L1815 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N VAL L1820 " --> pdb=" O PHE L1816 " (cutoff:3.500A) Processing helix chain 'L' and resid 1836 through 1854 removed outlier: 4.261A pdb=" N GLU L1842 " --> pdb=" O ARG L1838 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N LEU L1843 " --> pdb=" O TYR L1839 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU L1846 " --> pdb=" O GLU L1842 " (cutoff:3.500A) removed outlier: 4.076A pdb=" N LEU L1849 " --> pdb=" O GLN L1845 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N LYS L1852 " --> pdb=" O ALA L1848 " (cutoff:3.500A) Processing helix chain 'L' and resid 1859 through 1864 removed outlier: 3.830A pdb=" N ASP L1864 " --> pdb=" O ASP L1860 " (cutoff:3.500A) Processing helix chain 'L' and resid 1865 through 1870 Processing helix chain 'L' and resid 1871 through 1874 removed outlier: 3.537A pdb=" N LYS L1874 " --> pdb=" O ASN L1871 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 1871 through 1874' Processing helix chain 'L' and resid 1882 through 1893 removed outlier: 3.772A pdb=" N PHE L1891 " --> pdb=" O VAL L1887 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N SER L1893 " --> pdb=" O ALA L1889 " (cutoff:3.500A) Processing helix chain 'L' and resid 1902 through 1907 removed outlier: 4.411A pdb=" N PHE L1906 " --> pdb=" O THR L1902 " (cutoff:3.500A) Processing helix chain 'L' and resid 1917 through 1927 removed outlier: 3.581A pdb=" N LYS L1922 " --> pdb=" O ARG L1918 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN L1923 " --> pdb=" O TYR L1919 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ALA L1924 " --> pdb=" O LEU L1920 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LEU L1927 " --> pdb=" O GLN L1923 " (cutoff:3.500A) Processing helix chain 'L' and resid 1928 through 1933 removed outlier: 3.672A pdb=" N SER L1933 " --> pdb=" O ALA L1929 " (cutoff:3.500A) Processing helix chain 'L' and resid 1943 through 1949 removed outlier: 3.557A pdb=" N VAL L1949 " --> pdb=" O TRP L1945 " (cutoff:3.500A) Processing helix chain 'L' and resid 1961 through 1968 removed outlier: 3.776A pdb=" N ILE L1967 " --> pdb=" O ILE L1963 " (cutoff:3.500A) Processing helix chain 'L' and resid 1980 through 1994 Processing helix chain 'L' and resid 2001 through 2020 removed outlier: 3.865A pdb=" N LEU L2005 " --> pdb=" O GLU L2001 " (cutoff:3.500A) Processing helix chain 'L' and resid 2086 through 2102 removed outlier: 3.540A pdb=" N SER L2102 " --> pdb=" O TYR L2098 " (cutoff:3.500A) Processing helix chain 'L' and resid 2111 through 2124 Processing helix chain 'L' and resid 2134 through 2141 Processing helix chain 'L' and resid 2153 through 2168 Processing helix chain 'L' and resid 2174 through 2188 removed outlier: 3.521A pdb=" N LYS L2184 " --> pdb=" O SER L2180 " (cutoff:3.500A) Processing helix chain 'L' and resid 2196 through 2213 removed outlier: 3.773A pdb=" N ALA L2211 " --> pdb=" O ILE L2207 " (cutoff:3.500A) Processing helix chain 'L' and resid 2222 through 2239 Processing helix chain 'L' and resid 2249 through 2259 Processing helix chain 'L' and resid 2265 through 2286 Proline residue: L2271 - end of helix removed outlier: 3.560A pdb=" N MET L2274 " --> pdb=" O LEU L2270 " (cutoff:3.500A) Processing helix chain 'L' and resid 2304 through 2322 removed outlier: 3.541A pdb=" N ALA L2322 " --> pdb=" O ASN L2318 " (cutoff:3.500A) Processing helix chain 'L' and resid 2330 through 2344 Processing helix chain 'L' and resid 2347 through 2362 removed outlier: 3.564A pdb=" N ILE L2362 " --> pdb=" O VAL L2358 " (cutoff:3.500A) Processing helix chain 'L' and resid 2371 through 2383 removed outlier: 3.637A pdb=" N ILE L2383 " --> pdb=" O GLY L2379 " (cutoff:3.500A) Processing helix chain 'L' and resid 2384 through 2386 No H-bonds generated for 'chain 'L' and resid 2384 through 2386' Processing helix chain 'L' and resid 2392 through 2407 removed outlier: 3.613A pdb=" N VAL L2399 " --> pdb=" O LYS L2395 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ILE L2400 " --> pdb=" O PHE L2396 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N VAL L2401 " --> pdb=" O ASN L2397 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ASP L2402 " --> pdb=" O GLN L2398 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N PHE L2404 " --> pdb=" O ILE L2400 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LYS L2407 " --> pdb=" O ILE L2403 " (cutoff:3.500A) Processing helix chain 'L' and resid 2418 through 2423 removed outlier: 3.509A pdb=" N LEU L2423 " --> pdb=" O GLU L2419 " (cutoff:3.500A) Processing helix chain 'L' and resid 2430 through 2445 removed outlier: 3.746A pdb=" N LYS L2436 " --> pdb=" O SER L2432 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N LEU L2445 " --> pdb=" O LEU L2441 " (cutoff:3.500A) Processing helix chain 'L' and resid 2454 through 2459 removed outlier: 3.522A pdb=" N ASP L2459 " --> pdb=" O TYR L2455 " (cutoff:3.500A) Processing helix chain 'L' and resid 2470 through 2480 Processing helix chain 'L' and resid 2522 through 2535 removed outlier: 3.727A pdb=" N ALA L2526 " --> pdb=" O ILE L2522 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLU L2530 " --> pdb=" O ALA L2526 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N ASP L2533 " --> pdb=" O ASN L2529 " (cutoff:3.500A) Processing helix chain 'L' and resid 2540 through 2552 removed outlier: 3.514A pdb=" N LEU L2544 " --> pdb=" O ALA L2540 " (cutoff:3.500A) Proline residue: L2546 - end of helix removed outlier: 3.613A pdb=" N ASP L2549 " --> pdb=" O ASN L2545 " (cutoff:3.500A) Processing helix chain 'L' and resid 2554 through 2571 removed outlier: 4.203A pdb=" N ILE L2558 " --> pdb=" O SER L2554 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N HIS L2559 " --> pdb=" O ALA L2555 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N VAL L2563 " --> pdb=" O HIS L2559 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N VAL L2564 " --> pdb=" O ASN L2560 " (cutoff:3.500A) Proline residue: L2567 - end of helix Processing helix chain 'L' and resid 2577 through 2591 removed outlier: 3.685A pdb=" N LEU L2588 " --> pdb=" O ALA L2584 " (cutoff:3.500A) Processing helix chain 'L' and resid 2603 through 2613 removed outlier: 3.521A pdb=" N GLY L2611 " --> pdb=" O SER L2607 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N GLY L2613 " --> pdb=" O LEU L2609 " (cutoff:3.500A) Processing helix chain 'L' and resid 2621 through 2632 removed outlier: 3.541A pdb=" N TYR L2627 " --> pdb=" O HIS L2623 " (cutoff:3.500A) Processing helix chain 'L' and resid 2635 through 2645 removed outlier: 4.051A pdb=" N LEU L2641 " --> pdb=" O GLY L2637 " (cutoff:3.500A) Processing helix chain 'L' and resid 2653 through 2669 removed outlier: 3.697A pdb=" N ALA L2659 " --> pdb=" O LYS L2655 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N VAL L2667 " --> pdb=" O ALA L2663 " (cutoff:3.500A) Processing helix chain 'L' and resid 2676 through 2682 removed outlier: 3.795A pdb=" N ARG L2682 " --> pdb=" O TYR L2678 " (cutoff:3.500A) Processing helix chain 'L' and resid 2688 through 2694 Processing helix chain 'L' and resid 2694 through 2700 removed outlier: 3.743A pdb=" N ILE L2699 " --> pdb=" O SER L2695 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY L2700 " --> pdb=" O TYR L2696 " (cutoff:3.500A) Processing helix chain 'L' and resid 2702 through 2714 removed outlier: 3.907A pdb=" N LEU L2706 " --> pdb=" O TRP L2702 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLN L2707 " --> pdb=" O ASP L2703 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LEU L2708 " --> pdb=" O LYS L2704 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N ALA L2712 " --> pdb=" O LEU L2708 " (cutoff:3.500A) removed outlier: 3.683A pdb=" N ILE L2714 " --> pdb=" O GLU L2710 " (cutoff:3.500A) Processing helix chain 'L' and resid 2730 through 2742 removed outlier: 4.341A pdb=" N ILE L2736 " --> pdb=" O GLU L2732 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N CYS L2738 " --> pdb=" O HIS L2734 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N GLU L2740 " --> pdb=" O ILE L2736 " (cutoff:3.500A) Processing helix chain 'L' and resid 2746 through 2755 removed outlier: 3.855A pdb=" N GLU L2750 " --> pdb=" O GLU L2746 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA L2752 " --> pdb=" O LEU L2748 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N HIS L2754 " --> pdb=" O GLU L2750 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N GLU L2755 " --> pdb=" O LEU L2751 " (cutoff:3.500A) Processing helix chain 'L' and resid 2757 through 2767 Processing helix chain 'L' and resid 2774 through 2786 removed outlier: 3.662A pdb=" N GLN L2780 " --> pdb=" O GLU L2776 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N VAL L2785 " --> pdb=" O SER L2781 " (cutoff:3.500A) Processing helix chain 'L' and resid 2792 through 2806 removed outlier: 3.651A pdb=" N PHE L2796 " --> pdb=" O ARG L2792 " (cutoff:3.500A) Processing helix chain 'L' and resid 2812 through 2832 removed outlier: 3.718A pdb=" N SER L2816 " --> pdb=" O LEU L2812 