Starting phenix.real_space_refine on Mon Dec 30 11:47:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9e8k_47723/12_2024/9e8k_47723_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9e8k_47723/12_2024/9e8k_47723.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.08 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9e8k_47723/12_2024/9e8k_47723.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9e8k_47723/12_2024/9e8k_47723.map" model { file = "/net/cci-nas-00/data/ceres_data/9e8k_47723/12_2024/9e8k_47723_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9e8k_47723/12_2024/9e8k_47723_neut.cif" } resolution = 4.08 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= 0.002 sd= 0.023 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 15 5.49 5 Mg 1 5.21 5 S 328 5.16 5 C 39411 2.51 5 N 10739 2.21 5 O 11848 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 434 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 62343 Number of models: 1 Model: "" Number of chains: 34 Chain: "A" Number of atoms: 2804 Number of conformers: 1 Conformer: "" Number of residues, atoms: 359, 2804 Classifications: {'peptide': 359} Link IDs: {'PTRANS': 22, 'TRANS': 336} Chain: "C" Number of atoms: 2884 Number of conformers: 1 Conformer: "" Number of residues, atoms: 364, 2884 Classifications: {'peptide': 364} Link IDs: {'PTRANS': 16, 'TRANS': 347} Chain breaks: 1 Chain: "G" Number of atoms: 1811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1811 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 12} Link IDs: {'PTRANS': 8, 'TRANS': 229} Unresolved non-hydrogen bonds: 46 Unresolved non-hydrogen angles: 53 Unresolved non-hydrogen dihedrals: 41 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 3, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 24 Chain: "H" Number of atoms: 1715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 230, 1715 Classifications: {'peptide': 230} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 20} Link IDs: {'PTRANS': 10, 'TRANS': 219} Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 69 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 44 Chain: "I" Number of atoms: 1895 Number of conformers: 1 Conformer: "" Number of residues, atoms: 248, 1895 Classifications: {'peptide': 248} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 5, 'TRANS': 242} Unresolved non-hydrogen bonds: 59 Unresolved non-hydrogen angles: 66 Unresolved non-hydrogen dihedrals: 52 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLN:plan1': 2, 'GLU:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 15 Chain: "J" Number of atoms: 1704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1704 Classifications: {'peptide': 239} Incomplete info: {'truncation_to_alanine': 51} Link IDs: {'PTRANS': 6, 'TRANS': 232} Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 223 Unresolved non-hydrogen dihedrals: 151 Unresolved non-hydrogen chiralities: 17 Planarities with less than four sites: {'PHE:plan': 2, 'GLU:plan': 11, 'ARG:plan': 4, 'ASN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 82 Chain: "L" Number of atoms: 1838 Number of conformers: 1 Conformer: "" Number of residues, atoms: 236, 1838 Classifications: {'peptide': 236} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 9, 'TRANS': 226} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 11 Chain: "M" Number of atoms: 1839 Number of conformers: 1 Conformer: "" Number of residues, atoms: 238, 1839 Classifications: {'peptide': 238} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 5, 'TRANS': 232} Unresolved non-hydrogen bonds: 25 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 22 Planarities with less than four sites: {'GLU:plan': 1, 'ASN:plan1': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "O" Number of atoms: 355 Number of conformers: 1 Conformer: "" Number of residues, atoms: 44, 355 Classifications: {'peptide': 44} Link IDs: {'PTRANS': 1, 'TRANS': 42} Chain: "W" Number of atoms: 3570 Number of conformers: 1 Conformer: "" Number of residues, atoms: 438, 3570 Classifications: {'peptide': 438} Link IDs: {'PTRANS': 8, 'TRANS': 429} Chain: "X" Number of atoms: 2994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 2994 Classifications: {'peptide': 378} Link IDs: {'PTRANS': 10, 'TRANS': 367} Chain: "Y" Number of atoms: 3127 Number of conformers: 1 Conformer: "" Number of residues, atoms: 380, 3127 Classifications: {'peptide': 380} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 7, 'TRANS': 371} Chain: "a" Number of atoms: 2995 Number of conformers: 1 Conformer: "" Number of residues, atoms: 373, 2995 Classifications: {'peptide': 373} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 12, 'TRANS': 360} Chain: "b" Number of atoms: 1437 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1437 Classifications: {'peptide': 188} Link IDs: {'PTRANS': 9, 'TRANS': 178} Chain breaks: 1 Chain: "d" Number of atoms: 2188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 269, 2188 Classifications: {'peptide': 269} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 11, 'TRANS': 257} Chain: "u" Number of atoms: 1376 Number of conformers: 1 Conformer: "" Number of residues, atoms: 172, 1376 Classifications: {'peptide': 172} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 9, 'TRANS': 162} Chain: "v" Number of atoms: 40 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 40 Classifications: {'peptide': 8} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'TRANS': 7} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'UNK:plan-1': 8} Unresolved non-hydrogen planarities: 8 Chain: "D" Number of atoms: 2912 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2912 Classifications: {'peptide': 366} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 348} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 368, 2932 Classifications: {'peptide': 368} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 349} Chain breaks: 1 Chain: "F" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 2877 Classifications: {'peptide': 367} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 17, 'TRANS': 349} Chain breaks: 2 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 2544 Number of conformers: 1 Conformer: "" Number of residues, atoms: 326, 2544 Classifications: {'peptide': 326} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 310} Chain breaks: 3 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 1729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 228, 1729 Classifications: {'peptide': 228} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 7, 'TRANS': 220} Chain breaks: 1 Unresolved non-hydrogen bonds: 24 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 23 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "c" Number of atoms: 2145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 2145 Classifications: {'peptide': 271} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 2 Chain: "Z" Number of atoms: 2251 Number of conformers: 1 Conformer: "" Number of residues, atoms: 282, 2251 Classifications: {'peptide': 282} Link IDs: {'PTRANS': 9, 'TRANS': 272} Chain breaks: 1 Chain: "V" Number of atoms: 3525 Number of conformers: 1 Conformer: "" Number of residues, atoms: 439, 3525 Classifications: {'peptide': 439} Link IDs: {'PTRANS': 18, 'TRANS': 420} Chain breaks: 1 Chain: "e" Number of atoms: 349 Number of conformers: 1 Conformer: "" Number of residues, atoms: 41, 349 Classifications: {'peptide': 41} Link IDs: {'PTRANS': 1, 'TRANS': 39} Chain breaks: 1 Chain: "U" Number of atoms: 6331 Number of conformers: 1 Conformer: "" Number of residues, atoms: 811, 6331 Classifications: {'peptide': 811} Link IDs: {'PTRANS': 28, 'TRANS': 782} Chain breaks: 3 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N GLY Z 30 " occ=0.66 ... (2 atoms not shown) pdb=" O GLY Z 30 " occ=0.66 Time building chain proxies: 25.85, per 1000 atoms: 0.41 Number of scatterers: 62343 At special positions: 0 Unit cell: (178.16, 223.224, 183.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 328 16.00 P 15 15.00 Mg 1 11.99 O 11848 8.00 N 10739 7.00 C 39411 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS G 115 " - pdb=" SG CYS G 154 " distance=2.03 Simple disulfide: pdb=" SG CYS M 41 " - pdb=" SG CYS M 186 " distance=2.04 Simple disulfide: pdb=" SG CYS U 633 " - pdb=" SG CYS U 659 " distance=2.01 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 12.14 Conformation dependent library (CDL) restraints added in 6.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN c 501 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 115 " pdb="ZN ZN c 501 " - pdb=" NE2 HIS c 113 " 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 14916 Finding SS restraints... Secondary structure from input PDB file: 367 helices and 35 sheets defined 57.7% alpha, 8.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.30 Creating SS restraints... Processing helix chain 'A' and resid 74 through 78 Processing helix chain 'A' and resid 79 through 90 removed outlier: 4.506A pdb=" N LYS A 84 " --> pdb=" O LEU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 130 through 134 Processing helix chain 'A' and resid 160 through 165 Processing helix chain 'A' and resid 180 through 189 Processing helix chain 'A' and resid 192 through 197 Processing helix chain 'A' and resid 198 through 201 removed outlier: 3.541A pdb=" N PHE A 201 " --> pdb=" O PRO A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 201' Processing helix chain 'A' and resid 222 through 233 removed outlier: 4.374A pdb=" N ALA A 226 " --> pdb=" O LYS A 222 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 227 " --> pdb=" O THR A 223 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ALA A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 241 through 246 Processing helix chain 'A' and resid 251 through 267 removed outlier: 4.099A pdb=" N VAL A 257 " --> pdb=" O GLY A 253 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N ARG A 258 " --> pdb=" O ALA A 254 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 280 Processing helix chain 'A' and resid 285 through 289 Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.224A pdb=" N ARG A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N LEU A 300 " --> pdb=" O GLN A 296 " (cutoff:3.500A) removed outlier: 5.095A pdb=" N GLU A 301 " --> pdb=" O ARG A 297 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N LEU A 302 " --> pdb=" O THR A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 333 Processing helix chain 'A' and resid 347 through 359 removed outlier: 3.546A pdb=" N PHE A 355 " --> pdb=" O ARG A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 377 removed outlier: 4.474A pdb=" N ARG A 375 " --> pdb=" O GLU A 371 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 399 Processing helix chain 'A' and resid 405 through 418 removed outlier: 3.677A pdb=" N VAL A 416 " --> pdb=" O ALA A 412 " (cutoff:3.500A) Processing helix chain 'C' and resid 23 through 31 removed outlier: 3.980A pdb=" N ILE C 28 " --> pdb=" O TYR C 24 " (cutoff:3.500A) removed outlier: 4.215A pdb=" N GLU C 29 " --> pdb=" O LEU C 25 " (cutoff:3.500A) Processing helix chain 'C' and resid 31 through 66 removed outlier: 3.614A pdb=" N LEU C 45 " --> pdb=" O ASN C 41 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N LEU C 52 " --> pdb=" O GLN C 48 " (cutoff:3.500A) Processing helix chain 'C' and resid 104 through 108 Processing helix chain 'C' and resid 132 through 137 removed outlier: 3.680A pdb=" N LEU C 137 " --> pdb=" O PRO C 133 " (cutoff:3.500A) Processing helix chain 'C' and resid 147 through 151 Processing helix chain 'C' and resid 154 through 163 Processing helix chain 'C' and resid 171 through 177 removed outlier: 3.561A pdb=" N PHE C 175 " --> pdb=" O HIS C 171 " (cutoff:3.500A) Processing helix chain 'C' and resid 195 through 205 Processing helix chain 'C' and resid 217 through 219 No H-bonds generated for 'chain 'C' and resid 217 through 219' Processing helix chain 'C' and resid 227 through 233 Processing helix chain 'C' and resid 233 through 242 removed outlier: 4.522A pdb=" N ARG C 239 " --> pdb=" O PHE C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 251 through 256 Processing helix chain 'C' and resid 267 through 281 removed outlier: 3.567A pdb=" N MET C 273 " --> pdb=" O VAL C 269 " (cutoff:3.500A) Processing helix chain 'C' and resid 285 through 287 No H-bonds generated for 'chain 'C' and resid 285 through 287' Processing helix chain 'C' and resid 302 through 307 removed outlier: 4.261A pdb=" N LEU C 306 " --> pdb=" O ASP C 302 " (cutoff:3.500A) Processing helix chain 'C' and resid 321 through 333 Processing helix chain 'C' and resid 334 through 336 No H-bonds generated for 'chain 'C' and resid 334 through 336' Processing helix chain 'C' and resid 343 through 351 removed outlier: 3.803A pdb=" N ILE C 347 " --> pdb=" O ASN C 343 " (cutoff:3.500A) Processing helix chain 'C' and resid 356 through 372 Processing helix chain 'C' and resid 379 through 391 removed outlier: 3.832A pdb=" N PHE C 383 " --> pdb=" O THR C 379 " (cutoff:3.500A) Processing helix chain 'G' and resid 22 through 35 Processing helix chain 'G' and resid 83 through 105 Processing helix chain 'G' and resid 110 through 128 removed outlier: 3.710A pdb=" N ASN G 128 " --> pdb=" O VAL G 124 " (cutoff:3.500A) Processing helix chain 'G' and resid 171 through 183 Processing helix chain 'G' and resid 190 through 204 Processing helix chain 'G' and resid 231 through 240 Processing helix chain 'H' and resid 19 through 32 removed outlier: 4.236A pdb=" N GLU H 23 " --> pdb=" O LEU H 19 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N TYR H 24 " --> pdb=" O VAL H 20 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N ALA H 25 " --> pdb=" O GLN H 21 " (cutoff:3.500A) Processing helix chain 'H' and resid 79 through 101 removed outlier: 4.079A pdb=" N GLN H 96 " --> pdb=" O LYS H 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 106 through 120 Processing helix chain 'H' and resid 166 through 177 Processing helix chain 'H' and resid 183 through 199 removed outlier: 3.739A pdb=" N PHE H 199 " --> pdb=" O LEU H 195 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 231 removed outlier: 3.968A pdb=" N ASP H 228 " --> pdb=" O THR H 224 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR H 229 " --> pdb=" O GLU H 225 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA H 231 " --> pdb=" O LYS H 227 " (cutoff:3.500A) Processing helix chain 'I' and resid 4 through 8 removed outlier: 4.403A pdb=" N ARG I 8 " --> pdb=" O TYR I 5 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 27 Processing helix chain 'I' and resid 28 through 31 Processing helix chain 'I' and resid 79 through 102 removed outlier: 3.984A pdb=" N ASN I 88 " --> pdb=" O ASN I 84 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ARG I 91 " --> pdb=" O THR I 87 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 124 removed outlier: 3.826A pdb=" N ILE I 117 " --> pdb=" O ALA I 113 " (cutoff:3.500A) Processing helix chain 'I' and resid 167 through 178 Processing helix chain 'I' and resid 185 through 201 removed outlier: 4.343A pdb=" N LYS I 195 " --> pdb=" O ALA I 191 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N ASN I 198 " --> pdb=" O ILE I 194 " (cutoff:3.500A) Processing helix chain 'I' and resid 