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU L2825 " --> pdb=" O GLU L2821 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N ARG L2828 " --> pdb=" O GLN L2824 " (cutoff:3.500A) Processing helix chain 'L' and resid 2841 through 2853 removed outlier: 3.603A pdb=" N THR L2847 " --> pdb=" O GLY L2843 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN L2849 " --> pdb=" O LEU L2845 " (cutoff:3.500A) Processing helix chain 'L' and resid 2856 through 2861 Processing helix chain 'L' and resid 2878 through 2889 Processing helix chain 'L' and resid 2896 through 2918 removed outlier: 3.960A pdb=" N LEU L2903 " --> pdb=" O ILE L2899 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N TRP L2906 " --> pdb=" O ASP L2902 " (cutoff:3.500A) Processing helix chain 'L' and resid 2944 through 2960 removed outlier: 3.530A pdb=" N ARG L2957 " --> pdb=" O ALA L2953 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N GLU L2960 " --> pdb=" O ALA L2956 " (cutoff:3.500A) Processing helix chain 'L' and resid 3021 through 3035 removed outlier: 3.594A pdb=" N PHE L3025 " --> pdb=" O LYS L3021 " (cutoff:3.500A) removed outlier: 3.944A pdb=" N LEU L3035 " --> pdb=" O PHE L3031 " (cutoff:3.500A) Processing helix chain 'L' and resid 3037 through 3050 Processing helix chain 'L' and resid 3057 through 3073 removed outlier: 4.427A pdb=" N GLY L3063 " --> pdb=" O TRP L3059 " (cutoff:3.500A) Processing helix chain 'L' and resid 3080 through 3085 removed outlier: 3.946A pdb=" N SER L3085 " --> pdb=" O LYS L3081 " (cutoff:3.500A) Processing helix chain 'L' and resid 3099 through 3110 removed outlier: 4.285A pdb=" N ARG L3105 " --> pdb=" O LYS L3101 " (cutoff:3.500A) removed outlier: 4.175A pdb=" N TRP L3108 " --> pdb=" O CYS L3104 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LEU L3109 " --> pdb=" O ARG L3105 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ILE L3110 " --> pdb=" O ILE L3106 " (cutoff:3.500A) Processing helix chain 'L' and resid 3118 through 3124 Processing helix chain 'L' and resid 3132 through 3136 removed outlier: 3.954A pdb=" N TRP L3135 " --> pdb=" O VAL L3132 " (cutoff:3.500A) Processing helix chain 'L' and resid 3138 through 3146 removed outlier: 4.159A pdb=" N THR L3144 " --> pdb=" O PRO L3140 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER L3145 " --> pdb=" O GLN L3141 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU L3146 " --> pdb=" O LEU L3142 " (cutoff:3.500A) Processing helix chain 'L' and resid 3150 through 3157 removed outlier: 3.583A pdb=" N HIS L3156 " --> pdb=" O LYS L3152 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ILE L3157 " --> pdb=" O ILE L3153 " (cutoff:3.500A) Processing helix chain 'L' and resid 3158 through 3165 removed outlier: 3.713A pdb=" N LYS L3163 " --> pdb=" O ILE L3159 " (cutoff:3.500A) Processing helix chain 'L' and resid 3169 through 3174 Processing helix chain 'L' and resid 3285 through 3296 removed outlier: 3.553A pdb=" N ILE L3289 " --> pdb=" O ASP L3285 " (cutoff:3.500A) Processing helix chain 'L' and resid 3297 through 3314 removed outlier: 3.699A pdb=" N ALA L3301 " --> pdb=" O TYR L3297 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LEU L3302 " --> pdb=" O PRO L3298 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N GLU L3305 " --> pdb=" O ALA L3301 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N SER L3306 " --> pdb=" O LEU L3302 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LEU L3307 " --> pdb=" O SER L3303 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N GLN L3310 " --> pdb=" O SER L3306 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N ARG L3314 " --> pdb=" O GLN L3310 " (cutoff:3.500A) Processing helix chain 'L' and resid 3412 through 3416 Processing helix chain 'L' and resid 3416 through 3421 removed outlier: 3.742A pdb=" N SER L3420 " --> pdb=" O SER L3416 " (cutoff:3.500A) Processing helix chain 'L' and resid 3490 through 3509 removed outlier: 3.742A pdb=" N GLU L3495 " --> pdb=" O CYS L3491 " (cutoff:3.500A) removed outlier: 5.248A pdb=" N ARG L3496 " --> pdb=" O ARG L3492 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU L3500 " --> pdb=" O ARG L3496 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N PHE L3501 " --> pdb=" O ILE L3497 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ILE L3503 " --> pdb=" O GLN L3499 " (cutoff:3.500A) removed outlier: 4.471A pdb=" N ASP L3506 " --> pdb=" O ARG L3502 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N ALA L3507 " --> pdb=" O ILE L3503 " (cutoff:3.500A) Processing helix chain 'L' and