207 through 209 No H-bonds generated for 'chain 'I' and resid 207 through 209' Processing helix chain 'I' and resid 229 through 248 removed outlier: 3.577A pdb=" N LYS I 246 " --> pdb=" O GLU I 242 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 251 No H-bonds generated for 'chain 'I' and resid 249 through 251' Processing helix chain 'J' and resid 16 through 21 Processing helix chain 'J' and resid 21 through 28 Processing helix chain 'J' and resid 76 through 98 removed outlier: 3.833A pdb=" N VAL J 89 " --> pdb=" O ASN J 85 " (cutoff:3.500A) Processing helix chain 'J' and resid 103 through 120 Processing helix chain 'J' and resid 164 through 176 removed outlier: 3.774A pdb=" N VAL J 168 " --> pdb=" O GLY J 164 " (cutoff:3.500A) removed outlier: 4.242A pdb=" N ARG J 169 " --> pdb=" O ALA J 165 " (cutoff:3.500A) removed outlier: 4.865A pdb=" N GLU J 170 " --> pdb=" O LYS J 166 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N GLU J 173 " --> pdb=" O ARG J 169 " (cutoff:3.500A) Processing helix chain 'J' and resid 184 through 196 Processing helix chain 'J' and resid 224 through 239 removed outlier: 3.949A pdb=" N TYR J 228 " --> pdb=" O GLU J 224 " (cutoff:3.500A) Processing helix chain 'L' and resid 19 through 30 removed outlier: 3.948A pdb=" N GLU L 23 " --> pdb=" O ILE L 19 " (cutoff:3.500A) Processing helix chain 'L' and resid 80 through 100 Processing helix chain 'L' and resid 104 through 118 removed outlier: 4.030A pdb=" N LEU L 111 " --> pdb=" O ARG L 107 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE L 112 " --> pdb=" O LEU L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 119 through 122 Processing helix chain 'L' and resid 165 through 180 removed outlier: 5.243A pdb=" N SER L 177 " --> pdb=" O GLU L 173 " (cutoff:3.500A) removed outlier: 5.260A pdb=" N GLU L 178 " --> pdb=" O ARG L 174 " (cutoff:3.500A) removed outlier: 4.548A pdb=" N MET L 180 " --> pdb=" O MET L 176 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 197 Processing helix chain 'L' and resid 226 through 234 Proline residue: L 231 - end of helix Processing helix chain 'M' and resid 20 through 31 removed outlier: 3.988A pdb=" N ALA M 26 " --> pdb=" O GLN M 22 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLU M 31 " --> pdb=" O MET M 27 " (cutoff:3.500A) Processing helix chain 'M' and resid 80 through 103 removed outlier: 3.888A pdb=" N ASP M 89 " --> pdb=" O ARG M 85 " (cutoff:3.500A) removed outlier: 4.851A pdb=" N ILE M 90 " --> pdb=" O SER M 86 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N ALA M 91 " --> pdb=" O LEU M 87 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N SER M 96 " --> pdb=" O ARG M 92 " (cutoff:3.500A) Processing helix chain 'M' and resid 107 through 125 removed outlier: 3.841A pdb=" N ALA M 116 " --> pdb=" O ALA M 112 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N TYR M 118 " --> pdb=" O ARG M 114 " (cutoff:3.500A) removed outlier: 4.391A pdb=" N VAL M 119 " --> pdb=" O VAL M 115 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N THR M 123 " --> pdb=" O VAL M 119 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N LEU M 124 " --> pdb=" O HIS M 120 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N TYR M 125 " --> pdb=" O ALA M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 172 through 177 Processing helix chain 'M' and resid 185 through 200 removed outlier: 4.251A pdb=" N LYS M 191 " --> pdb=" O ARG M 187 " (cutoff:3.500A) Processing helix chain 'M' and resid 219 through 221 No H-bonds generated for 'chain 'M' and resid 219 through 221' Processing helix chain 'M' and resid 233 through 242 removed outlier: 3.681A pdb=" N SER M 242 " --> pdb=" O TYR M 238 " (cutoff:3.500A) Processing helix chain 'O' and resid 54 through 71 removed outlier: 4.155A pdb=" N LEU O 58 " --> pdb=" O MET O 54 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER O 61 " --> pdb=" O GLN O 57 " (cutoff:3.500A) Processing helix chain 'O' and resid 76 through 88 removed outlier: 3.957A pdb=" N LYS O 84 " --> pdb=" O ASN O 80 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N GLN O 85 " --> pdb=" O ARG O 81 " (cutoff:3.500A) Processing helix chain 'O' and resid 89 through 91 No H-bonds generated for 'chain 'O' and resid 89 through 91' Processing helix chain 'W' and resid 20 through 25 removed outlier: 4.422A pdb=" N VAL W 24 " --> pdb=" O TYR W 20 " (cutoff:3.500A) Processing helix chain 'W' and resid 27 through 37 removed outlier: 4.751A pdb=" N LYS W 33 " --> pdb=" O PRO W 29 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N LEU W 34 " --> pdb=" O GLU W 30 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA W 35 " --> pdb=" O CYS W 31 " (cutoff:3.500A) Processing helix chain 'W' and resid 43 through 55 Processing helix chain 'W' and resid 62 through 77 removed outlier: 3.986A pdb=" N VAL W 71 " --> pdb=" O LEU W 67 " (cutoff:3.500A) Processing helix chain 'W' and resid 79 through 93 removed outlier: 4.203A pdb=" N LEU W 83 " --> pdb=" O GLU W 79 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N MET W 88 " --> pdb=" O ASN W 84 " (cutoff:3.500A) Processing helix chain 'W' and resid 100 through 113 removed outlier: 3.597A pdb=" N MET W 104 " --> pdb=" O ALA W 100 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N THR W 110 " --> pdb=" O GLN W 106 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N GLU W 113 " --> pdb=" O CYS W 109 " (cutoff:3.500A) Processing helix chain 'W' and resid 117 through 129 removed outlier: 4.269A pdb=" N LEU W 122 " --> pdb=" O LEU W 118 " (cutoff:3.500A) removed outlier: 6.059A pdb=" N ARG W 123 " --> pdb=" O PRO W 119 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LEU W 124 " --> pdb=" O ILE W 120 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ILE W 125 " --> pdb=" O LYS W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 141 through 156 removed outlier: 4.200A pdb=" N LEU W 145 " --> pdb=" O GLU W 141 " (cutoff:3.500A) Processing helix chain 'W' and resid 158 through 167 removed outlier: 3.766A pdb=" N ALA W 162 " --> pdb=" O ASP W 158 " (cutoff:3.500A) Processing helix chain 'W' and resid 170 through 174 Processing helix chain 'W' and resid 178 through 196 removed outlier: 4.641A pdb=" N LEU W 192 " --> pdb=" O GLU W 188 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N CYS W 193 " --> pdb=" O GLN W 189 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU W 194 " --> pdb=" O MET W 190 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ALA W 195 " --> pdb=" O ARG W 191 " (cutoff:3.500A) Processing helix chain 'W' and resid 198 through 209 Processing helix chain 'W' and resid 210 through 215 removed outlier: 3.788A pdb=" N PHE W 214 " --> pdb=" O ASN W 210 " (cutoff:3.500A) Processing helix chain 'W' and resid 216 through 238 removed outlier: 4.749A pdb=" N LYS W 221 " --> pdb=" O GLU W 217 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU W 222 " --> pdb=" O ASN W 218 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS W 225 " --> pdb=" O LYS W 221 " (cutoff:3.500A) removed outlier: 4.805A pdb=" N GLN W 232 " --> pdb=" O ASN W 228 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU W 233 " --> pdb=" O LEU W 229 " (cutoff:3.500A) Processing helix chain 'W' and resid 239 through 252 Processing helix chain 'W' and resid 255 through 258 Processing helix chain 'W' and resid 259 through 277 removed outlier: 4.637A pdb=" N LEU W 272 " --> pdb=" O LYS W 268 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ILE W 275 " --> pdb=" O VAL W 271 " (cutoff:3.500A) Processing helix chain 'W' and resid 280 through 292 Processing helix chain 'W' and resid 294 through 299 Processing helix chain 'W' and resid 300 through 311 removed outlier: 3.814A pdb=" N ASP W 304 " --> pdb=" O PRO W 300 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU W 306 " --> pdb=" O TYR W 302 " (cutoff:3.500A) removed outlier: 4.364A pdb=" N LYS W 307 " --> pdb=" O LYS W 303 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N PHE W 309 " --> pdb=" O LEU W 305 " (cutoff:3.500A) Processing helix chain 'W' and resid 316 through 324 removed outlier: 3.810A pdb=" N GLU W 322 " --> pdb=" O SER W 318 " (cutoff:3.500A) Processing helix chain 'W' and resid 324 through 329 Processing helix chain 'W' and resid 344 through 369 removed outlier: 3.593A pdb=" N TYR W 369 " --> pdb=" O ILE W 365 " (cutoff:3.500A) Processing helix chain 'W' and resid 375 through 382 removed outlier: 3.734A pdb=" N GLN W 380 " --> pdb=" O LYS W 376 " (cutoff:3.500A) Processing helix chain 'W' and resid 385 through 399 Processing helix chain 'W' and resid 420 through 454 Processing helix chain 'X' and resid 47 through 60 removed outlier: 4.824A pdb=" N LEU X 53 " --> pdb=" O SER X 49 " (cutoff:3.500A) Processing helix chain 'X' and resid 62 through 73 Processing helix chain 'X' and resid 73 through 79 Processing helix chain 'X' and resid 81 through 98 removed outlier: 3.765A pdb=" N ARG X 87 " --> pdb=" O ALA X 83 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N LEU X 88 " --> pdb=" O LYS X 84 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N SER X 91 " --> pdb=" O ARG X 87 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N PHE X 96 " --> pdb=" O LEU X 92 " (cutoff:3.500A) Processing helix chain 'X' and resid 105 through 120 Processing helix chain 'X' and resid 122 through 140 Processing helix chain 'X' and resid 142 through 160 removed outlier: 3.650A pdb=" N ARG X 155 " --> pdb=" O SER X 151 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N MET X 160 " --> pdb=" O GLU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 162 through 180 Processing helix chain 'X' and resid 182 through 199 Processing helix chain 'X' and resid 203 through 221 Processing helix chain 'X' and resid 224 through 241 removed outlier: 3.718A pdb=" N ALA X 228 " --> pdb=" O ASP X 224 " (cutoff:3.500A) Processing helix chain 'X' and resid 245 through 261 removed outlier: 4.136A pdb=" N THR X 249 " --> pdb=" O PRO X 245 " (cutoff:3.500A) Processing helix chain 'X' and resid 264 through 272 removed outlier: 3.999A pdb=" N GLN X 268 " --> pdb=" O PRO X 264 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ALA X 269 " --> pdb=" O GLU X 265 " (cutoff:3.500A) Processing helix chain 'X' and resid 273 through 279 Processing helix chain 'X' and resid 282 through 296 removed outlier: 3.690A pdb=" N LEU X 287 " --> pdb=" O GLN X 283 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL X 290 " --> pdb=" O ALA X 286 " (cutoff:3.500A) Processing helix chain 'X' and resid 298 through 309 Processing helix chain 'X' and resid 310 through 313 Processing helix chain 'X' and resid 316 through 339 removed outlier: 4.431A pdb=" N ARG X 337 " --> pdb=" O GLN X 333 " (cutoff:3.500A) Processing helix chain 'X' and resid 347 through 355 Processing helix chain 'X' and resid 357 through 371 removed outlier: 3.847A pdb=" N ARG X 363 " --> pdb=" O ALA X 359 " (cutoff:3.500A) Processing helix chain 'X' and resid 394 through 415 removed outlier: 4.143A pdb=" N LEU X 401 " --> pdb=" O TYR X 397 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N GLU X 402 " --> pdb=" O GLU X 398 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N TYR X 415 " --> pdb=" O VAL X 411 " (cutoff:3.500A) Processing helix chain 'Y' and resid 16 through 26 removed outlier: 3.605A pdb=" N ALA Y 20 " --> pdb=" O ASP Y 16 " (cutoff:3.500A) Processing helix chain 'Y' and resid 28 through 33 Processing helix chain 'Y' and resid 34 through 36 No H-bonds generated for 'chain 'Y' and resid 34 through 36' Processing helix chain 'Y' and resid 37 through 47 removed outlier: 4.643A pdb=" N ALA Y 43 " --> pdb=" O ASP Y 39 " (cutoff:3.500A) Processing helix chain 'Y' and resid 50 through 59 removed outlier: 3.622A pdb=" N ALA Y 56 " --> pdb=" O PRO Y 52 " (cutoff:3.500A) Processing helix chain 'Y' and resid 68 through 93 removed outlier: 3.530A pdb=" N ASP Y 79 " --> pdb=" O LYS Y 75 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU Y 80 " --> pdb=" O ALA Y 76 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASP Y 90 " --> pdb=" O GLU Y 86 " (cutoff:3.500A) Processing helix chain 'Y' and resid 98 through 115 removed outlier: 4.925A pdb=" N MET Y 104 " --> pdb=" O ILE Y 100 " (cutoff:3.500A) Processing helix chain 'Y' and resid 116 through 129 Processing helix chain 'Y' and resid 135 through 151 removed outlier: 5.138A pdb=" N VAL Y 141 " --> pdb=" O ARG Y 137 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N TYR Y 143 " --> pdb=" O ASP Y 139 " (cutoff:3.500A) Processing helix chain 'Y' and resid 153 through 169 removed outlier: 3.724A pdb=" N THR Y 158 " --> pdb=" O ASN Y 154 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N ARG Y 159 " --> pdb=" O ASP Y 155 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N GLU Y 162 " --> pdb=" O THR Y 158 " (cutoff:3.500A) removed outlier: 5.200A pdb=" N LEU Y 167 " --> pdb=" O LYS Y 163 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N ILE Y 168 " --> pdb=" O ALA Y 164 " (cutoff:3.500A) Processing helix chain 'Y' and resid 173 through 191 Processing helix chain 'Y' and resid 193 through 205 Processing helix chain 'Y' and resid 206 through 208 No H-bonds generated for 'chain 'Y' and resid 206 through 208' Processing helix chain 'Y' and resid 215 through 231 Processing helix chain 'Y' and resid 232 through 240 removed outlier: 4.565A pdb=" N GLU Y 238 " --> pdb=" O PRO Y 234 " (cutoff:3.500A) Processing helix chain 'Y' and resid 243 through 252 removed outlier: 3.921A pdb=" N SER Y 252 " --> pdb=" O GLU Y 248 " (cutoff:3.500A) Processing helix chain 'Y' and resid 253 through 265 Processing helix chain 'Y' and resid 267 through 285 removed outlier: 4.260A pdb=" N VAL Y 277 " --> pdb=" O GLN Y 273 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N GLN Y 280 " --> pdb=" O ALA Y 276 " (cutoff:3.500A) Processing helix chain 'Y' and resid 288 through 290 No H-bonds generated for 'chain 'Y' and resid 288 through 290' Processing helix chain 'Y' and resid 291 through 309 removed outlier: 3.517A pdb=" N LEU Y 307 " --> pdb=" O ALA Y 303 " (cutoff:3.500A) Processing helix chain 'Y' and resid 316 through 324 Processing helix chain 'Y' and resid 326 through 339 removed outlier: 4.372A pdb=" N ARG Y 336 " --> pdb=" O GLN Y 332 " (cutoff:3.500A) Processing helix chain 'Y' and resid 360 through 384 Processing helix chain 'a' and resid 6 through 11 removed outlier: 4.465A pdb=" N GLN a 10 " --> pdb=" O GLY a 6 " (cutoff:3.500A) Processing helix chain 'a' and resid 17 through 31 removed outlier: 3.832A pdb=" N VAL a 21 " --> pdb=" O GLY a 17 " (cutoff:3.500A) Processing helix chain 'a' and resid 33 through 44 removed outlier: 3.693A pdb=" N LEU a 37 " --> pdb=" O LEU a 33 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU a 42 " --> pdb=" O THR a 38 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N PHE a 44 " --> pdb=" O GLN a 40 " (cutoff:3.500A) Processing helix chain 'a' and resid 45 through 47 No H-bonds generated for 'chain 'a' and resid 45 through 47' Processing helix chain 'a' and resid 52 through 65 removed outlier: 3.555A pdb=" N LEU a 56 " --> pdb=" O GLN a 52 " (cutoff:3.500A) removed outlier: 4.286A pdb=" N LEU a 59 " --> pdb=" O GLY a 55 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU a 61 " --> pdb=" O ILE a 57 " (cutoff:3.500A) removed outlier: 5.560A pdb=" N ASN a 62 " --> pdb=" O LYS a 58 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N PHE a 63 " --> pdb=" O LEU a 59 " (cutoff:3.500A) Processing helix chain 'a' and resid 72 through 82 removed outlier: 3.697A pdb=" N ILE a 80 " --> pdb=" O LEU a 76 " (cutoff:3.500A) Processing helix chain 'a' and resid 83 through 88 Processing helix chain 'a' and resid 89 through 98 Processing helix chain 'a' and resid 100 through 105 removed outlier: 4.331A pdb=" N LYS a 105 " --> pdb=" O ARG a 101 " (cutoff:3.500A) Processing helix chain 'a' and resid 110 through 123 Processing helix chain 'a' and resid 130 through 137 Processing helix chain 'a' and resid 138 through 143 Processing helix chain 'a' and resid 149 through 162 removed outlier: 3.866A pdb=" N TYR a 162 " --> pdb=" O LEU a 158 " (cutoff:3.500A) Processing helix chain 'a' and resid 163 through 165 No H-bonds generated for 'chain 'a' and resid 163 through 165' Processing helix chain 'a' and resid 168 through 183 removed outlier: 3.531A pdb=" N VAL a 183 " --> pdb=" O PHE a 179 " (cutoff:3.500A) Processing helix chain 'a' and resid 189 through 207 removed outlier: 4.017A pdb=" N GLN a 193 " --> pdb=" O PRO a 189 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLU a 195 " --> pdb=" O SER a 191 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N PHE a 198 " --> pdb=" O GLN a 194 " (cutoff:3.500A) Processing helix chain 'a' and resid 231 through 243 removed outlier: 3.645A pdb=" N LEU a 237 " --> pdb=" O LEU a 233 " (cutoff:3.500A) Processing helix chain 'a' and resid 246 through 257 removed outlier: 3.609A pdb=" N THR a 250 " --> pdb=" O GLU a 246 " (cutoff:3.500A) Processing helix chain 'a' and resid 261 through 263 No H-bonds generated for 'chain 'a' and resid 261 through 263' Processing helix chain 'a' and resid 264 through 284 removed outlier: 4.224A pdb=" N LEU a 277 " --> pdb=" O GLN a 273 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N MET a 278 " --> pdb=" O LEU a 274 " (cutoff:3.500A) Processing helix chain 'a' and resid 292 through 298 removed outlier: 3.957A pdb=" N ILE a 296 " --> pdb=" O THR a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 306 through 317 Processing helix chain 'a' and resid 342 through 376 removed outlier: 3.607A pdb=" N PHE a 355 " --> pdb=" O ASP a 351 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N TRP a 356 " --> pdb=" O ARG a 352 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N HIS a 369 " --> pdb=" O MET a 365 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N GLN a 370 " --> pdb=" O LEU a 366 " (cutoff:3.500A) removed outlier: 5.348A pdb=" N ASP a 373 " --> pdb=" O HIS a 369 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N ILE a 374 " --> pdb=" O GLN a 370 " (cutoff:3.500A) Processing helix chain 'b' and resid 13 through 18 Processing helix chain 'b' and resid 24 through 44 removed outlier: 3.570A pdb=" N ALA b 28 " --> pdb=" O THR b 24 " (cutoff:3.500A) Processing helix chain 'b' and resid 67 through 76 removed outlier: 4.011A pdb=" N ILE b 71 " --> pdb=" O ASP b 67 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS b 74 " --> pdb=" O ARG b 70 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N HIS b 76 " --> pdb=" O LEU b 72 " (cutoff:3.500A) Processing helix chain 'b' and resid 85 through 99 removed outlier: 3.826A pdb=" N ALA b 93 " --> pdb=" O GLY b 89 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N HIS b 99 " --> pdb=" O LEU b 95 " (cutoff:3.500A) Processing helix chain 'b' and resid 120 through 132 removed outlier: 3.900A pdb=" N LEU b 124 " --> pdb=" O ASN b 120 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N VAL b 125 " --> pdb=" O GLU b 121 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N LYS b 126 " --> pdb=" O LYS b 122 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N LYS b 129 " --> pdb=" O VAL b 125 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N LEU b 131 " --> pdb=" O LEU b 127 " (cutoff:3.500A) Processing helix chain 'b' and resid 150 through 161 Processing helix chain 'b' and resid 179 through 186 Processing helix chain 'd' and resid 83 through 104 removed outlier: 3.692A pdb=" N ARG d 104 " --> pdb=" O GLY d 100 " (cutoff:3.500A) Processing helix chain 'd' and resid 108 through 123 Processing helix chain 'd' and resid 137 through 158 removed outlier: 3.704A pdb=" N ALA d 144 " --> pdb=" O GLN d 140 " (cutoff:3.500A) Processing helix chain 'd' and resid 160 through 177 removed outlier: 4.479A pdb=" N CYS d 173 " --> pdb=" O ALA d 169 " (cutoff:3.500A) removed outlier: 4.009A pdb=" N TYR d 174 " --> pdb=" O GLN d 170 " (cutoff:3.500A) Processing helix chain 'd' and resid 187 through 202 Processing helix chain 'd' and resid 204 through 214 Processing helix chain 'd' and resid 216 through 222 removed outlier: 3.679A pdb=" N ILE d 220 " --> pdb=" O PRO d 216 " (cutoff:3.500A) Processing helix chain 'd' and resid 223 through 238 Proline residue: d 229 - end of helix removed outlier: 3.623A pdb=" N GLN d 234 " --> pdb=" O VAL d 230 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N TYR d 235 " --> pdb=" O SER d 231 " (cutoff:3.500A) Processing helix chain 'd' and resid 240 through 247 removed outlier: 3.594A pdb=" N LEU d 246 " --> pdb=" O ASN d 242 " (cutoff:3.500A) Processing helix chain 'd' and resid 248 through 251 removed outlier: 3.784A pdb=" N ILE d 251 " --> pdb=" O LYS d 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 248 through 251' Processing helix chain 'd' and resid 253 through 255 No H-bonds generated for 'chain 'd' and resid 253 through 255' Processing helix chain 'd' and resid 256 through 279 removed outlier: 3.827A pdb=" N ILE d 262 " --> pdb=" O PHE d 258 " (cutoff:3.500A) removed outlier: 5.018A pdb=" N GLU d 276 " --> pdb=" O ALA d 272 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N LYS d 277 " --> pdb=" O GLY d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 284 through 291 Processing helix chain 'd' and resid 296 through 307 Processing helix chain 'd' and resid 318 through 323 Processing helix chain 'd' and resid 332 through 348 Processing helix chain 'u' and resid 141 through 151 removed outlier: 3.661A pdb=" N GLY u 145 " --> pdb=" O ASP u 142 " (cutoff:3.500A) removed outlier: 7.668A pdb=" N PHE u 146 " --> pdb=" O GLU u 143 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASP u 147 " --> pdb=" O HIS u 144 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N CYS u 149 " --> pdb=" O PHE u 146 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU u 150 " --> pdb=" O ASP u 147 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG u 151 " --> pdb=" O ASN u 148 " (cutoff:3.500A) Processing helix chain 'u' and resid 205 through 212 removed outlier: 3.915A pdb=" N ARG u 211 " --> pdb=" O GLU u 207 " (cutoff:3.500A) Processing helix chain 'u' and resid 234 through 239 removed outlier: 4.164A pdb=" N GLN u 239 " --> pdb=" O VAL u 236 " (cutoff:3.500A) Processing helix chain 'D' and resid 40 through 83 removed outlier: 3.630A pdb=" N TYR D 44 " --> pdb=" O LEU D 40 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N GLU D 52 " --> pdb=" O GLN D 48 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TYR D 60 " --> pdb=" O VAL D 56 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASP D 63 " --> pdb=" O GLU D 59 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 83 " --> pdb=" O VAL D 79 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 170 through 186 removed outlier: 3.751A pdb=" N LEU D 183 " --> pdb=" O GLU D 179 " (cutoff:3.500A) Proline residue: D 184 - end of helix Processing helix chain 'D' and resid 187 through 195 removed outlier: 3.729A pdb=" N GLN D 193 " --> pdb=" O GLU D 189 " (cutoff:3.500A) Processing helix chain 'D' and resid 212 through 223 Processing helix chain 'D' and resid 231 through 235 Processing helix chain 'D' and resid 241 through 258 removed outlier: 3.803A pdb=" N ARG D 245 " --> pdb=" O GLY D 241 " (cutoff:3.500A) Processing helix chain 'D' and resid 267 through 271 Processing helix chain 'D' and resid 279 through 297 Processing helix chain 'D' and resid 318 through 323 Processing helix chain 'D' and resid 324 through 327 Processing helix chain 'D' and resid 339 through 352 removed outlier: 3.795A pdb=" N LYS D 351 " --> pdb=" O THR D 347 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N MET D 352 " --> pdb=" O ILE D 348 " (cutoff:3.500A) Processing helix chain 'D' and resid 359 through 366 removed outlier: 3.967A pdb=" N TYR D 363 " --> pdb=" O ASP D 359 " (cutoff:3.500A) Processing helix chain 'D' and resid 371 through 389 Processing helix chain 'D' and resid 395 through 406 Processing helix chain 'E' and resid 16 through 51 removed outlier: 4.018A pdb=" N ILE E 22 " --> pdb=" O GLU E 18 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N ASP E 23 " --> pdb=" O HIS E 19 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N LYS E 38 " --> pdb=" O LYS E 34 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N LEU E 47 " --> pdb=" O SER E 43 " (cutoff:3.500A) Processing helix chain 'E' and resid 88 through 92 Processing helix chain 'E' and resid 116 through 124 Processing helix chain 'E' and resid 139 through 148 Processing helix chain 'E' and resid 149 through 155 Processing helix chain 'E' and resid 155 through 163 removed outlier: 4.307A pdb=" N PHE E 159 " --> pdb=" O ASN E 155 " (cutoff:3.500A) Processing helix chain 'E' and resid 179 through 190 removed outlier: 4.204A pdb=" N ALA E 184 " --> pdb=" O LYS E 180 " (cutoff:3.500A) Processing helix chain 'E' and resid 201 through 204 Processing helix chain 'E' and resid 209 through 225 Processing helix chain 'E' and resid 234 through 238 Processing helix chain 'E' and resid 251 through 264 Processing helix chain 'E' and resid 286 through 291 removed outlier: 4.042A pdb=" N LEU E 290 " --> pdb=" O ASP E 286 " (cutoff:3.500A) Processing helix chain 'E' and resid 305 through 316 Processing helix chain 'E' and resid 327 through 335 removed outlier: 4.034A pdb=" N ILE E 331 " --> pdb=" O ASP E 327 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 357 removed outlier: 4.024A pdb=" N ASN E 345 " --> pdb=" O ALA E 341 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N VAL E 346 " --> pdb=" O ASP E 342 " (cutoff:3.500A) Processing helix chain 'E' and resid 363 through 381 removed outlier: 3.562A pdb=" N PHE E 367 " --> pdb=" O VAL E 363 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LYS E 379 " --> pdb=" O ALA E 375 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N LEU E 380 " --> pdb=" O ASP E 376 " (cutoff:3.500A) Processing helix chain 'F' and resid 53 through 82 removed outlier: 3.801A pdb=" N GLU F 58 " --> pdb=" O ILE F 54 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N VAL F 59 " --> pdb=" O MET F 55 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N HIS F 64 " --> pdb=" O LEU F 60 " (cutoff:3.500A) Processing helix chain 'F' and resid 141 through 145 Processing helix chain 'F' and resid 170 through 175 Processing helix chain 'F' and resid 184 through 188 Processing helix chain 'F' and resid 191 through 203 removed outlier: 4.045A pdb=" N GLU F 197 " --> pdb=" O LYS F 193 " (cutoff:3.500A) Processing helix chain 'F' and resid 203 through 208 Processing helix chain 'F' and resid 209 through 216 Processing helix chain 'F' and resid 232 through 244 Processing helix chain 'F' and resid 254 through 257 Processing helix chain 'F' and resid 262 through 278 Processing helix chain 'F' and resid 287 through 291 Processing helix chain 'F' and resid 304 through 316 removed outlier: 4.841A pdb=" N LEU F 311 " --> pdb=" O GLN F 307 " (cutoff:3.500A) Processing helix chain 'F' and resid 358 through 374 Processing helix chain 'F' and resid 380 through 388 Processing helix chain 'F' and resid 392 through 410 removed outlier: 4.025A pdb=" N VAL F 401 " --> pdb=" O LYS F 397 " (cutoff:3.500A) Processing helix chain 'F' and resid 416 through 428 removed outlier: 4.053A pdb=" N GLU F 426 " --> pdb=" O GLU F 422 " (cutoff:3.500A) Processing helix chain 'F' and resid 434 through 438 Processing helix chain 'B' and resid 92 through 97 Processing helix chain 'B' and resid 98 through 103 Processing helix chain 'B' and resid 170 through 175 Processing helix chain 'B' and resid 191 through 202 removed outlier: 3.502A pdb=" N GLN B 195 " --> pdb=" O ASP B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 207 removed outlier: 4.026A pdb=" N HIS B 207 " --> pdb=" O PRO B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 213 Processing helix chain 'B' and resid 231 through 242 Processing helix chain 'B' and resid 261 through 273 removed outlier: 5.405A pdb=" N LEU B 270 " --> pdb=" O LEU B 266 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N PHE B 271 " --> pdb=" O VAL B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 286 through 291 removed outlier: 4.198A pdb=" N GLY B 291 " --> pdb=" O ASP B 288 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 317 Processing helix chain 'B' and resid 333 through 337 Processing helix chain 'B' and resid 338 through 343 Processing helix chain 'B' and resid 357 through 370 Processing helix chain 'B' and resid 375 through 379 Processing helix chain 'B' and resid 380 through 385 removed outlier: 3.599A pdb=" N ILE B 384 " --> pdb=" O LEU B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 409 Processing helix chain 'B' and resid 415 through 427 Processing helix chain 'K' and resid 23 through 31 Processing helix chain 'K' and resid 32 through 34 No H-bonds generated for 'chain 'K' and resid 32 through 34' Processing helix chain 'K' and resid 81 through 104 removed outlier: 3.583A pdb=" N THR K 87 " --> pdb=" O ALA K 83 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU K 88 " --> pdb=" O ASP K 84 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N THR K 96 " --> pdb=" O ALA K 92 " (cutoff:3.500A) removed outlier: 4.156A pdb=" N GLN K 97 " --> pdb=" O ARG K 93 " (cutoff:3.500A) Processing helix chain 'K' and resid 108 through 121 Processing helix chain 'K' and resid 173 through 182 Processing helix chain 'K' and resid 190 through 206 removed outlier: 3.613A pdb=" N ILE K 201 " --> pdb=" O SER K 197 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N GLN K 204 " --> pdb=" O ILE K 200 " (cutoff:3.500A) Processing helix chain 'K' and resid 236 through 240 Processing helix chain 'c' and resid 34 through 48 Processing helix chain 'c' and resid 83 through 87 Processing helix chain 'c' and resid 88 through 102 Processing helix chain 'c' and resid 123 through 137 Processing helix chain 'c' and resid 179 through 184 removed outlier: 3.650A pdb=" N LEU c 184 " --> pdb=" O ASN c 180 " (cutoff:3.500A) Processing helix chain 'c' and resid 188 through 193 Processing helix chain 'c' and resid 194 through 198 removed outlier: 5.653A pdb=" N ASN c 197 " --> pdb=" O HIS c 194 " (cutoff:3.500A) Processing helix chain 'c' and resid 210 through 222 removed outlier: 4.071A pdb=" N HIS c 221 " --> pdb=" O LEU c 217 " (cutoff:3.500A) Processing helix chain 'c' and resid 224 through 230 Processing helix chain 'c' and resid 233 through 259 removed outlier: 4.639A pdb=" N GLU c 247 " --> pdb=" O SER c 243 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU c 250 " --> pdb=" O LYS c 246 " (cutoff:3.500A) Processing helix chain 'c' and resid 280 through 309 removed outlier: 4.042A