resid 3544 through 3556 Processing helix chain 'L' and resid 3604 through 3612 removed outlier: 3.963A pdb=" N THR L3610 " --> pdb=" O LYS L3606 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N GLU L3611 " --> pdb=" O ASP L3607 " (cutoff:3.500A) Processing helix chain 'L' and resid 3615 through 3639 removed outlier: 3.847A pdb=" N TYR L3619 " --> pdb=" O ASN L3615 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA L3631 " --> pdb=" O THR L3627 " (cutoff:3.500A) removed outlier: 4.307A pdb=" N SER L3632 " --> pdb=" O ALA L3628 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N MET L3636 " --> pdb=" O SER L3632 " (cutoff:3.500A) Processing helix chain 'L' and resid 3706 through 3714 removed outlier: 4.224A pdb=" N PHE L3712 " --> pdb=" O ASN L3708 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N GLY L3714 " --> pdb=" O GLN L3710 " (cutoff:3.500A) Processing helix chain 'L' and resid 3721 through 3734 removed outlier: 3.979A pdb=" N ILE L3726 " --> pdb=" O LEU L3722 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N LEU L3727 " --> pdb=" O SER L3723 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N ALA L3730 " --> pdb=" O ILE L3726 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER L3732 " --> pdb=" O VAL L3728 " (cutoff:3.500A) Processing helix chain 'L' and resid 3751 through 3760 removed outlier: 3.651A pdb=" N ALA L3757 " --> pdb=" O ILE L3753 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N HIS L3760 " --> pdb=" O PHE L3756 " (cutoff:3.500A) Processing helix chain 'L' and resid 3768 through 3785 removed outlier: 3.678A pdb=" N GLU L3778 " --> pdb=" O ARG L3774 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N LEU L3780 " --> pdb=" O ASN L3776 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N VAL L3784 " --> pdb=" O LEU L3780 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N LEU L3785 " --> pdb=" O THR L3781 " (cutoff:3.500A) Processing helix chain 'L' and resid 3786 through 3788 No H-bonds generated for 'chain 'L' and resid 3786 through 3788' Processing helix chain 'L' and resid 3800 through 3809 Processing helix chain 'L' and resid 3810 through 3816 removed outlier: 3.618A pdb=" N ALA L3815 " --> pdb=" O PRO L3811 " (cutoff:3.500A) Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 463 through 471 Processing helix chain 'B' and resid 510 through 522 Processing helix chain 'B' and resid 530 through 538 Processing helix chain 'B' and resid 546 through 557 Processing sheet with id=AA1, first strand: chain 'M' and resid 102 through 106 removed outlier: 3.640A pdb=" N THR M 111 " --> pdb=" O ILE M 106 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N GLY M 125 " --> pdb=" O ILE M 70 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N ILE M 70 " --> pdb=" O GLY M 125 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N LEU M 67 " --> pdb=" O GLY M 162 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLY M 162 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 6.899A pdb=" N ASN M 69 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ILE M 160 " --> pdb=" O ASN M 69 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N VAL M 71 " --> pdb=" O GLN M 158 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N ILE M 160 " --> pdb=" O GLY M 216 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N GLY M 216 " --> pdb=" O ILE M 160 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N ILE M 202 " --> pdb=" O MET M 197 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N LEU M 193 " --> pdb=" O ILE M 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 92 through 94 removed outlier: 4.494A pdb=" N TYR F 145 " --> pdb=" O PHE F 85 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ILE F 87 " --> pdb=" O TYR F 145 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE F 140 " --> pdb=" O LEU F 190 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N LEU F 190 " --> pdb=" O ILE F 140 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N LEU F 142 " --> pdb=" O THR F 188 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N THR F 188 " --> pdb=" O LEU F 142 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'G' and resid 703 through 706 removed outlier: 6.823A pdb=" N GLY G 717 " --> pdb=" O TYR G 704 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N TYR G 384 " --> pdb=" O GLY G 718 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'G' and resid 393 through 398 removed outlier: 3.594A pdb=" N CYS G 395 " --> pdb=" O GLY G 408 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N