pdb=" N GLU c 285 " --> pdb=" O LYS c 281 " (cutoff:3.500A) Processing helix chain 'Z' and resid 12 through 28 removed outlier: 4.151A pdb=" N LEU Z 16 " --> pdb=" O HIS Z 12 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N VAL Z 20 " --> pdb=" O LEU Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 71 through 86 Processing helix chain 'Z' and resid 104 through 114 removed outlier: 3.610A pdb=" N ILE Z 108 " --> pdb=" O ASN Z 104 " (cutoff:3.500A) Processing helix chain 'Z' and resid 165 through 176 removed outlier: 3.664A pdb=" N GLY Z 171 " --> pdb=" O ALA Z 167 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 217 removed outlier: 3.581A pdb=" N GLN Z 194 " --> pdb=" O ARG Z 190 " (cutoff:3.500A) Processing helix chain 'Z' and resid 226 through 236 removed outlier: 4.021A pdb=" N ASP Z 232 " --> pdb=" O TYR Z 228 " (cutoff:3.500A) Processing helix chain 'Z' and resid 242 through 288 removed outlier: 3.510A pdb=" N VAL Z 259 " --> pdb=" O ASP Z 255 " (cutoff:3.500A) Processing helix chain 'V' and resid 30 through 35 removed outlier: 3.712A pdb=" N ASP V 34 " --> pdb=" O PRO V 30 " (cutoff:3.500A) Processing helix chain 'V' and resid 35 through 53 removed outlier: 4.955A pdb=" N ALA V 41 " --> pdb=" O MET V 37 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N GLY V 49 " --> pdb=" O GLY V 45 " (cutoff:3.500A) Processing helix chain 'V' and resid 60 through 72 removed outlier: 4.182A pdb=" N GLN V 64 " --> pdb=" O ALA V 60 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N LEU V 67 " --> pdb=" O SER V 63 " (cutoff:3.500A) Processing helix chain 'V' and resid 73 through 77 Processing helix chain 'V' and resid 89 through 94 Processing helix chain 'V' and resid 147 through 164 Proline residue: V 158 - end of helix Proline residue: V 161 - end of helix Processing helix chain 'V' and resid 170 through 191 removed outlier: 4.167A pdb=" N PHE V 174 " --> pdb=" O LEU V 170 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ASN V 177 " --> pdb=" O ILE V 173 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS V 179 " --> pdb=" O MET V 175 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG V 180 " --> pdb=" O MET V 176 " (cutoff:3.500A) Processing helix chain 'V' and resid 198 through 216 removed outlier: 4.271A pdb=" N ALA V 202 " --> pdb=" O GLN V 198 " (cutoff:3.500A) removed outlier: 4.087A pdb=" N LYS V 209 " --> pdb=" O LEU V 205 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N TYR V 212 " --> pdb=" O ALA V 208 " (cutoff:3.500A) Processing helix chain 'V' and resid 216 through 221 Processing helix chain 'V' and resid 224 through 240 removed outlier: 3.587A pdb=" N ALA V 233 " --> pdb=" O SER V 229 " (cutoff:3.500A) Processing helix chain 'V' and resid 245 through 257 removed outlier: 4.231A pdb=" N LEU V 251 " --> pdb=" O GLN V 247 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU V 255 " --> pdb=" O LEU V 251 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ASN V 257 " --> pdb=" O LEU V 253 " (cutoff:3.500A) Processing helix chain 'V' and resid 264 through 271 Processing helix chain 'V' and resid 282 through 299 Processing helix chain 'V' and resid 301 through 316 removed outlier: 3.520A pdb=" N ARG V 314 " --> pdb=" O THR V 310 " (cutoff:3.500A) Processing helix chain 'V' and resid 321 through 340 Processing helix chain 'V' and resid 346 through 349 Processing helix chain 'V' and resid 350 through 368 Proline residue: V 359 - end of helix Processing helix chain 'V' and resid 371 through 389 removed outlier: 3.801A pdb=" N ASN V 376 " --> pdb=" O LEU V 372 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU V 379 " --> pdb=" O PHE V 375 " (cutoff:3.500A) removed outlier: 6.052A pdb=" N GLU V 384 " --> pdb=" O ASP V 380 " (cutoff:3.500A) removed outlier: 6.185A pdb=" N LYS V 385 " --> pdb=" O GLN V 381 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE V 386 " --> pdb=" O PHE V 382 " (cutoff:3.500A) Processing helix chain 'V' and resid 391 through 393 No H-bonds generated for 'chain 'V' and resid 391 through 393' Processing helix chain 'V' and resid 394 through 414 removed outlier: 5.984A pdb=" N HIS V 400 " --> pdb=" O ILE V 396 " (cutoff:3.500A) removed outlier: 4.992A pdb=" N ILE V 403 " --> pdb=" O ARG V 399 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N LYS V 404 " --> pdb=" O HIS V 400 " (cutoff:3.500A) Processing helix chain 'V' and resid 420 through 425 Processing helix chain 'V' and resid 430 through 444 removed outlier: 3.621A pdb=" N ALA V 434 " --> pdb=" O SER V 430 " (cutoff:3.500A) Processing helix chain 'V' and resid 453 through 455 No H-bonds generated for 'chain 'V' and resid 453 through 455' Processing helix chain 'V' and resid 470 through 493 removed outlier: 3.537A pdb=" N ALA V 493 " --> pdb=" O MET V 489 " (cutoff:3.500A) Processing helix chain 'e' and resid 42 through 47 Processing helix chain 'e' and resid 51 through 64 Processing helix chain 'U' and resid 7 through 11 removed outlier: 3.602A pdb=" N LEU U 11 " --> pdb=" O GLY U 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'U' and resid 7 through 11' Processing helix chain 'U' and resid 12 through 14 No H-bonds generated for 'chain 'U' and resid 12 through 14' Processing helix chain 'U' and resid 16 through 31 Processing helix chain 'U' and resid 34 through 39 Processing helix chain 'U' and resid 40 through 49 removed outlier: 4.603A pdb=" N ILE U 45 " --> pdb=" O VAL U 42 " (cutoff:3.500A) Processing helix chain 'U' and resid 56 through 72 removed outlier: 4.044A pdb=" N SER U 65 " --> pdb=" O ALA U 61 " (cutoff:3.500A) Processing helix chain 'U' and resid 73 through 82 Processing helix chain 'U' and resid 94 through 118 removed outlier: 3.606A pdb=" N ALA U 102 " --> pdb=" O GLU U 98 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE U 105 " --> pdb=" O ILE U 101 " (cutoff:3.500A) removed outlier: 4.707A pdb=" N ASP U 106 " --> pdb=" O ALA U 102 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N GLU U 114 " --> pdb=" O LYS U 110 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 143 Processing helix chain 'U' and resid 146 through 157 removed outlier: 5.748A pdb=" N GLY U 152 " --> pdb=" O LYS U 148 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE U 153 " --> pdb=" O GLN U 149 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LEU U 155 " --> pdb=" O ILE U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 159 through 167 Processing helix chain 'U' and resid 173 through 188 removed outlier: 4.130A pdb=" N LEU U 177 " --> pdb=" O VAL U 173 " (cutoff:3.500A) Processing helix chain 'U' and resid 190 through 208 Processing helix chain 'U' and resid 212 through 221 removed outlier: 3.568A pdb=" N CYS U 219 " --> pdb=" O ASN U 215 " (cutoff:3.500A) Processing helix chain 'U' and resid 225 through 239 removed outlier: 3.650A pdb=" N VAL U 229 " --> pdb=" O ASP U 225 " (cutoff:3.500A) Processing helix chain 'U' and resid 242 through 256 removed outlier: 3.705A pdb=" N GLN U 247 " --> pdb=" O LEU U 243 " (cutoff:3.500A) Processing helix chain 'U' and resid 257 through 268 Processing helix chain 'U' and resid 321 through 330 removed outlier: 3.716A pdb=" N ILE U 328 " --> pdb=" O LYS U 324 " (cutoff:3.500A) Processing helix chain 'U' and resid 331 through 345 Processing helix chain 'U' and resid 349 through 358 removed outlier: 3.643A pdb=" N LEU U 353 " --> pdb=" O ASP U 349 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N THR U 356 " --> pdb=" O ILE U 352 " (cutoff:3.500A) Processing helix chain 'U' and resid 363 through 377 removed outlier: 4.236A pdb=" N THR U 367 " --> pdb=" O SER U 363 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N THR U 369 " --> pdb=" O CYS U 365 " (cutoff:3.500A) Processing helix chain 'U' and resid 383 through 388 Processing helix chain 'U' and resid 390 through 395 Processing helix chain 'U' and resid 398 through 412 removed outlier: 4.135A pdb=" N LEU U 408 " --> pdb=" O ALA U 404 " (cutoff:3.500A) removed outlier: 4.209A pdb=" N GLY U 409 " --> pdb=" O THR U 405 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N VAL U 410 " --> pdb=" O ALA U 406 " (cutoff:3.500A) Processing helix chain 'U' and resid 415 through 427 removed outlier: 5.286A pdb=" N GLN U 421 " --> pdb=" O LYS U 417 " (cutoff:3.500A) removed outlier: 5.078A pdb=" N ALA U 424 " --> pdb=" O LEU U 420 " (cutoff:3.500A) Processing helix chain 'U' and resid 436 through 450 Processing helix chain 'U' and resid 454 through 466 removed outlier: 3.972A pdb=" N LYS U 466 " --> pdb=" O LEU U 462 " (cutoff:3.500A) Processing helix chain 'U' and resid 471 through 485 Processing helix chain 'U' and resid 490 through 502 removed outlier: 4.434A pdb=" N LEU U 496 " --> pdb=" O ASP U 492 " (cutoff:3.500A) Processing helix chain 'U' and resid 505 through 520 removed outlier: 3.939A pdb=" N GLU U 510 " --> pdb=" O ALA U 506 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N ALA U 511 " --> pdb=" O VAL U 507 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N GLY U 517 " --> pdb=" O GLY U 513 " (cutoff:3.500A) Processing helix chain 'U' and resid 525 through 537 removed outlier: 4.384A pdb=" N ILE U 529 " --> pdb=" O ASN U 525 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLU U 530 " --> pdb=" O ALA U 526 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N GLY U 534 " --> pdb=" O GLU U 530 " (cutoff:3.500A) Processing helix chain 'U' and resid 541 through 555 removed outlier: 3.690A pdb=" N VAL U 550 " --> pdb=" O ARG U 546 " (cutoff:3.500A) removed outlier: 4.225A pdb=" N ALA U 553 " --> pdb=" O ALA U 549 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N VAL U 555 " --> pdb=" O GLY U 551 " (cutoff:3.500A) Processing helix chain 'U' and resid 563 through 571 removed outlier: 3.644A pdb=" N SER U 569 " --> pdb=" O ALA U 565 " (cutoff:3.500A) Processing helix chain 'U' and resid 575 through 590 Processing helix chain 'U' and resid 597 through 609 removed outlier: 3.663A pdb=" N HIS U 604 " --> pdb=" O ARG U 600 " (cutoff:3.500A) Processing helix chain 'U' and resid 611 through 627 removed outlier: 3.973A pdb=" N LEU U 622 " --> pdb=" O ALA U 618 " (cutoff:3.500A) removed outlier: 4.354A pdb=" N GLY U 623 " --> pdb=" O VAL U 619 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N PHE U 624 " --> pdb=" O GLU U 620 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N ILE U 625 " --> pdb=" O SER U 621 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE U 627 " --> pdb=" O GLY U 623 " (cutoff:3.500A) Processing helix chain 'U' and resid 632 through 641 removed outlier: 5.224A pdb=" N LEU U 639 " --> pdb=" O SER U 635 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N LEU U 640 " --> pdb=" O VAL U 636 " (cutoff:3.500A) Processing helix chain 'U' and resid 645 through 660 Processing helix chain 'U' and resid 666 through 676 removed outlier: 3.994A pdb=" N LEU U 671 " --> pdb=" O GLU U 667 " (cutoff:3.500A) Proline residue: U 674 - end of helix Processing helix chain 'U' and resid 680 through 696 removed outlier: 4.468A pdb=" N ILE U 694 " --> pdb=" O ALA U 690 " (cutoff:3.500A) Processing helix chain 'U' and resid 705 through 718 removed outlier: 3.772A pdb=" N VAL U 716 " --> pdb=" O LEU U 712 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ASN U 718 " --> pdb=" O SER U 714 " (cutoff:3.500A) Processing helix chain 'U' and resid 723 through 738 Processing helix chain 'U' and resid 739 through 742 Processing helix chain 'U' and resid 756 through 768 removed outlier: 3.793A pdb=" N GLN U 768 " --> pdb=" O LEU U 764 " (cutoff:3.500A) Processing helix chain 'U' and resid 769 through 771 No H-bonds generated for 'chain 'U' and resid 769 through 771' Processing helix chain 'U' and resid 772 through 782 Processing helix chain 'U' and resid 887 through 892 removed outlier: 3.971A pdb=" N LYS U 890 " --> pdb=" O ALA U 887 " (cutoff:3.500A) Processing helix chain 'U' and resid 905 through 909 Processing sheet with id=AA1, first strand: chain 'A' and resid 93 through 98 removed outlier: 6.013A pdb=" N CYS A 98 " --> pdb=" O MET A 138 " (cutoff:3.500A) removed outlier: 4.728A pdb=" N MET A 138 " --> pdb=" O CYS A 98 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N ASP A 143 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N ILE A 149 " --> pdb=" O ASP A 143 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 149 through 151 current: chain 'C' and resid 86 through 89 removed outlier: 4.942A pdb=" N LYS C 94 " --> pdb=" O VAL B 109 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ILE B 122 " --> pdb=" O GLU B 113 " (cutoff:3.500A) removed outlier: 5.206A pdb=" N ILE B 115 " --> pdb=" O HIS B 120 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N HIS B 120 " --> pdb=" O ILE B 115 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 130 through 134 current: chain 'B' and resid 159 through 162 Processing sheet with id=AA2, first strand: chain 'A' and resid 111 through 115 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 119 through 123 current: chain 'D' and resid 100 through 105 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 110 through 114 current: chain 'D' and resid 139 through 142 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 139 through 142 current: chain 'E' and resid 68 through 72 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 78 through 81 current: chain 'E' and resid 107 through 110 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 107 through 110 current: chain 'F' and resid 121 through 126 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 131 through 134 current: chain 'F' and resid 160 through 163 Processing sheet with id=AA3, first strand: chain 'A' and resid 237 through 240 removed outlier: 6.315A pdb=" N VAL A 212 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 115 through 116 Processing sheet with id=AA5, first strand: chain 'C' and resid 186 through 189 removed outlier: 6.586A pdb=" N LEU C 187 " --> pdb=" O ILE C 315 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 210 through 215 removed outlier: 6.652A pdb=" N THR C 210 " --> pdb=" O ILE C 245 " (cutoff:3.500A) removed outlier: 7.563A pdb=" N PHE C 247 " --> pdb=" O THR C 210 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N ILE C 212 " --> pdb=" O PHE C 247 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N ASP C 249 " --> pdb=" O ILE C 212 " (cutoff:3.500A) removed outlier: 6.217A pdb=" N VAL C 214 " --> pdb=" O ASP C 249 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N SER C 244 " --> pdb=" O LYS C 290 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 165 through 169 removed outlier: 5.459A pdb=" N THR G 221 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 5.315A pdb=" N LYS G 226 " --> pdb=" O THR G 221 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 82 removed outlier: 3.667A pdb=" N ASP G 155 " --> pdb=" O TYR G 159 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 160 through 163 Processing sheet with id=AB1, first strand: chain 'H' and resid 66 through 69 removed outlier: 3.575A pdb=" N ILE H 68 " --> pdb=" O ILE H 72 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ILE H 72 " --> pdb=" O ILE H 68 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'I' and resid 162 through 164 Processing sheet with id=AB3, first strand: chain 'I' and resid 65 through 69 removed outlier: 6.446A pdb=" N MET I 72 " --> pdb=" O LEU I 68 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N GLY I 138 " --> pdb=" O GLN I 146 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LEU I 147 " --> pdb=" O TRP I 159 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'J' and resid 158 through 162 removed outlier: 4.106A pdb=" N THR J 31 " --> pdb=" O GLU J 46 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'J' and resid 63 through 66 removed outlier: 5.679A pdb=" N ALA J 64 " --> pdb=" O MET J 71 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET J 71 " --> pdb=" O ALA J 64 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 69 through 71 current: chain 'J' and resid 129 through 135 removed outlier: 4.260A pdb=" N LEU J 144 " --> pdb=" O TRP J 156 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'L' and resid 158 through 159 removed outlier: 4.152A pdb=" N SER L 211 " --> pdb=" O ALA L 48 " (cutoff:3.500A) removed outlier: 4.900A pdb=" N GLY L 216 " --> pdb=" O GLU L 220 " (cutoff:3.500A) removed outlier: 4.999A pdb=" N GLU L 220 " --> pdb=" O GLY L 216 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'L' and resid 63 through 67 removed outlier: 6.695A pdb=" N ILE L 70 " --> pdb=" O VAL L 66 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE L 144 " --> pdb=" O CYS L 156 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'M' and resid 36 through 40 WARNING: can't find start of bonding for strands! previous: chain 'M' and resid 44 through 52 current: chain 'M' and resid 224 through 225 Processing sheet with id=AB9, first strand: chain 'M' and resid 74 through 79 removed outlier: 4.036A pdb=" N LEU M 148 " --> pdb=" O TYR M 160 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR M 158 " --> pdb=" O MET M 150 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'Y' and resid 345 through 348 removed outlier: 7.331A pdb=" N ARG Y 312 " --> pdb=" O THR Y 356 " (cutoff:3.500A) removed outlier: 7.406A pdb=" N ARG Y 312 " --> pdb=" O GLY X 376 " (cutoff:3.500A) removed outlier: 7.692A pdb=" N LEU X 378 " --> pdb=" O ARG Y 312 " (cutoff:3.500A) removed outlier: 5.798A pdb=" N LEU Y 314 " --> pdb=" O LEU X 378 " (cutoff:3.500A) removed outlier: 6.787A pdb=" N GLN X 380 " --> pdb=" O LEU Y 314 " (cutoff:3.500A) removed outlier: 5.256A pdb=" N SER X 343 " --> pdb=" O ILE X 387 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N VAL W 406 " --> pdb=" O SER X 343 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N VAL X 345 " --> pdb=" O VAL W 406 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU a 326 " --> pdb=" O THR W 371 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ILE W 373 " --> pdb=" O GLU a 326 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'b' and resid 62 through 65 removed outlier: 5.654A pdb=" N THR b 63 " --> pdb=" O LEU b 51 " (cutoff:3.500A) removed outlier: 5.301A pdb=" N LEU b 51 " --> pdb=" O THR b 63 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ASN b 48 " --> pdb=" O GLU b 4 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N MET b 107 " --> pdb=" O ASN b 137 " (cutoff:3.500A) removed outlier: 8.023A pdb=" N ASP b 139 " --> pdb=" O MET b 107 " (cutoff:3.500A) removed outlier: 6.305A pdb=" N ILE b 109 " --> pdb=" O ASP b 139 " (cutoff:3.500A) removed outlier: 8.045A pdb=" N ILE b 141 " --> pdb=" O ILE b 109 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N ALA b 111 " --> pdb=" O ILE b 141 " (cutoff:3.500A) removed outlier: 8.055A pdb=" N VAL b 171 " --> pdb=" O VAL b 138 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE b 140 " --> pdb=" O VAL b 171 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'd' and resid 281 through 283 Processing sheet with id=AC4, first strand: chain 'u' and resid 124 through 125 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 124 through 125 current: chain 'u' and resid 165 through 180 WARNING: can't find start of bonding for strands! previous: chain 'u' and resid 165 through 180 current: chain 'u' and resid 216 through 219 No H-bonds generated for sheet with id=AC4 Processing sheet with id=AC5, first strand: chain 'u' and resid 157 through 158 Processing sheet with id=AC6, first strand: chain 'D' and resid 226 through 229 removed outlier: 7.317A pdb=" N ALA D 226 " --> pdb=" O ILE D 261 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N PHE D 263 " --> pdb=" O ALA D 226 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N ILE D 228 " --> pdb=" O PHE D 263 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ASP D 265 " --> pdb=" O ILE D 228 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL D 202 " --> pdb=" O MET D 309 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 194 through 199 removed outlier: 6.688A pdb=" N ASN E 194 " --> pdb=" O ILE E 229 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N PHE E 231 " --> pdb=" O ASN E 194 " (cutoff:3.500A) removed outlier: 6.028A pdb=" N LEU E 196 " --> pdb=" O PHE E 231 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N ASP E 233 " --> pdb=" O LEU E 196 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N VAL E 198 " --> pdb=" O ASP E 233 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N GLY E 169 " --> pdb=" O ARG E 297 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N ILE E 299 " --> pdb=" O GLY E 169 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU E 171 " --> pdb=" O ILE E 299 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'F' and resid 247 through 252 removed outlier: 6.789A pdb=" N GLY F 222 " --> pdb=" O ARG F 350 " (cutoff:3.500A) removed outlier: 8.187A pdb=" N ILE F 352 " --> pdb=" O GLY F 222 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N LEU F 224 " --> pdb=" O ILE F 352 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'B' and resid 246 through 251 removed outlier: 7.600A pdb=" N GLY B 221 " --> pdb=" O ASP B 348 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LYS B 350 " --> pdb=" O GLY B 221 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ILE B 223 " --> pdb=" O LYS B 350 " (cutoff:3.500A) removed outlier: 5.404A pdb=" N GLU B 352 " --> pdb=" O ILE B 223 " (cutoff:3.500A) removed outlier: 6.309A pdb=" N TYR B 225 " --> pdb=" O GLU B 352 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'K' and resid 167 through 170 Processing sheet with id=AD2, first strand: chain 'K' and resid 67 through 71 removed outlier: 6.754A pdb=" N ILE K 74 " --> pdb=" O ILE K 70 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N LEU K 153 " --> pdb=" O CYS K 165 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'c' and resid 31 through 33 removed outlier: 6.740A pdb=" N THR c 66 " --> pdb=" O VAL c 62 " (cutoff:3.500A) removed outlier: 4.638A pdb=" N LEU c 58 " --> pdb=" O ILE c 70 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N VAL c 72 " --> pdb=" O LEU c 56 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU c 56 " --> pdb=" O VAL c 72 " (cutoff:3.500A) removed outlier: 5.231A pdb=" N ALA c 74 " --> pdb=" O MET c 54 " (cutoff:3.500A) removed outlier: 7.868A pdb=" N MET c 54 " --> pdb=" O ALA c 74 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N GLY c 110 " --> pdb=" O MET c 57 " (cutoff:3.500A) removed outlier: 6.262A pdb=" N GLY c 59 " --> pdb=" O VAL c 108 " (cutoff:3.500A) removed outlier: 5.747A pdb=" N VAL c 108 " --> pdb=" O GLY c 59 " (cutoff:3.500A) removed outlier: 10.149A pdb=" N VAL c 141 " --> pdb=" O MET c 107 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N VAL c 109 " --> pdb=" O VAL c 141 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N VAL c 143 " --> pdb=" O VAL c 109 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N TRP c 111 " --> pdb=" O VAL c 143 " (cutoff:3.500A) removed outlier: 8.156A pdb=" N VAL c 145 " --> pdb=" O TRP c 111 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N HIS c 113 " --> pdb=" O VAL c 145 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ALA c 159 " --> pdb=" O ILE c 203 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'Z' and resid 154 through 157 removed outlier: 5.288A pdb=" N ILE Z 91 " --> pdb=" O GLY Z 41 " (cutoff:3.500A) removed outlier: 6.037A pdb=" N GLY Z 41 " --> pdb=" O ILE Z 91 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N VAL Z 36 " --> pdb=" O ALA Z 55 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N ALA Z 55 " --> pdb=" O VAL Z 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N VAL Z 38 " --> pdb=" O SER Z 53 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER Z 53 " --> pdb=" O VAL Z 38 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N LEU Z 40 " --> pdb=" O SER Z 51 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LYS Z 8 " --> pdb=" O LEU Z 48 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N VAL Z 50 " --> pdb=" O LYS Z 8 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N VAL Z 10 " --> pdb=" O VAL Z 50 " (cutoff:3.500A) removed outlier: 7.677A pdb=" N ASN Z 52 " --> pdb=" O VAL Z 10 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Z' and resid 58 through 60 Processing sheet with id=AD6, first strand: chain 'V' and resid 416 through 418 Processing sheet with id=AD7, first strand: chain 'U' and resid 744 through 745 Processing sheet with id=AD8, first strand: chain 'U' and resid 881 through 882 removed outlier: 6.387A pdb=" N ILE U 789 " --> pdb=" O ILE U 912 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU U 914 " --> pdb=" O ILE U 789 " (cutoff:3.500A) removed outlier: 6.316A pdb=" N LEU U 791 " --> pdb=" O LEU U 914 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N GLN U 901 " --> pdb=" O LYS U 915 " (cutoff:3.500A) 3197 hydrogen bonds defined for protein. 9156 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: 27.76 Time building geometry restraints manager: 14.38 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.13 - 1.27: 10696 1.27 - 1.41: 14408 1.41 - 1.55: 37486 1.55 - 1.69: 250 1.69 - 1.83: 546 Bond restraints: 63386 Sorted by residual: bond pdb=" C PRO D 145 " pdb=" O PRO D 145 " ideal model delta sigma weight residual 1.235 1.125 0.110 1.30e-02 5.92e+03 7.14e+01 bond pdb=" C4 ADP B 501 " pdb=" C5 ADP B 501 " ideal model delta sigma weight residual 1.490 1.354 0.136 2.00e-02 2.50e+03 4.65e+01 bond pdb=" CA ASP V 140 " pdb=" C ASP V 140 " ideal model delta sigma weight residual 1.519 1.550 -0.031 5.30e-03 3.56e+04 3.43e+01 bond pdb=" C4 ADP F 501 " pdb=" C5 ADP F 501 " ideal model delta sigma weight residual 1.490 1.380 0.110 2.00e-02 2.50e+03 3.00e+01 bond pdb=" C4 ADP A 501 " pdb=" C5 ADP A 501 " ideal model delta sigma weight residual 1.490 1.381 0.109 2.00e-02 2.50e+03 2.97e+01 ... (remaining 63381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.55: 83345 4.55 - 9.10: 2283 9.10 - 13.65: 42 13.65 - 18.21: 5 18.21 - 22.76: 3 Bond angle restraints: 85678 Sorted by residual: angle pdb=" PB ATP C 501 " pdb=" O3B ATP C 501 " pdb=" PG ATP C 501 " ideal model delta sigma weight residual 139.87 125.11 14.76 1.00e+00 1.00e+00 2.18e+02 angle pdb=" PB ATP D 501 " pdb=" O3B ATP D 501 " pdb=" PG ATP D 501 " ideal model delta sigma weight residual 139.87 125.94 13.93 1.00e+00 1.00e+00 1.94e+02 angle pdb=" CA VAL C 220 " pdb=" CB VAL C 220 " pdb=" CG1 VAL C 220 " ideal model delta sigma weight residual 110.40 133.16 -22.76 1.70e+00 3.46e-01 1.79e+02 angle pdb=" O PRO D 145 " pdb=" C PRO D 145 " pdb=" N GLU D 146 " ideal model delta sigma weight residual 122.64 104.90 17.74 1.35e+00 5.49e-01 1.73e+02 angle pdb=" PA ATP C 501 " pdb=" O3A ATP C 501 " pdb=" PB ATP C 501 " ideal model delta sigma weight residual 136.83 125.37 11.46 1.00e+00 1.00e+00 1.31e+02 ... (remaining 85673 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 28.25: 36998 28.25 - 56.50: 1647 56.50 - 84.75: 249 84.75 - 113.00: 30 113.00 - 141.25: 4 Dihedral angle restraints: 38928 sinusoidal: 15888 harmonic: 23040 Sorted by residual: dihedral pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CA PRO B 169 " pdb=" CB PRO B 169 " ideal model delta harmonic sigma weight residual 115.10 141.10 -26.00 0 2.50e+00 1.60e-01 1.08e+02 dihedral pdb=" C PRO B 169 " pdb=" N PRO B 169 " pdb=" CA PRO B 169 " pdb=" CB PRO B 169 " ideal model delta harmonic sigma weight residual -120.70 -143.35 22.65 0 2.50e+00 1.60e-01 8.21e+01 dihedral pdb=" C ASP B 168 " pdb=" N ASP B 168 " pdb=" CA ASP B 168 " pdb=" CB ASP B 168 " ideal model delta harmonic sigma weight residual -122.60 -141.49 18.89 0 2.50e+00 1.60e-01 5.71e+01 ... (remaining 38925 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.234: 9442 0.234 - 0.467: 326 0.467 - 0.701: 17 0.701 - 0.934: 2 0.934 - 1.168: 1 Chirality restraints: 9788 Sorted by residual: chirality pdb=" CA PRO B 169 " pdb=" N PRO B 169 " pdb=" C PRO B 169 " pdb=" CB PRO B 169 " both_signs ideal model delta sigma weight residual False 2.72 1.55 1.17 2.00e-01 2.50e+01 3.41e+01 chirality pdb=" CB VAL C 220 " pdb=" CA VAL C 220 " pdb=" CG1 VAL C 220 " pdb=" CG2 VAL C 220 " both_signs ideal model delta sigma weight residual False -2.63 -1.72 -0.91 2.00e-01 2.50e+01 2.07e+01 chirality pdb=" CA ASP B 168 " pdb=" N ASP B 168 " pdb=" C ASP B 168 " pdb=" CB ASP B 168 " both_signs ideal model delta sigma weight residual False 2.51 1.74 0.77 2.00e-01 2.50e+01 1.50e+01 ... (remaining 9785 not shown) Planarity restraints: 11038 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR V 360 " -0.249 2.00e-02 2.50e+03 1.33e-01 3.53e+02 pdb=" CG TYR V 360 " 0.087 2.00e-02 2.50e+03 pdb=" CD1 TYR V 360 " 0.125 2.00e-02 2.50e+03 pdb=" CD2 TYR V 360 " 0.097 2.00e-02 2.50e+03 pdb=" CE1 TYR V 360 " 0.059 2.00e-02 2.50e+03 pdb=" CE2 TYR V 360 " 0.081 2.00e-02 2.50e+03 pdb=" CZ TYR V 360 " -0.010 2.00e-02 2.50e+03 pdb=" OH TYR V 360 " -0.190 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 78 " -0.222 2.00e-02 2.50e+03 1.10e-01 3.03e+02 pdb=" CG TRP A 78 " 0.047 2.00e-02 2.50e+03 pdb=" CD1 TRP A 78 " 0.165 2.00e-02 2.50e+03 pdb=" CD2 TRP A 78 " 0.062 2.00e-02 2.50e+03 pdb=" NE1 TRP A 78 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 78 " -0.033 2.00e-02 2.50e+03 pdb=" CE3 TRP A 78 " 0.112 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 78 " -0.124 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 78 " 0.066 2.00e-02 2.50e+03 pdb=" CH2 TRP A 78 " -0.074 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 158 " 0.233 2.00e-02 2.50e+03 1.23e-01 3.01e+02 pdb=" CG TYR F 158 " -0.083 2.00e-02 2.50e+03 pdb=" CD1 TYR F 158 " -0.111 2.00e-02 2.50e+03 pdb=" CD2 TYR F 158 " -0.105 2.00e-02 2.50e+03 pdb=" CE1 TYR F 158 " -0.055 2.00e-02 2.50e+03 pdb=" CE2 TYR F 158 " -0.060 2.00e-02 2.50e+03 pdb=" CZ TYR F 158 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 158 " 0.171 2.00e-02 2.50e+03 ... (remaining 11035 not shown) Histogram of nonbonded interaction distances: 0.84 - 1.66: 3 1.66 - 2.47: 117 2.47 - 3.28: 73944 3.28 - 4.09: 166056 4.09 - 4.90: 287598 Warning: very small nonbonded interaction distances. Nonbonded interactions: 527718 Sorted by model distance: nonbonded pdb=" OE1 GLU D 242 " pdb=" NH2 ARG D 245 " model vdw 0.845 3.120 nonbonded pdb=" CZ PHE C 283 " pdb=" OE2 GLU C 284 " model vdw 1.469 3.340 nonbonded pdb=" CE1 PHE C 283 " pdb=" OE2 GLU C 284 " model vdw 1.655 3.340 nonbonded pdb=" OD1 ASP c 126 " pdb="ZN ZN c 501 " model vdw 1.707 2.230 nonbonded pdb=" OD2 ASP c 126 " pdb="ZN ZN c 501 " model vdw 1.717 2.230 ... (remaining 527713 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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=0.00 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: 1.490 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: 0.080 Extract box with map and model: 1.810 Check model and map are aligned: 0.360 Set scattering table: 0.450 Process input model: 124.130 Find NCS groups from input model: 1.740 Set up NCS constraints: 0.230 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: 0.030 Load rotamer database and sin/cos tables:2.