SER G 407 " --> pdb=" O LYS G 415 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 456 through 461 removed outlier: 3.987A pdb=" N GLY G 458 " --> pdb=" O CYS G 471 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG G 478 " --> pdb=" O SER G 470 " (cutoff:3.500A) removed outlier: 6.650A pdb=" N VAL G 477 " --> pdb=" O SER G 490 " (cutoff:3.500A) removed outlier: 4.686A pdb=" N SER G 490 " --> pdb=" O VAL G 477 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LEU G 479 " --> pdb=" O LEU G 488 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'G' and resid 498 through 503 removed outlier: 6.330A pdb=" N ALA G 513 " --> pdb=" O TRP G 499 " (cutoff:3.500A) removed outlier: 4.348A pdb=" N VAL G 501 " --> pdb=" O ALA G 511 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA G 511 " --> pdb=" O VAL G 501 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N PHE G 503 " --> pdb=" O TYR G 509 " (cutoff:3.500A) removed outlier: 7.139A pdb=" N TYR G 509 " --> pdb=" O PHE G 503 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N ARG G 520 " --> pdb=" O THR G 512 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG G 531 " --> pdb=" O LEU G 521 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 540 through 545 removed outlier: 4.560A pdb=" N THR G 560 " --> pdb=" O SER G 556 " (cutoff:3.500A) removed outlier: 4.019A pdb=" N ARG G 573 " --> pdb=" O MET G 563 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N ASP G 565 " --> pdb=" O CYS G 571 " (cutoff:3.500A) removed outlier: 6.783A pdb=" N CYS G 571 " --> pdb=" O ASP G 565 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 584 through 587 removed outlier: 6.196A pdb=" N ASP G 607 " --> pdb=" O ARG G 613 " (cutoff:3.500A) removed outlier: 6.016A pdb=" N ARG G 613 " --> pdb=" O ASP G 607 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 625 through 630 removed outlier: 3.650A pdb=" N ARG G 647 " --> pdb=" O SER G 639 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N SER G 645 " --> pdb=" O GLY G 641 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N SER G 694 " --> pdb=" O VAL G 648 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 954 through 956 Processing sheet with id=AB2, first strand: chain 'L' and resid 3410 through 3411 Processing sheet with id=AB3, first strand: chain 'L' and resid 3451 through 3452 Processing sheet with id=AB4, first strand: chain 'L' and resid 3459 through 3460 removed outlier: 3.665A pdb=" N VAL L3459 " --> pdb=" O TYR L3466 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N TYR L3466 " --> pdb=" O VAL L3459 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'L' and resid 3481 through 3484 removed outlier: 3.524A pdb=" N GLN L3484 " --> pdb=" O ARG L3534 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG L3534 " --> pdb=" O GLN L3484 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 3650 through 3652 1875 hydrogen bonds defined for protein. 5541 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: 22.17 Time building geometry restraints manager: 16.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.34: 13167 1.34 - 1.50: 11020 1.50 - 1.65: 17038 1.65 - 1.81: 221 1.81 - 1.97: 27 Bond restraints: 41473 Sorted by residual: bond pdb=" C ILE M 194 " pdb=" N TYR M 195 " ideal model delta sigma weight residual 1.332 1.966 -0.634 1.25e-02 6.40e+03 2.57e+03 bond pdb=" C SER M 183 " pdb=" N SER M 184 " ideal model delta sigma weight residual 1.332 1.483 -0.151 1.25e-02 6.40e+03 1.46e+02 bond pdb=" C ARG L 828 " pdb=" N PRO L 829 " ideal model delta sigma weight residual 1.333 1.375 -0.042 7.80e-03 1.64e+04 2.92e+01 bond pdb=" C ILE L 340 " pdb=" N PRO L 341 " ideal model delta sigma weight residual 1.337 1.389 -0.052 9.80e-03 1.04e+04 2.81e+01 bond pdb=" N PRO D 67 " pdb=" CA PRO D 67 " ideal model delta sigma weight residual 1.469 1.532 -0.064 1.28e-02 6.10e+03 2.46e+01 ... (remaining 41468 not shown) Histogram of bond angle deviations from ideal: 95.63 - 103.39: 469 103.39 - 111.16: 15963 111.16 - 118.92: 17866 118.92 - 126.68: 21438 126.68 - 134.45: 510 Bond angle restraints: 56246 Sorted by residual: angle pdb=" CA ILE M 194 " pdb=" C ILE M 194 " pdb=" N TYR M 195 " ideal model delta sigma weight residual 116.60 103.71 12.89 1.45e+00 4.76e-01 7.90e+01 angle pdb=" N GLY M 62 " pdb=" CA GLY M 62 " pdb=" C GLY M 62 " ideal model delta sigma weight residual 113.18 130.46 -17.28 2.37e+00 1.78e-01 5.32e+01 angle pdb=" N ILE L2595 " pdb=" CA ILE L2595 " pdb=" C ILE L2595 " ideal model delta sigma weight residual 111.91 105.46 6.45 8.90e-01 1.26e+00 5.25e+01 angle pdb=" C LYS K 453 " pdb=" N PRO K 454 " pdb=" CA PRO K 454 " ideal model delta sigma weight residual 120.38 127.39 -7.01 1.03e+00 9.43e-01 4.63e+01 angle pdb=" N LYS D 323 " pdb=" CA LYS D 323 " pdb=" C LYS D 323 " ideal model delta sigma weight residual 113.18 105.04 8.14 1.21e+00 6.83e-01 4.53e+01 ... (remaining 56241 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.90: 22274 17.90 - 35.80: 2257 35.80 - 53.70: 435 53.70 - 71.60: 88 71.60 - 89.50: 25 Dihedral angle restraints: 25079 sinusoidal: 9359 harmonic: 15720 Sorted by residual: dihedral pdb=" C LYS E 930 " pdb=" N LYS E 930 " pdb=" CA LYS E 930 " pdb=" CB LYS E 930 " ideal model delta harmonic sigma weight residual -122.60 -137.83 15.23 0 2.50e+00 1.60e-01 3.71e+01 dihedral pdb=" CA LEU F 124 " pdb=" C LEU F 124 " pdb=" N ILE F 125 " pdb=" CA ILE F 125 " ideal model delta harmonic sigma weight residual -180.00 -150.12 -29.88 0 5.00e+00 4.00e-02 3.57e+01 dihedral pdb=" CA ARG G 592 " pdb=" C ARG G 592 " pdb=" N TRP G 593 " pdb=" CA TRP G 593 " ideal model delta harmonic sigma weight residual -180.00 -150.68 -29.32 0 5.00e+00 4.00e-02 3.44e+01 ... (remaining 25076 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.107: 6013 0.107 - 0.214: 484 0.214 - 0.321: 59 0.321 - 0.428: 5 0.428 - 0.535: 5 Chirality restraints: 6566 Sorted by residual: chirality pdb=" CB ILE K 462 " pdb=" CA ILE K 462 " pdb=" CG1 ILE K 462 " pdb=" CG2 ILE K 462 " both_signs ideal model delta sigma weight residual False 2.64 2.11 0.53 2.00e-01 2.50e+01 7.15e+00 chirality pdb=" CA LYS E 930 " pdb=" N LYS E 930 " pdb=" C LYS E 930 " pdb=" CB LYS E 930 " both_signs ideal model delta sigma weight residual False 2.51 1.99 0.52 2.00e-01 2.50e+01 6.76e+00 chirality pdb=" CA ILE M 63 " pdb=" N ILE M 63 " pdb=" C ILE M 63 " pdb=" CB ILE M 63 " both_signs ideal model delta sigma weight residual False 2.43 2.93 -0.49 2.00e-01 2.50e+01 6.11e+00 ... (remaining 6563 not shown) Planarity restraints: 7196 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE M 194 " 0.093 2.00e-02 2.50e+03 1.70e-01 2.88e+02 pdb=" C ILE M 194 " -0.291 2.00e-02 2.50e+03 pdb=" O ILE M 194 " 0.134 2.00e-02 2.50e+03 pdb=" N TYR M 195 " 0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER M 183 " -0.038 2.00e-02 2.50e+03 7.25e-02 5.26e+01 pdb=" C SER M 183 " 0.125 2.00e-02 2.50e+03 pdb=" O SER M 183 " -0.049 2.00e-02 2.50e+03 pdb=" N SER M 184 " -0.039 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 935 " 0.020 2.00e-02 2.50e+03 4.12e-02 1.70e+01 pdb=" C SER E 935 " -0.071 2.00e-02 2.50e+03 pdb=" O SER E 935 " 0.026 2.00e-02 2.50e+03 pdb=" N LYS E 936 " 0.025 2.00e-02 2.50e+03 ... (remaining 7193 not shown) Histogram of nonbonded interaction distances: 2.04 - 2.62: 575 2.62 - 3.19: 36755 3.19 - 3.76: 62844 3.76 - 4.33: 83321 4.33 - 4.90: 132208 Nonbonded interactions: 315703 Sorted by model distance: nonbonded pdb=" OG SER G 462 " pdb=" OD1 ASP G 464 " model vdw 2.044 2.440 nonbonded pdb=" O ARG G 67 " pdb=" OG SER G 70 " model vdw 2.073 2.440 nonbonded pdb=" OE2 GLU M 188 " pdb=" NH2 ARG D 85 " model vdw 2.075 2.520 nonbonded pdb=" O LEU F 202 " pdb=" OG1 THR F 205 " model vdw 2.077 2.440 nonbonded pdb=" O PHE L1425 " pdb=" N LEU L1428 " model vdw 2.098 2.520 ... (remaining 315698 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: 5.630 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.020 Extract box with map and model: 29.460 Check model and map are aligned: 0.580 Set scattering table: 0.370 Process input model: 107.740 Find NCS groups from input model: 1.190 Set up NCS constraints: 0.160 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: 0.000 Load rotamer database and sin/cos tables:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 148.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5590 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 : 0.008 0.634 41473 Z= 0.570 Angle : 1.078 17.280 56246 Z= 0.651 Chirality : 0.064 0.535 6566 Planarity : 0.007 0.170 7196 Dihedral : 15.271 89.500 14797 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 11.25 Ramachandran Plot: Outliers : 0.76 % Allowed : 9.76 % Favored : 89.48 % Rotamer: Outliers : 2.05 % Allowed : 9.79 % Favored : 88.16 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.38 (0.09), residues: 5123 helix: -3.48 (0.06), residues: 2895 sheet: -2.54 (0.34), residues: 210 loop : -3.64 (0.11), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP L1251 HIS 0.009 0.001 HIS G 578 PHE 0.043 