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.136 63386 Z= 0.815 Angle : 1.968 22.757 85678 Z= 1.290 Chirality : 0.110 1.168 9788 Planarity : 0.017 0.248 11038 Dihedral : 16.419 141.248 24003 Min Nonbonded Distance : 0.845 Molprobity Statistics. All-atom Clashscore : 7.46 Ramachandran Plot: Outliers : 2.54 % Allowed : 9.48 % Favored : 87.98 % Rotamer: Outliers : 5.57 % Allowed : 8.67 % Favored : 85.77 % Cbeta Deviations : 0.86 % Peptide Plane: Cis-proline : 1.04 % 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: -3.31 (0.08), residues: 7806 helix: -2.20 (0.06), residues: 3983 sheet: -0.97 (0.22), residues: 532 loop : -2.25 (0.11), residues: 3291 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.222 0.029 TRP A 78 HIS 0.025 0.004 HIS c 183 PHE 0.121 0.017 PHE G 210 TYR 0.249 0.026 TYR V 360 ARG 0.014 0.002 ARG D 114 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1412 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 375 poor density : 1037 time to evaluate : 5.408 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 206 ILE cc_start: 0.7200 (OUTLIER) cc_final: 0.6818 (mm) REVERT: A 362 MET cc_start: 0.3830 (mpp) cc_final: 0.3347 (mpp) REVERT: A 371 GLU cc_start: 0.5702 (OUTLIER) cc_final: 0.3896 (pp20) REVERT: A 372 LEU cc_start: 0.6434 (tp) cc_final: 0.6002 (tp) REVERT: C 64 GLN cc_start: 0.8697 (OUTLIER) cc_final: 0.8403 (mp10) REVERT: C 275 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.8228 (tm-30) REVERT: C 385 MET cc_start: 0.8698 (ptm) cc_final: 0.7824 (ptm) REVERT: G 159 TYR cc_start: 0.0394 (OUTLIER) cc_final: -0.1926 (t80) REVERT: H 219 ARG cc_start: 0.6492 (OUTLIER) cc_final: 0.5492 (ppt-90) REVERT: L 123 TYR cc_start: 0.6587 (OUTLIER) cc_final: 0.6387 (p90) REVERT: L 140 MET cc_start: 0.5437 (mtp) cc_final: 0.5235 (mpp) REVERT: L 146 GLN cc_start: -0.1880 (OUTLIER) cc_final: -0.2733 (tt0) REVERT: M 69 VAL cc_start: 0.1754 (OUTLIER) cc_final: 0.1470 (t) REVERT: M 151 ILE cc_start: 0.5591 (OUTLIER) cc_final: 0.5366 (mp) REVERT: M 181 MET cc_start: 0.3751 (mtm) cc_final: 0.3492 (mpp) REVERT: W 88 MET cc_start: 0.1941 (tmm) cc_final: 0.1573 (ttp) REVERT: W 172 GLU cc_start: 0.7478 (OUTLIER) cc_final: 0.7197 (pm20) REVERT: W 207 LYS cc_start: 0.7960 (tptt) cc_final: 0.7579 (tmtt) REVERT: W 255 CYS cc_start: 0.7845 (p) cc_final: 0.7280 (t) REVERT: Y 200 LEU cc_start: 0.8643 (mt) cc_final: 0.8423 (mm) REVERT: Y 228 MET cc_start: 0.8104 (mtp) cc_final: 0.7897 (mtp) REVERT: a 54 ASP cc_start: 0.7132 (OUTLIER) cc_final: 0.6823 (p0) REVERT: a 94 LEU cc_start: 0.8307 (OUTLIER) cc_final: 0.7869 (mm) REVERT: b 107 MET cc_start: 0.7206 (mtm) cc_final: 0.6858 (mtp) REVERT: u 123 TYR cc_start: 0.1944 (m-10) cc_final: 0.1688 (m-80) REVERT: u 180 MET cc_start: 0.6134 (OUTLIER) cc_final: 0.5855 (ppp) REVERT: u 214 PRO cc_start: 0.5382 (Cg_endo) cc_final: 0.4869 (Cg_exo) REVERT: D 235 PHE cc_start: 0.8171 (m-80) cc_final: 0.7967 (m-80) REVERT: D 312 ASN cc_start: 0.8456 (OUTLIER) cc_final: 0.8053 (p0) REVERT: D 381 GLU cc_start: 0.8365 (OUTLIER) cc_final: 0.7592 (mm-30) REVERT: E 130 VAL cc_start: 0.8606 (OUTLIER) cc_final: 0.8185 (t) REVERT: E 196 LEU cc_start: 0.9028 (mt) cc_final: 0.6636 (mt) REVERT: E 231 PHE cc_start: 0.8630 (t80) cc_final: 0.8055 (t80) REVERT: E 332 VAL cc_start: 0.8548 (t) cc_final: 0.8136 (t) REVERT: F 88 TYR cc_start: 0.7152 (OUTLIER) cc_final: 0.6540 (p90) REVERT: F 206 MET cc_start: 0.9082 (mpp) cc_final: 0.8675 (mpp) REVERT: F 254 PRO cc_start: 0.8888 (Cg_exo) cc_final: 0.8428 (Cg_endo) REVERT: B 202 GLU cc_start: 0.4442 (OUTLIER) cc_final: 0.3751 (tm-30) REVERT: B 203 LEU cc_start: 0.5035 (OUTLIER) cc_final: 0.4633 (mt) REVERT: B 258 LYS cc_start: 0.3866 (OUTLIER) cc_final: 0.3091 (tptt) REVERT: c 130 GLN cc_start: 0.8201 (tp40) cc_final: 0.7819 (tp-100) REVERT: c 178 THR cc_start: 0.8543 (OUTLIER) cc_final: 0.8266 (p) REVERT: Z 81 MET cc_start: 0.8360 (mpm) cc_final: 0.7400 (mmp) REVERT: Z 82 PHE cc_start: 0.8374 (m-80) cc_final: 0.7552 (m-10) REVERT: V 37 MET cc_start: 0.6642 (mtp) cc_final: 0.3952 (tpp) REVERT: V 64 GLN cc_start: 0.8748 (tt0) cc_final: 0.8382 (tm-30) REVERT: V 182 LYS cc_start: 0.7633 (OUTLIER) cc_final: 0.7036 (tptp) REVERT: U 69 TYR cc_start: 0.7822 (OUTLIER) cc_final: 0.6297 (t80) REVERT: U 176 MET cc_start: 0.5572 (tmm) cc_final: 0.5181 (tmm) REVERT: U 694 ILE cc_start: 0.8162 (OUTLIER) cc_final: 0.7686 (pt) REVERT: U 797 MET cc_start: 0.7989 (mpp) cc_final: 0.7732 (mpp) outliers start: 375 outliers final: 119 residues processed: 1346 average time/residue: 0.6277 time to fit residues: 1382.9898 Evaluate side-chains 771 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 144 poor density : 627 time to evaluate : 5.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 654 optimal weight: 5.9990 chunk 587 optimal weight: 4.9990 chunk 325 optimal weight: 7.9990 chunk 200 optimal weight: 8.9990 chunk 396 optimal weight: 8.9990 chunk 313 optimal weight: 5.9990 chunk 607 optimal weight: 8.9990 chunk 235 optimal weight: 4.9990 chunk 369 optimal weight: 5.9990 chunk 452 optimal weight: 0.9980 chunk 703 optimal weight: 6.9990 overall best weight: 4.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 150 HIS A 353 HIS C 64 GLN C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 42 ASN H 102 GLN I 166 ASN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 8 ASN L 143 HIS O 66 HIS W 53 GLN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 426 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 440 ASN X 62 GLN ** X 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 405 GLN ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 332 HIS ** b 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 228 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 289 HIS D 83 GLN D 135 HIS D 295 GLN E 32 GLN E 262 ASN E 300 HIS E 345 ASN F 417 HIS F 428 GLN B 242 GLN K 23 GLN ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 204 GLN ** c 44 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 101 GLN ** c 183 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN ** Z 145 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 174 HIS V 329 HIS V 477 HIS e 47 ASN e 63 HIS ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** U 321 GLN U 347 ASN ** U 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 467 ASN Total number of N/Q/H flips: 40 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 moved from start: 0.3115 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 63386 Z= 0.299 Angle : 0.892 11.030 85678 Z= 0.471 Chirality : 0.050 0.356 9788 Planarity : 0.006 0.079 11038 Dihedral : 9.118 119.495 8684 Min Nonbonded Distance : 1.889 Molprobity Statistics. All-atom Clashscore : 14.33 Ramachandran Plot: Outliers : 0.67 % Allowed : 7.70 % Favored : 91.63 % Rotamer: Outliers : 0.18 % Allowed : 4.57 % Favored : 95.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -2.08 (0.09), residues: 7806 helix: -1.09 (0.07), residues: 4075 sheet: -0.92 (0.18), residues: 737 loop : -1.72 (0.12), residues: 2994 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.003 TRP W 263 HIS 0.017 0.002 HIS c 183 PHE 0.042 0.003 PHE U 59 TYR 0.051 0.003 TYR W 174 ARG 0.020 0.001 ARG E 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 871 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 859 time to evaluate : 5.353 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 160 THR cc_start: 0.6257 (OUTLIER) cc_final: 0.5542 (m) REVERT: A 299 MET cc_start: 0.3990 (ppp) cc_final: 0.3673 (ppp) REVERT: C 76 VAL cc_start: 0.6627 (t) cc_final: 0.6350 (m) REVERT: C 347 ILE cc_start: 0.8633 (mm) cc_final: 0.8210 (tp) REVERT: L 176 MET cc_start: 0.7057 (ppp) cc_final: 0.6698 (ppp) REVERT: W 60 MET cc_start: -0.3672 (ptt) cc_final: -0.4223 (mtm) REVERT: W 207 LYS cc_start: 0.7770 (tptt) cc_final: 0.7407 (tmtt) REVERT: X 251 LEU cc_start: 0.8042 (tp) cc_final: 0.7830 (tp) REVERT: b 107 MET cc_start: 0.7196 (mtm) cc_final: 0.6930 (mtt) REVERT: d 109 LEU cc_start: 0.7568 (pt) cc_final: 0.7301 (pt) REVERT: d 219 ASP cc_start: 0.7782 (p0) cc_final: 0.7559 (p0) REVERT: u 172 ASN cc_start: 0.7027 (m-40) cc_final: 0.6639 (m-40) REVERT: D 267 ILE cc_start: 0.8213 (tp) cc_final: 0.7885 (tp) REVERT: D 292 LEU cc_start: 0.8375 (tt) cc_final: 0.7919 (tt) REVERT: E 368 MET cc_start: 0.8655 (mmt) cc_final: 0.7930 (mmp) REVERT: B 119 ASN cc_start: 0.8465 (p0) cc_final: 0.8254 (p0) REVERT: B 405 MET cc_start: 0.7557 (mtp) cc_final: 0.6776 (mtp) REVERT: c 160 PHE cc_start: 0.7984 (m-80) cc_final: 0.7595 (m-80) REVERT: V 37 MET cc_start: 0.6471 (mtp) cc_final: 0.5212 (tpp) REVERT: V 64 GLN cc_start: 0.8635 (tt0) cc_final: 0.8433 (tm-30) REVERT: V 309 MET cc_start: 0.4822 (mmp) cc_final: 0.4086 (mmm) REVERT: U 550 VAL cc_start: 0.9080 (t) cc_final: 0.8757 (t) REVERT: U 560 MET cc_start: 0.7215 (tpt) cc_final: 0.6847 (tpp) REVERT: U 797 MET cc_start: 0.7736 (mpp) cc_final: 0.7408 (mpp) outliers start: 12 outliers final: 1 residues processed: 868 average time/residue: 0.6022 time to fit residues: 870.7883 Evaluate side-chains 581 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 579 time to evaluate : 5.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 391 optimal weight: 8.9990 chunk 218 optimal weight: 30.0000 chunk 585 optimal weight: 6.9990 chunk 479 optimal weight: 9.9990 chunk 194 optimal weight: 7.9990 chunk 705 optimal weight: 8.9990 chunk 761 optimal weight: 6.9990 chunk 627 optimal weight: 5.9990 chunk 699 optimal weight: 7.9990 chunk 240 optimal weight: 6.9990 chunk 565 optimal weight: 10.0000 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 305 GLN C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN O 62 ASN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 35 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 169 HIS d 190 GLN D 83 GLN ** D 294 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 155 ASN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 316 HIS ** F 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 417 HIS F 428 GLN K 23 GLN ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 152 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 178 GLN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 223 ASN e 47 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 63386 Z= 0.321 Angle : 0.829 13.024 85678 Z= 0.436 Chirality : 0.048 0.246 9788 Planarity : 0.006 0.090 11038 Dihedral : 8.706 113.908 8684 Min Nonbonded Distance : 1.832 Molprobity Statistics. All-atom Clashscore : 17.49 Ramachandran Plot: Outliers : 0.58 % Allowed : 8.02 % Favored : 91.40 % Rotamer: Outliers : 0.04 % Allowed : 4.59 % Favored : 95.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.09), residues: 7806 helix: -0.82 (0.08), residues: 4069 sheet: -1.00 (0.18), residues: 779 loop : -1.57 (0.12), residues: 2958 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP W 263 HIS 0.011 0.002 HIS W 288 PHE 0.034 0.003 PHE K 22 TYR 0.035 0.002 TYR W 174 ARG 0.011 0.001 ARG D 252 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 738 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 735 time to evaluate : 5.455 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 299 MET cc_start: 0.3918 (ppp) cc_final: 0.3486 (ppp) REVERT: C 347 ILE cc_start: 0.8511 (mm) cc_final: 0.8178 (tp) REVERT: L 176 MET cc_start: 0.7090 (ppp) cc_final: 0.6575 (ppp) REVERT: W 47 LEU cc_start: 0.1912 (mm) cc_final: 0.0589 (mm) REVERT: W 60 MET cc_start: -0.3535 (ptt) cc_final: -0.4311 (mtm) REVERT: W 177 MET cc_start: 0.5856 (ptm) cc_final: 0.5248 (ptm) REVERT: W 207 LYS cc_start: 0.7732 (tptt) cc_final: 0.7423 (tmtt) REVERT: b 107 MET cc_start: 0.7297 (mtm) cc_final: 0.7064 (mtt) REVERT: u 264 THR cc_start: 0.5358 (t) cc_final: 0.4678 (t) REVERT: D 214 MET cc_start: 0.7912 (ttp) cc_final: 0.7691 (ttp) REVERT: D 315 ASP cc_start: 0.7928 (p0) cc_final: 0.7707 (p0) REVERT: F 310 MET cc_start: 0.8683 (ptm) cc_final: 0.8390 (ptm) REVERT: V 37 MET cc_start: 0.6339 (mtp) cc_final: 0.5489 (tpp) REVERT: V 64 GLN cc_start: 0.8670 (tt0) cc_final: 0.8449 (tm-30) REVERT: U 9 ILE cc_start: 0.6282 (mt) cc_final: 0.5946 (mt) REVERT: U 550 VAL cc_start: 0.9134 (t) cc_final: 0.8862 (t) REVERT: U 560 MET cc_start: 0.7197 (tpt) cc_final: 0.6817 (tpt) REVERT: U 588 MET cc_start: 0.6188 (mmp) cc_final: 0.5959 (mmp) REVERT: U 757 MET cc_start: 0.8376 (tmm) cc_final: 0.7969 (tmm) REVERT: U 797 MET cc_start: 0.7883 (mpp) cc_final: 0.7350 (mpp) outliers start: 3 outliers final: 0 residues processed: 737 average time/residue: 0.5843 time to fit residues: 726.7981 Evaluate side-chains 536 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 536 time to evaluate : 5.365 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 696 optimal weight: 10.0000 chunk 530 optimal weight: 10.0000 chunk 365 optimal weight: 7.9990 chunk 78 optimal weight: 20.0000 chunk 336 optimal weight: 0.1980 chunk 473 optimal weight: 9.9990 chunk 707 optimal weight: 10.0000 chunk 749 optimal weight: 0.1980 chunk 369 optimal weight: 10.0000 chunk 670 optimal weight: 10.0000 chunk 201 optimal weight: 50.0000 overall best weight: 5.6788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 GLN A 117 GLN C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 21 GLN ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 146 GLN W 86 ASN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 375 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 136 HIS a 249 GLN b 34 ASN b 76 HIS ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 135 HIS ** D 295 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN E 316 HIS F 358 ASN ** B 241 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 118 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 152 GLN c 44 HIS ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 283 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6392 moved from start: 0.4235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.080 63386 Z= 0.287 Angle : 0.782 12.004 85678 Z= 0.409 Chirality : 0.047 0.239 9788 Planarity : 0.005 0.116 11038 Dihedral : 8.378 111.427 8684 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 17.45 Ramachandran Plot: Outliers : 0.56 % Allowed : 7.65 % Favored : 91.79 % Rotamer: Outliers : 0.06 % Allowed : 3.78 % Favored : 96.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.59 (0.09), residues: 7806 helix: -0.61 (0.08), residues: 4087 sheet: -1.09 (0.18), residues: 777 loop : -1.50 (0.12), residues: 2942 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP Z 94 HIS 0.010 0.002 HIS U 450 PHE 0.035 0.002 PHE E 219 TYR 0.031 0.002 TYR V 360 ARG 0.011 0.001 ARG A 139 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 732 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 728 time to evaluate : 5.413 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 REVERT: A 299 MET cc_start: 0.4277 (ppp) cc_final: 0.3817 (ppp) REVERT: A 362 MET cc_start: 0.3711 (mpp) cc_final: 0.3288 (mpp) REVERT: C 347 ILE cc_start: 0.8488 (mm) cc_final: 0.8142 (tp) REVERT: I 174 MET cc_start: 0.6355 (ptp) cc_final: 0.5511 (ppp) REVERT: L 176 MET cc_start: 0.7054 (ppp) cc_final: 0.6502 (ppp) REVERT: W 177 MET cc_start: 0.6234 (ptm) cc_final: 0.5660 (ptm) REVERT: W 207 LYS cc_start: 0.7371 (tptt) cc_final: 0.6809 (tmtt) REVERT: Y 228 MET cc_start: 0.8196 (ptp) cc_final: 0.7930 (mtm) REVERT: Y 389 MET cc_start: 0.7490 (mtt) cc_final: 0.7240 (mtm) REVERT: u 177 LEU cc_start: 0.7001 (mt) cc_final: 0.6778 (mt) REVERT: u 264 THR cc_start: 0.5281 (t) cc_final: 0.4680 (t) REVERT: D 246 MET cc_start: 0.7897 (ptp) cc_final: 0.7311 (ptt) REVERT: D 315 ASP cc_start: 0.7737 (p0) cc_final: 0.7503 (p0) REVERT: E 219 PHE cc_start: 0.8914 (m-80) cc_final: 0.8616 (m-80) REVERT: F 310 MET cc_start: 0.8718 (ptm) cc_final: 0.8508 (ptm) REVERT: F 422 GLU cc_start: 0.6590 (pt0) cc_final: 0.6376 (pt0) REVERT: V 64 GLN cc_start: 0.8644 (tt0) cc_final: 0.8435 (tm-30) REVERT: U 9 ILE cc_start: 0.6322 (mt) cc_final: 0.5987 (mt) REVERT: U 176 MET cc_start: 0.5671 (tmm) cc_final: 0.3885 (tpp) REVERT: U 333 MET cc_start: 0.8521 (mtm) cc_final: 0.8164 (mtp) REVERT: U 550 VAL cc_start: 0.9183 (t) cc_final: 0.8890 (t) REVERT: U 560 MET cc_start: 0.7130 (tpt) cc_final: 0.6807 (tpt) REVERT: U 588 MET cc_start: 0.6148 (mmp) cc_final: 0.5744 (mmp) REVERT: U 797 MET cc_start: 0.7821 (mpp) cc_final: 0.7126 (mpp) REVERT: U 894 MET cc_start: 0.7817 (mpp) cc_final: 0.6468 (tpp) outliers start: 4 outliers final: 1 residues processed: 732 average time/residue: 0.5766 time to fit residues: 720.9134 Evaluate side-chains 528 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 527 time to evaluate : 5.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 623 optimal weight: 10.0000 chunk 425 optimal weight: 20.0000 chunk 10 optimal weight: 8.9990 chunk 557 optimal weight: 6.9990 chunk 309 optimal weight: 10.0000 chunk 639 optimal weight: 10.0000 chunk 517 optimal weight: 7.9990 chunk 0 optimal weight: 30.0000 chunk 382 optimal weight: 7.9990 chunk 672 optimal weight: 7.9990 chunk 189 optimal weight: 8.9990 overall best weight: 7.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 ASN C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 116 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 107 GLN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 264 GLN Y 178 ASN ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 129 GLN b 76 HIS ** u 172 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** E 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 307 GLN E 316 HIS B 195 GLN B 207 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 109 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.4577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 63386 Z= 0.343 Angle : 0.813 14.545 85678 Z= 0.423 Chirality : 0.047 0.235 9788 Planarity : 0.006 0.100 11038 Dihedral : 8.373 112.705 8684 Min Nonbonded Distance : 1.782 Molprobity Statistics. All-atom Clashscore : 20.19 Ramachandran Plot: Outliers : 0.53 % Allowed : 8.43 % Favored : 91.05 % Rotamer: Outliers : 0.01 % Allowed : 3.80 % Favored : 96.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: -1.61 (0.09), residues: 7806 helix: -0.59 (0.08), residues: 4068 sheet: -1.21 (0.17), residues: 831 loop : -1.54 (0.12), residues: 2907 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP W 263 HIS 0.012 0.002 HIS U 450 PHE 0.032 0.003 PHE U 88 TYR 0.034 0.002 TYR V 360 ARG 0.012 0.001 ARG E 255 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 666 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 665 time to evaluate : 5.430 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: A 362 MET cc_start: 0.3571 (mpp) cc_final: 0.3301 (mpp) REVERT: C 347 ILE cc_start: 0.8347 (mm) cc_final: 0.7954 (tp) REVERT: C 350 LEU cc_start: 0.8825 (tp) cc_final: 0.8617 (tp) REVERT: G 80 MET cc_start: 0.1643 (tpp) cc_final: 0.1258 (tpp) REVERT: I 174 MET cc_start: 0.6331 (ptp) cc_final: 0.5416 (ppp) REVERT: L 176 MET cc_start: 0.7082 (ppp) cc_final: 0.6544 (ppp) REVERT: W 177 MET cc_start: 0.6139 (ptm) cc_final: 0.5669 (ptm) REVERT: W 207 LYS cc_start: 0.7543 (tptt) cc_final: 0.6886 (tmtt) REVERT: Y 228 MET cc_start: 0.7899 (ptp) cc_final: 0.7590 (mtm) REVERT: Y 389 MET cc_start: 0.7551 (mtt) cc_final: 0.6952 (mmm) REVERT: b 31 ASP cc_start: 0.9267 (m-30) cc_final: 0.8757 (p0) REVERT: u 264 THR cc_start: 0.5473 (t) cc_final: 0.4682 (t) REVERT: D 87 LEU cc_start: 0.7875 (mt) cc_final: 0.7645 (mt) REVERT: D 315 ASP cc_start: 0.7809 (p0) cc_final: 0.7596 (p0) REVERT: E 281 ARG cc_start: 0.7788 (ttt180) cc_final: 0.7490 (ttp80) REVERT: F 422 GLU cc_start: 0.6694 (pt0) cc_final: 0.6432 (pt0) REVERT: B 119 ASN cc_start: 0.8528 (p0) cc_final: 0.8301 (p0) REVERT: K 156 MET cc_start: 0.6196 (mpp) cc_final: 0.5714 (mpp) REVERT: c 234 TYR cc_start: 0.6173 (m-80) cc_final: 0.5894 (m-10) REVERT: Z 21 ASP cc_start: 0.7279 (t70) cc_final: 0.7034 (t0) REVERT: Z 78 MET cc_start: 0.7695 (tpt) cc_final: 0.7022 (tpt) REVERT: V 37 MET cc_start: 0.7000 (ttt) cc_final: 0.6667 (tpp) REVERT: V 64 GLN cc_start: 0.8684 (tt0) cc_final: 0.8448 (tm-30) REVERT: U 9 ILE cc_start: 0.6420 (mt) cc_final: 0.6080 (mt) REVERT: U 176 MET cc_start: 0.5569 (tmm) cc_final: 0.3866 (tpp) REVERT: U 333 MET cc_start: 0.8516 (mtm) cc_final: 0.8248 (mtp) REVERT: U 560 MET cc_start: 0.7259 (tpt) cc_final: 0.6827 (tpp) REVERT: U 588 MET cc_start: 0.6265 (mmp) cc_final: 0.5890 (mmp) REVERT: U 797 MET cc_start: 0.7957 (mpp) cc_final: 0.7292 (mpp) outliers start: 1 outliers final: 1 residues processed: 666 average time/residue: 0.5788 time to fit residues: 656.1158 Evaluate side-chains 493 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 5.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 252 optimal weight: 30.0000 chunk 674 optimal weight: 5.9990 chunk 148 optimal weight: 9.9990 chunk 439 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 749 optimal weight: 7.9990 chunk 622 optimal weight: 10.0000 chunk 347 optimal weight: 7.9990 chunk 62 optimal weight: 0.0370 chunk 248 optimal weight: 8.9990 chunk 393 optimal weight: 8.9990 overall best weight: 4.6066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 12 HIS ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 88 HIS ** H 95 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 116 GLN J 146 GLN ** W 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 207 GLN ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 76 HIS ** b 94 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 139 ASN u 172 ASN D 67 ASN D 83 GLN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 263 GLN E 316 HIS F 316 GLN B 207 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN K 118 ASN c 237 HIS c 254 ASN c 295 ASN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 ASN e 47 ASN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 24 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.4833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 63386 Z= 0.249 Angle : 0.759 12.978 85678 Z= 0.392 Chirality : 0.046 0.331 9788 Planarity : 0.005 0.121 11038 Dihedral : 8.134 112.974 8684 Min Nonbonded Distance : 1.817 Molprobity Statistics. All-atom Clashscore : 17.91 Ramachandran Plot: Outliers : 0.47 % Allowed : 7.80 % Favored : 91.72 % Rotamer: Outliers : 0.04 % Allowed : 2.69 % Favored : 97.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.39 (0.09), residues: 7806 helix: -0.38 (0.08), residues: 4070 sheet: -1.16 (0.17), residues: 823 loop : -1.46 (0.12), residues: 2913 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 78 HIS 0.009 0.001 HIS U 450 PHE 0.037 0.002 PHE D 345 TYR 0.035 0.002 TYR X 397 ARG 0.009 0.001 ARG D 339 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 698 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 695 time to evaluate : 5.527 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 revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 347 ILE cc_start: 0.8317 (mm) cc_final: 0.7947 (tp) REVERT: C 365 GLU cc_start: 0.7651 (tt0) cc_final: 0.7424 (tt0) REVERT: G 80 MET cc_start: 0.1457 (tpp) cc_final: 0.1064 (tpp) REVERT: I 174 MET cc_start: 0.6616 (ptp) cc_final: 0.5728 (ppp) REVERT: W 177 MET cc_start: 0.6317 (ptm) cc_final: 0.5756 (ptm) REVERT: Y 152 MET cc_start: 0.5107 (mpp) cc_final: 0.4822 (mtm) REVERT: Y 389 MET cc_start: 0.7488 (mtt) cc_final: 0.7181 (mtm) REVERT: b 7 MET cc_start: 0.6068 (tmm) cc_final: 0.5845 (tmm) REVERT: b 107 MET cc_start: 0.4307 (mtt) cc_final: 0.3949 (mtp) REVERT: b 164 ASP cc_start: 0.8504 (m-30) cc_final: 0.8295 (m-30) REVERT: u 264 THR cc_start: 0.5465 (t) cc_final: 0.4714 (t) REVERT: D 87 LEU cc_start: 0.7796 (mt) cc_final: 0.7587 (mt) REVERT: D 315 ASP cc_start: 0.7744 (p0) cc_final: 0.7538 (p0) REVERT: E 281 ARG cc_start: 0.7698 (ttt180) cc_final: 0.7365 (ttp80) REVERT: F 236 LEU cc_start: 0.8654 (tp) cc_final: 0.8306 (tp) REVERT: F 422 GLU cc_start: 0.6646 (pt0) cc_final: 0.6337 (pt0) REVERT: B 119 ASN cc_start: 0.8554 (p0) cc_final: 0.8298 (p0) REVERT: K 156 MET cc_start: 0.6022 (mpp) cc_final: 0.5781 (mpp) REVERT: V 37 MET cc_start: 0.7110 (ttt) cc_final: 0.6305 (tpt) REVERT: V 38 LYS cc_start: 0.9177 (mtmt) cc_final: 0.8785 (mmtt) REVERT: V 64 GLN cc_start: 0.8643 (tt0) cc_final: 0.8251 (pm20) REVERT: U 137 MET cc_start: 0.7989 (mmm) cc_final: 0.7404 (mmm) REVERT: U 176 MET cc_start: 0.5518 (tmm) cc_final: 0.3802 (tpp) REVERT: U 333 MET cc_start: 0.8533 (mtm) cc_final: 0.8171 (mtp) REVERT: U 423 MET cc_start: 0.8568 (mmm) cc_final: 0.7848 (mmm) REVERT: U 560 MET cc_start: 0.7223 (tpt) cc_final: 0.6826 (tpp) REVERT: U 588 MET cc_start: 0.6176 (mmp) cc_final: 0.5745 (mmp) REVERT: U 797 MET cc_start: 0.7864 (mpp) cc_final: 0.7176 (mpp) outliers start: 3 outliers final: 0 residues processed: 698 average time/residue: 0.5840 time to fit residues: 693.6875 Evaluate side-chains 525 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 525 time to evaluate : 5.409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 722 optimal weight: 20.0000 chunk 84 optimal weight: 50.0000 chunk 427 optimal weight: 6.9990 chunk 547 optimal weight: 20.0000 chunk 424 optimal weight: 40.0000 chunk 631 optimal weight: 0.7980 chunk 418 optimal weight: 9.9990 chunk 746 optimal weight: 9.9990 chunk 467 optimal weight: 10.0000 chunk 455 optimal weight: 9.9990 chunk 344 optimal weight: 20.0000 overall best weight: 7.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 75 ASN H 21 GLN H 95 GLN J 146 GLN W 155 GLN W 356 ASN ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 249 GLN ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 94 HIS D 83 GLN ** D 127 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 237 GLN B 207 HIS ** B 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 157 HIS Z 278 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** U 89 ASN ** U 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6473 moved from start: 0.5044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 63386 Z= 0.332 Angle : 0.810 15.519 85678 Z= 0.418 Chirality : 0.047 0.227 9788 Planarity : 0.006 0.099 11038 Dihedral : 8.191 113.566 8684 Min Nonbonded Distance : 1.774 Molprobity Statistics. All-atom Clashscore : 21.53 Ramachandran Plot: Outliers : 0.47 % Allowed : 8.40 % Favored : 91.12 % Rotamer: Outliers : 0.04 % Allowed : 2.46 % Favored : 97.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.50 (0.09), residues: 7806 helix: -0.46 (0.08), residues: 4069 sheet: -1.22 (0.17), residues: 848 loop : -1.51 (0.12), residues: 2889 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP W 263 HIS 0.011 0.002 HIS U 450 PHE 0.030 0.002 PHE K 22 TYR 0.059 0.002 TYR G 27 ARG 0.021 0.001 ARG F 371 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 648 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 645 time to evaluate : 5.459 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: A 229 VAL cc_start: 0.7533 (t) cc_final: 0.7199 (t) REVERT: A 362 MET cc_start: 0.3305 (mpp) cc_final: 0.2642 (mpp) REVERT: I 72 MET cc_start: 0.5629 (mpp) cc_final: 0.5098 (mpp) REVERT: I 174 MET cc_start: 0.6637 (ptp) cc_final: 0.5747 (ppp) REVERT: W 177 MET cc_start: 0.6874 (ptm) cc_final: 0.6324 (ptm) REVERT: W 326 MET cc_start: 0.6274 (mmp) cc_final: 0.5619 (tpt) REVERT: Y 152 MET cc_start: 0.5227 (mpp) cc_final: 0.4988 (mtm) REVERT: Y 200 LEU cc_start: 0.8798 (mt) cc_final: 0.8562 (mm) REVERT: Y 389 MET cc_start: 0.7515 (mtt) cc_final: 0.7218 (mtm) REVERT: b 164 ASP cc_start: 0.8510 (m-30) cc_final: 0.8285 (m-30) REVERT: u 264 THR cc_start: 0.5400 (t) cc_final: 0.4643 (t) REVERT: D 87 LEU cc_start: 0.7800 (mt) cc_final: 0.7557 (mt) REVERT: D 315 ASP cc_start: 0.7740 (p0) cc_final: 0.7492 (p0) REVERT: E 234 GLU cc_start: 0.8339 (mt-10) cc_final: 0.7914 (mt-10) REVERT: E 281 ARG cc_start: 0.7895 (ttt180) cc_final: 0.7531 (ttp80) REVERT: E 372 ARG cc_start: 0.8837 (ttt-90) cc_final: 0.8587 (tmm160) REVERT: F 422 GLU cc_start: 0.6742 (pt0) cc_final: 0.6316 (pt0) REVERT: B 119 ASN cc_start: 0.8597 (p0) cc_final: 0.8385 (p0) REVERT: B 385 MET cc_start: 0.6345 (mmt) cc_final: 0.5360 (mmt) REVERT: K 107 MET cc_start: 0.5298 (pmm) cc_final: 0.4996 (pmm) REVERT: c 41 MET cc_start: 0.8755 (mmt) cc_final: 0.8538 (mmp) REVERT: Z 73 ASP cc_start: 0.7110 (m-30) cc_final: 0.6856 (m-30) REVERT: V 37 MET cc_start: 0.6869 (ttt) cc_final: 0.6531 (tpp) REVERT: V 64 GLN cc_start: 0.8666 (tt0) cc_final: 0.8279 (pm20) REVERT: U 137 MET cc_start: 0.8049 (mmm) cc_final: 0.7499 (mmm) REVERT: U 176 MET cc_start: 0.5585 (tmm) cc_final: 0.3921 (tpp) REVERT: U 333 MET cc_start: 0.8550 (mtm) cc_final: 0.8201 (mtp) REVERT: U 423 MET cc_start: 0.8630 (mmm) cc_final: 0.7847 (mmm) REVERT: U 560 MET cc_start: 0.7271 (tpt) cc_final: 0.6889 (tpp) REVERT: U 588 MET cc_start: 0.6193 (mmp) cc_final: 0.5799 (mmp) REVERT: U 797 MET cc_start: 0.7864 (mpp) cc_final: 0.7305 (mpp) outliers start: 3 outliers final: 0 residues processed: 647 average time/residue: 0.5849 time to fit residues: 645.9667 Evaluate side-chains 494 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 494 time to evaluate : 5.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 462 optimal weight: 3.9990 chunk 298 optimal weight: 0.0670 chunk 446 optimal weight: 3.9990 chunk 225 optimal weight: 1.9990 chunk 146 optimal weight: 5.9990 chunk 144 optimal weight: 50.0000 chunk 474 optimal weight: 6.9990 chunk 508 optimal weight: 0.5980 chunk 369 optimal weight: 30.0000 chunk 69 optimal weight: 7.9990 chunk 587 optimal weight: 1.9990 overall best weight: 1.7324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 117 GLN C 124 HIS ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN J 146 GLN W 423 ASN ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN D 127 ASN E 86 GLN E 316 HIS ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN K 118 ASN K 152 GLN c 130 GLN c 237 HIS Z 52 ASN ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 278 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 452 ASN e 47 ASN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6323 moved from start: 0.5282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 63386 Z= 0.210 Angle : 0.751 13.340 85678 Z= 0.385 Chirality : 0.046 0.223 9788 Planarity : 0.005 0.094 11038 Dihedral : 7.855 112.396 8684 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 16.51 Ramachandran Plot: Outliers : 0.47 % Allowed : 6.96 % Favored : 92.57 % Rotamer: Outliers : 0.04 % Allowed : 1.08 % Favored : 98.