0.002 PHE M 168 TYR 0.054 0.002 TYR M 224 ARG 0.022 0.001 ARG M 137 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 706 residues out of total 4728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 622 time to evaluate : 4.712 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: M 239 LYS cc_start: -0.1294 (OUTLIER) cc_final: -0.1592 (ttpt) REVERT: D 17 ILE cc_start: 0.6733 (OUTLIER) cc_final: 0.6250 (mp) REVERT: D 212 GLN cc_start: 0.4556 (OUTLIER) cc_final: 0.4327 (mm-40) REVERT: D 329 PHE cc_start: 0.6319 (OUTLIER) cc_final: 0.5886 (m-80) REVERT: G 560 THR cc_start: 0.5112 (OUTLIER) cc_final: 0.4072 (p) REVERT: G 571 CYS cc_start: 0.3814 (OUTLIER) cc_final: 0.2708 (t) REVERT: L 823 ILE cc_start: 0.6892 (mm) cc_final: 0.6356 (mm) REVERT: L 912 LEU cc_start: 0.8170 (tp) cc_final: 0.7936 (tp) REVERT: L 2438 MET cc_start: 0.7230 (mmm) cc_final: 0.6908 (mmm) REVERT: L 2678 TYR cc_start: 0.6933 (m-80) cc_final: 0.6296 (m-80) REVERT: L 2784 THR cc_start: 0.7994 (p) cc_final: 0.7660 (t) REVERT: L 2913 VAL cc_start: 0.7152 (OUTLIER) cc_final: 0.6819 (m) outliers start: 84 outliers final: 11 residues processed: 698 average time/residue: 0.5568 time to fit residues: 637.2305 Evaluate side-chains 345 residues out of total 4728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 327 time to evaluate : 4.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 181 THR Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain M residue 239 LYS Chi-restraints excluded: chain D residue 17 ILE Chi-restraints excluded: chain D residue 87 TYR Chi-restraints excluded: chain D residue 212 GLN Chi-restraints excluded: chain D residue 329 PHE Chi-restraints excluded: chain E residue 938 ILE Chi-restraints excluded: chain E residue 949 LYS Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain G residue 566 ILE Chi-restraints excluded: chain G residue 571 CYS Chi-restraints excluded: chain H residue 362 ILE Chi-restraints excluded: chain L residue 1358 VAL Chi-restraints excluded: chain L residue 1419 LYS Chi-restraints excluded: chain L residue 2887 ARG Chi-restraints excluded: chain L residue 2913 VAL Chi-restraints excluded: chain L residue 2914 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 447 optimal weight: 1.9990 chunk 401 optimal weight: 9.9990 chunk 222 optimal weight: 0.8980 chunk 137 optimal weight: 10.0000 chunk 270 optimal weight: 0.9990 chunk 214 optimal weight: 7.9990 chunk 415 optimal weight: 10.0000 chunk 160 optimal weight: 9.9990 chunk 252 optimal weight: 3.9990 chunk 309 optimal weight: 3.9990 chunk 481 optimal weight: 0.3980 overall best weight: 1.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 91 ASN A 213 ASN A 227 HIS F 86 HIS ** F 97 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 194 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 267 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 274 ASN ** D 82 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 317 GLN E 982 GLN K 464 ASN K 594 ASN ** G 390 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 391 ASN G 410 GLN G 465 ASN G 508 HIS ** H 157 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 161 ASN I 56 HIS ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 397 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 399 GLN L 450 ASN L 669 HIS L 698 HIS ** L1333 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L1563 ASN L1632 HIS L2460 GLN L2623 HIS L2661 GLN L2698 GLN ** L2808 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L2892 ASN L2898 ASN L3418 HIS ** L3435 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L3484 GLN L3625 GLN ** L3742 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L3794 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 30 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6004 moved from start: 0.2793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 41473 Z= 0.279 Angle : 0.771 12.312 56246 Z= 0.397 Chirality : 0.045 0.370 6566 Planarity : 0.006 0.071 7196 Dihedral : 6.376 81.521 5749 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.25 % Allowed : 8.35 % Favored : 91.39 % Rotamer: Outliers : 2.81 % Allowed : 15.79 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.93 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.33 (0.10), residues: 5123 helix: -1.60 (0.08), residues: 2971 sheet: -1.78 (0.33), residues: 235 loop : -3.15 (0.13), residues: 1917 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L1251 HIS 0.011 0.001 HIS A 278 PHE 0.031 0.002 PHE G 156 TYR 0.031 0.002 TYR L2942 ARG 0.008 0.001 ARG G 592 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 10246 Ramachandran restraints generated. 