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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 (0.10), residues: 7806 helix: -0.28 (0.08), residues: 4081 sheet: -1.13 (0.17), residues: 841 loop : -1.36 (0.12), residues: 2884 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP c 111 HIS 0.010 0.001 HIS a 69 PHE 0.038 0.002 PHE D 345 TYR 0.033 0.002 TYR G 27 ARG 0.019 0.001 ARG C 374 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 711 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 708 time to evaluate : 5.497 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: A 229 VAL cc_start: 0.7425 (t) cc_final: 0.7102 (t) REVERT: A 362 MET cc_start: 0.2872 (mpp) cc_final: 0.2465 (mpp) REVERT: C 347 ILE cc_start: 0.8183 (mm) cc_final: 0.7766 (tp) REVERT: C 365 GLU cc_start: 0.7807 (tt0) cc_final: 0.7209 (tt0) REVERT: I 72 MET cc_start: 0.5573 (mpp) cc_final: 0.4903 (mpp) REVERT: I 174 MET cc_start: 0.6537 (ptp) cc_final: 0.5580 (ppp) REVERT: W 177 MET cc_start: 0.6413 (ptm) cc_final: 0.5565 (tpp) REVERT: W 326 MET cc_start: 0.6031 (mmp) cc_final: 0.5513 (tpt) REVERT: Y 152 MET cc_start: 0.4933 (mpp) cc_final: 0.4566 (mtm) REVERT: Y 200 LEU cc_start: 0.8766 (mt) cc_final: 0.8512 (mm) REVERT: Y 389 MET cc_start: 0.7632 (mtt) cc_final: 0.7340 (mtm) REVERT: b 7 MET cc_start: 0.6124 (tmm) cc_final: 0.5882 (tmm) REVERT: b 164 ASP cc_start: 0.8482 (m-30) cc_final: 0.8241 (m-30) REVERT: u 212 SER cc_start: 0.6886 (t) cc_final: 0.6672 (p) REVERT: u 264 THR cc_start: 0.5496 (t) cc_final: 0.4655 (t) REVERT: D 315 ASP cc_start: 0.7582 (p0) cc_final: 0.7300 (p0) REVERT: E 113 ARG cc_start: 0.6946 (ttp80) cc_final: 0.6326 (ttp80) REVERT: E 224 ASP cc_start: 0.7903 (m-30) cc_final: 0.7138 (m-30) REVERT: E 231 PHE cc_start: 0.8527 (t80) cc_final: 0.7966 (t80) REVERT: E 281 ARG cc_start: 0.7615 (ttt180) cc_final: 0.7318 (ttp80) REVERT: E 372 ARG cc_start: 0.8775 (ttt-90) cc_final: 0.8456 (tmm160) REVERT: F 422 GLU cc_start: 0.6416 (pt0) cc_final: 0.6148 (pt0) REVERT: B 119 ASN cc_start: 0.8468 (p0) cc_final: 0.8198 (p0) REVERT: K 107 MET cc_start: 0.4924 (pmm) cc_final: 0.4111 (ptp) REVERT: V 64 GLN cc_start: 0.8620 (tt0) cc_final: 0.8221 (pm20) REVERT: V 309 MET cc_start: 0.4951 (mmt) cc_final: 0.4083 (mtp) REVERT: U 137 MET cc_start: 0.8024 (mmm) cc_final: 0.7507 (mmm) REVERT: U 176 MET cc_start: 0.5434 (tmm) cc_final: 0.3748 (tpp) REVERT: U 333 MET cc_start: 0.8478 (mtm) cc_final: 0.8124 (mtp) REVERT: U 423 MET cc_start: 0.8509 (mmm) cc_final: 0.7768 (mmm) REVERT: U 550 VAL cc_start: 0.9159 (t) cc_final: 0.8849 (t) REVERT: U 560 MET cc_start: 0.7099 (tpt) cc_final: 0.6786 (tpp) REVERT: U 797 MET cc_start: 0.7768 (mpp) cc_final: 0.7034 (mpp) outliers start: 3 outliers final: 0 residues processed: 711 average time/residue: 0.5850 time to fit residues: 716.3166 Evaluate side-chains 540 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 540 time to evaluate : 5.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 679 optimal weight: 7.9990 chunk 715 optimal weight: 20.0000 chunk 652 optimal weight: 2.9990 chunk 696 optimal weight: 30.0000 chunk 418 optimal weight: 8.9990 chunk 303 optimal weight: 5.9990 chunk 546 optimal weight: 8.9990 chunk 213 optimal weight: 9.9990 chunk 629 optimal weight: 6.9990 chunk 658 optimal weight: 0.3980 chunk 693 optimal weight: 7.9990 overall best weight: 4.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 207 ASN J 146 GLN ** W 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** X 375 HIS ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 249 GLN ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN E 86 GLN E 263 GLN E 316 HIS ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 207 HIS B 257 GLN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 278 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6393 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 63386 Z= 0.254 Angle : 0.761 13.623 85678 Z= 0.391 Chirality : 0.046 0.410 9788 Planarity : 0.005 0.081 11038 Dihedral : 7.844 111.747 8684 Min Nonbonded Distance : 1.826 Molprobity Statistics. All-atom Clashscore : 18.72 Ramachandran Plot: Outliers : 0.44 % Allowed : 7.71 % Favored : 91.85 % Rotamer: Outliers : 0.04 % Allowed : 0.71 % Favored : 99.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.05 % 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: -1.21 (0.10), residues: 7806 helix: -0.22 (0.08), residues: 4065 sheet: -1.17 (0.17), residues: 844 loop : -1.37 (0.12), residues: 2897 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP W 263 HIS 0.011 0.001 HIS a 69 PHE 0.028 0.002 PHE K 22 TYR 0.048 0.002 TYR Y 222 ARG 0.011 0.001 ARG A 375 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 648 time to evaluate : 5.651 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: A 229 VAL cc_start: 0.7389 (t) cc_final: 0.7051 (t) REVERT: A 362 MET cc_start: 0.2891 (mpp) cc_final: 0.2467 (mpp) REVERT: C 347 ILE cc_start: 0.8267 (mm) cc_final: 0.7767 (tp) REVERT: C 365 GLU cc_start: 0.7876 (tt0) cc_final: 0.7352 (tt0) REVERT: C 368 MET cc_start: 0.7475 (mmp) cc_final: 0.7096 (mmp) REVERT: C 385 MET cc_start: 0.8389 (ptp) cc_final: 0.8129 (ptp) REVERT: I 72 MET cc_start: 0.5580 (mpp) cc_final: 0.4871 (mpp) REVERT: I 174 MET cc_start: 0.6576 (ptp) cc_final: 0.5809 (ppp) REVERT: W 177 MET cc_start: 0.6278 (ptm) cc_final: 0.6008 (ptm) REVERT: W 326 MET cc_start: 0.6087 (mmp) cc_final: 0.5523 (tpt) REVERT: Y 152 MET cc_start: 0.5175 (mpp) cc_final: 0.4879 (mtm) REVERT: Y 200 LEU cc_start: 0.8806 (mt) cc_final: 0.8553 (mm) REVERT: Y 389 MET cc_start: 0.7639 (mtt) cc_final: 0.7343 (mtm) REVERT: b 7 MET cc_start: 0.6064 (tmm) cc_final: 0.5860 (tmm) REVERT: u 251 ASN cc_start: 0.6200 (p0) cc_final: 0.5977 (p0) REVERT: u 264 THR cc_start: 0.5453 (t) cc_final: 0.4838 (t) REVERT: D 246 MET cc_start: 0.7669 (ptp) cc_final: 0.6931 (ptp) REVERT: D 315 ASP cc_start: 0.7644 (p0) cc_final: 0.7349 (p0) REVERT: E 281 ARG cc_start: 0.7774 (ttt180) cc_final: 0.7416 (ttp80) REVERT: E 372 ARG cc_start: 0.8808 (ttt-90) cc_final: 0.8533 (tmm160) REVERT: F 422 GLU cc_start: 0.6535 (pt0) cc_final: 0.6228 (pt0) REVERT: B 119 ASN cc_start: 0.8527 (p0) cc_final: 0.8304 (p0) REVERT: K 107 MET cc_start: 0.5157 (pmm) cc_final: 0.4315 (ptp) REVERT: c 71 ASP cc_start: 0.5223 (m-30) cc_final: 0.4980 (m-30) REVERT: c 98 MET cc_start: 0.7339 (ppp) cc_final: 0.7053 (ppp) REVERT: V 64 GLN cc_start: 0.8637 (tt0) cc_final: 0.8243 (pm20) REVERT: V 309 MET cc_start: 0.5323 (mmt) cc_final: 0.4705 (mmm) REVERT: V 409 MET cc_start: 0.5323 (ptt) cc_final: 0.4482 (ppp) REVERT: U 137 MET cc_start: 0.8052 (mmm) cc_final: 0.7542 (mmm) REVERT: U 176 MET cc_start: 0.5488 (tmm) cc_final: 0.3853 (tpp) REVERT: U 333 MET cc_start: 0.8477 (mtm) cc_final: 0.8156 (mtp) REVERT: U 423 MET cc_start: 0.8572 (mmm) cc_final: 0.7784 (mmm) REVERT: U 560 MET cc_start: 0.7140 (tpt) cc_final: 0.6816 (tpp) REVERT: U 797 MET cc_start: 0.7821 (mpp) cc_final: 0.7294 (mpp) outliers start: 3 outliers final: 0 residues processed: 651 average time/residue: 0.5879 time to fit residues: 659.1422 Evaluate side-chains 507 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 507 time to evaluate : 6.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 457 optimal weight: 0.3980 chunk 736 optimal weight: 20.0000 chunk 449 optimal weight: 8.9990 chunk 349 optimal weight: 20.0000 chunk 511 optimal weight: 0.8980 chunk 772 optimal weight: 20.0000 chunk 710 optimal weight: 6.9990 chunk 614 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 474 optimal weight: 9.9990 chunk 376 optimal weight: 5.9990 overall best weight: 4.6586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 212 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 101 GLN ** u 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 207 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 257 GLN ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 114 GLN K 118 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 221 HIS c 237 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 278 ASN ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6391 moved from start: 0.5533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 63386 Z= 0.247 Angle : 0.760 12.616 85678 Z= 0.391 Chirality : 0.046 0.348 9788 Planarity : 0.005 0.112 11038 Dihedral : 7.835 111.214 8684 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 18.42 Ramachandran Plot: Outliers : 0.45 % Allowed : 7.89 % Favored : 91.66 % Rotamer: Outliers : 0.01 % Allowed : 0.49 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % 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: -1.20 (0.10), residues: 7806 helix: -0.20 (0.08), residues: 4074 sheet: -1.15 (0.17), residues: 855 loop : -1.38 (0.12), residues: 2877 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP W 263 HIS 0.015 0.001 HIS E 316 PHE 0.030 0.002 PHE D 345 TYR 0.052 0.002 TYR C 121 ARG 0.013 0.001 ARG E 113 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 15612 Ramachandran restraints generated. 7806 Oldfield, 0 Emsley, 7806 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 654 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 653 time to evaluate : 5.530 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: A 229 VAL cc_start: 0.7425 (t) cc_final: 0.7116 (t) REVERT: A 362 MET cc_start: 0.2199 (mpp) cc_final: 0.1953 (mpp) REVERT: C 365 GLU cc_start: 0.7806 (tt0) cc_final: 0.7245 (tt0) REVERT: C 368 MET cc_start: 0.7525 (mmp) cc_final: 0.7142 (mmp) REVERT: I 72 MET cc_start: 0.5599 (mpp) cc_final: 0.4893 (mpp) REVERT: I 174 MET cc_start: 0.6473 (ptp) cc_final: 0.5586 (ppp) REVERT: O 82 MET cc_start: 0.6967 (mmm) cc_final: 0.6721 (mmm) REVERT: W 73 MET cc_start: 0.6843 (ptp) cc_final: 0.5470 (tpt) REVERT: W 177 MET cc_start: 0.6386 (ptm) cc_final: 0.5986 (ptm) REVERT: W 326 MET cc_start: 0.6085 (mmp) cc_final: 0.5527 (tpt) REVERT: X 260 MET cc_start: 0.7248 (mmt) cc_final: 0.6743 (mmt) REVERT: Y 152 MET cc_start: 0.5090 (mpp) cc_final: 0.4772 (mtm) REVERT: Y 200 LEU cc_start: 0.8810 (mt) cc_final: 0.8567 (mm) REVERT: Y 389 MET cc_start: 0.7659 (mtt) cc_final: 0.7339 (mtm) REVERT: u 180 MET cc_start: 0.5724 (tmm) cc_final: 0.5158 (tmm) REVERT: u 251 ASN cc_start: 0.6291 (p0) cc_final: 0.6081 (p0) REVERT: u 262 TYR cc_start: 0.7983 (t80) cc_final: 0.7620 (t80) REVERT: u 264 THR cc_start: 0.5357 (t) cc_final: 0.5035 (t) REVERT: D 87 LEU cc_start: 0.7591 (mt) cc_final: 0.7328 (mt) REVERT: D 267 ILE cc_start: 0.8903 (pt) cc_final: 0.8474 (pt) REVERT: D 315 ASP cc_start: 0.7636 (p0) cc_final: 0.7358 (p0) REVERT: E 102 MET cc_start: 0.7114 (ttp) cc_final: 0.6815 (ttp) REVERT: E 113 ARG cc_start: 0.7548 (ttp80) cc_final: 0.7194 (ttp-170) REVERT: E 281 ARG cc_start: 0.7737 (ttt180) cc_final: 0.7366 (ttp80) REVERT: E 372 ARG cc_start: 0.8829 (ttt-90) cc_final: 0.8523 (tmm160) REVERT: F 422 GLU cc_start: 0.6528 (pt0) cc_final: 0.6165 (pt0) REVERT: B 119 ASN cc_start: 0.8560 (p0) cc_final: 0.8313 (p0) REVERT: B 405 MET cc_start: 0.6895 (ptt) cc_final: 0.6554 (ptt) REVERT: K 107 MET cc_start: 0.5207 (pmm) cc_final: 0.4391 (ptp) REVERT: c 98 MET cc_start: 0.7286 (ppp) cc_final: 0.6632 (ppp) REVERT: V 64 GLN cc_start: 0.8655 (tt0) cc_final: 0.8242 (pm20) REVERT: V 409 MET cc_start: 0.5151 (ptt) cc_final: 0.4464 (ppp) REVERT: U 137 MET cc_start: 0.8062 (mmm) cc_final: 0.7548 (mmm) REVERT: U 176 MET cc_start: 0.5448 (tmm) cc_final: 0.4084 (tpt) REVERT: U 333 MET cc_start: 0.8510 (mtm) cc_final: 0.8190 (mtp) REVERT: U 423 MET cc_start: 0.8578 (mmm) cc_final: 0.7819 (mmm) REVERT: U 556 MET cc_start: 0.8581 (mmp) cc_final: 0.7410 (mmp) REVERT: U 560 MET cc_start: 0.7131 (tpt) cc_final: 0.6842 (tpp) REVERT: U 797 MET cc_start: 0.7941 (mpp) cc_final: 0.7400 (mpp) outliers start: 1 outliers final: 0 residues processed: 654 average time/residue: 0.5945 time to fit residues: 669.5161 Evaluate side-chains 515 residues out of total 6859 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 515 time to evaluate : 5.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 775 random chunks: chunk 488 optimal weight: 5.9990 chunk 654 optimal weight: 6.9990 chunk 188 optimal weight: 5.9990 chunk 566 optimal weight: 10.0000 chunk 90 optimal weight: 30.0000 chunk 170 optimal weight: 30.0000 chunk 615 optimal weight: 6.9990 chunk 257 optimal weight: 0.9980 chunk 632 optimal weight: 5.9990 chunk 77 optimal weight: 6.9990 chunk 113 optimal weight: 6.9990 overall best weight: 5.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 94 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 247 GLN C 124 HIS ** C 296 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 423 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 257 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** u 271 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 GLN ** D 135 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 366 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 118 ASN ** c 130 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 237 HIS ** Z 96 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 104 ASN Z 109 ASN Z 278 ASN V 33 GLN ** V 62 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 242 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 47 ASN ** U 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 500 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 685 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 697 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.070239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.056488 restraints weight = 521716.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.056726 restraints weight = 310385.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.057011 restraints weight = 224517.926| |-----------------------------------------------------------------------------| r_work (final): 0.3543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3543 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3543 r_free = 0.3543 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 6 | |-----------------------------------------------------------------------------| r_final: 0.3543 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7735 moved from start: 0.5626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 63386 Z= 0.263 Angle : 0.765 11.775 85678 Z= 0.393 Chirality : 0.046 0.383 9788 Planarity : 0.005 0.104 11038 Dihedral : 7.861 110.163 8684 Min Nonbonded Distance : 1.787 Molprobity Statistics. All-atom Clashscore : 19.24 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.05 % Favored : 91.54 % Rotamer: Outliers : 0.01 % Allowed : 0.42 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.04 % Cis-general : 0.00 % 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: -1.20 (0.10), residues: 7806 helix: -0.20 (0.08), residues: 4084 sheet: -1.14 (0.17), residues: 849 loop : -1.39 (0.12), residues: 2873 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP W 263 HIS 0.011 0.001 HIS a 69 PHE 0.026 0.002 PHE K 22 TYR 0.024 0.002 TYR M 58 ARG 0.013 0.001 ARG E 113 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12702.82 seconds wall clock time: 225 minutes 34.54 seconds (13534.54 seconds total)