5123 Oldfield, 0 Emsley, 5123 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 456 residues out of total 4728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 115 poor density : 341 time to evaluate : 4.982 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: M 240 MET cc_start: 0.2496 (pmm) cc_final: 0.2212 (pmm) REVERT: F 301 MET cc_start: 0.7399 (mmm) cc_final: 0.6991 (mmm) REVERT: D 21 MET cc_start: 0.6621 (mtt) cc_final: 0.6152 (mtt) REVERT: G 560 THR cc_start: 0.5112 (OUTLIER) cc_final: 0.4409 (t) REVERT: L 1204 ASP cc_start: 0.6510 (OUTLIER) cc_final: 0.5611 (m-30) REVERT: L 1943 LEU cc_start: 0.6824 (OUTLIER) cc_final: 0.6431 (tt) REVERT: L 2438 MET cc_start: 0.7545 (mmm) cc_final: 0.7327 (mmm) REVERT: L 3475 ASP cc_start: 0.7624 (p0) cc_final: 0.7417 (p0) outliers start: 115 outliers final: 54 residues processed: 427 average time/residue: 0.4345 time to fit residues: 317.6986 Evaluate side-chains 329 residues out of total 4728 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 272 time to evaluate : 3.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain M residue 63 ILE Chi-restraints excluded: chain M residue 197 MET Chi-restraints excluded: chain M residue 215 THR Chi-restraints excluded: chain A residue 189 MET Chi-restraints excluded: chain C residue 298 ASP Chi-restraints excluded: chain F residue 215 SER Chi-restraints excluded: chain D residue 294 PHE Chi-restraints excluded: chain K residue 462 ILE Chi-restraints excluded: chain K residue 464 ASN Chi-restraints excluded: chain K residue 537 VAL Chi-restraints excluded: chain G residue 542 CYS Chi-restraints excluded: chain G residue 560 THR Chi-restraints excluded: chain H residue 264 TYR Chi-restraints excluded: chain I residue 73 ASN Chi-restraints excluded: chain L residue 362 THR Chi-restraints excluded: chain L residue 403 LEU Chi-restraints excluded: chain L residue 414 LEU Chi-restraints excluded: chain L residue 416 LEU Chi-restraints excluded: chain L residue 439 ILE Chi-restraints excluded: chain L residue 574 THR Chi-restraints excluded: chain L residue 668 ILE Chi-restraints excluded: chain L residue 690 MET Chi-restraints excluded: chain L residue 886 THR Chi-restraints excluded: chain L residue 899 ASP Chi-restraints excluded: chain L residue 940 VAL Chi-restraints excluded: chain L residue 945 THR Chi-restraints excluded: chain L residue 953 VAL Chi-restraints excluded: chain L residue 980 LEU Chi-restraints excluded: chain L residue 1097 MET Chi-restraints excluded: chain L residue 1122 ASN Chi-restraints excluded: chain L residue 1193 CYS Chi-restraints excluded: chain L residue 1204 ASP Chi-restraints excluded: chain L residue 1272 LEU Chi-restraints excluded: chain L residue 1313 LEU Chi-restraints excluded: chain L residue 1334 ILE Chi-restraints excluded: chain L residue 1358 VAL Chi-restraints excluded: chain L residue 1418 VAL Chi-restraints excluded: chain L residue 1419 LYS Chi-restraints excluded: chain L residue 1563 ASN Chi-restraints excluded: chain L residue 1621 LEU Chi-restraints excluded: chain L residue 1668 LEU Chi-restraints excluded: chain L residue 1943 LEU Chi-restraints excluded: chain L residue 1962 ASN Chi-restraints excluded: chain L residue 1972 ASP Chi-restraints excluded: chain L residue 2401 VAL Chi-restraints excluded: chain L residue 2448 ASP Chi-restraints excluded: chain L residue 2535 VAL Chi-restraints excluded: chain L residue 2558 ILE Chi-restraints excluded: chain L residue 2758 THR Chi-restraints excluded: chain L residue 2760 LEU Chi-restraints excluded: chain L residue 2823 ILE Chi-restraints excluded: chain L residue 3139 VAL Chi-restraints excluded: chain L residue 3161 ILE Chi-restraints excluded: chain L residue 3173 LEU Chi-restraints excluded: chain L residue 3512 VAL Chi-restraints excluded: chain L residue 3605 LEU Chi-restraints excluded: chain L residue 3801 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 530 random chunks: chunk 267 optimal weight: 3.9990 chunk 149 optimal weight: 20.0000 chunk 400 optimal weight: 30.0000 chunk 327 optimal weight: 5.9990 chunk 132 optimal weight: 8.9990 chunk 482 optimal weight: 7.9990 chunk 520 optimal weight: 0.8980 chunk 429 optimal weight: 0.1980 chunk 478 optimal weight: 2.9990 chunk 164 optimal weight: 10.0000 chunk 386 optimal weight: 6.9990 overall best weight: 2.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: