Starting phenix.real_space_refine on Tue Aug 26 03:02:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8iog_35618/08_2025/8iog_35618.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iog_35618/08_2025/8iog_35618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.88 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8iog_35618/08_2025/8iog_35618.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iog_35618/08_2025/8iog_35618.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8iog_35618/08_2025/8iog_35618.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iog_35618/08_2025/8iog_35618.map" } resolution = 2.88 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs 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= 0.004 sd= 0.113 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Fe 10 7.16 5 P 7 5.49 5 S 171 5.16 5 C 21407 2.51 5 N 5696 2.21 5 O 6122 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 62 residue(s): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 33413 Number of models: 1 Model: "" Number of chains: 29 Chain: "A" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3017 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 21, 'TRANS': 355} Chain: "B" Number of atoms: 1920 Number of conformers: 1 Conformer: "" Number of residues, atoms: 241, 1920 Classifications: {'peptide': 241} Link IDs: {'PTRANS': 21, 'TRANS': 219} Chain: "C" Number of atoms: 1502 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1502 Classifications: {'peptide': 194} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 183} Chain: "D" Number of atoms: 3452 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3452 Classifications: {'peptide': 445} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 426} Chain: "E" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3134 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 406} 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: "F" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "G" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 921 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "H" Number of atoms: 608 Number of conformers: 1 Conformer: "" Number of residues, atoms: 71, 608 Classifications: {'peptide': 71} Link IDs: {'PTRANS': 5, 'TRANS': 65} Chain: "I" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 507 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "J" Number of atoms: 405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 49, 405 Classifications: {'peptide': 49} Link IDs: {'PTRANS': 3, 'TRANS': 45} Chain: "K" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 404 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "a" Number of atoms: 3017 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3017 Classifications: {'peptide': 378} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 22, 'TRANS': 355} Chain: "b" Number of atoms: 1904 Number of conformers: 1 Conformer: "" Number of residues, atoms: 239, 1904 Classifications: {'peptide': 239} Link IDs: {'PTRANS': 20, 'TRANS': 218} Chain: "c" Number of atoms: 1517 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1517 Classifications: {'peptide': 196} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 185} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 3459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 446, 3459 Classifications: {'peptide': 446} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 16, 'TRANS': 427} Chain: "e" Number of atoms: 3134 Number of conformers: 1 Conformer: "" Number of residues, atoms: 418, 3134 Classifications: {'peptide': 418} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 406} 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: "f" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 62} Chain: "g" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 921 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "h" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 666 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Chain: "i" Number of atoms: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 507 Classifications: {'peptide': 62} Link IDs: {'PTRANS': 1, 'TRANS': 60} Chain: "j" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 421 Classifications: {'peptide': 51} Link IDs: {'PTRANS': 3, 'TRANS': 47} Chain: "k" Number of atoms: 404 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 404 Classifications: {'peptide': 57} Link IDs: {'PTRANS': 5, 'TRANS': 51} Chain: "A" Number of atoms: 131 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 131 Unusual residues: {'HEM': 2, 'PEE': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 6 Chain: "B" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 113 Unusual residues: {'CDL': 1, 'PEE': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "a" Number of atoms: 199 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 199 Unusual residues: {'CDL': 1, 'HEM': 2, 'PEE': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 38 Unresolved non-hydrogen angles: 38 Unresolved non-hydrogen dihedrals: 38 Chain: "b" Number of atoms: 43 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 43 Unusual residues: {'HEC': 1} Classifications: {'undetermined': 1} Chain: "c" Number of atoms: 4 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 4 Unusual residues: {'FES': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 6013 SG CYS C 217 101.837 87.749 39.576 1.00124.50 S ATOM 6048 SG CYS C 222 99.172 90.665 38.820 1.00123.35 S ATOM 6048 SG CYS C 222 99.172 90.665 38.820 1.00123.35 S ATOM 22445 SG CYS c 222 46.447 57.418 33.732 1.00123.37 S Time building chain proxies: 6.92, per 1000 atoms: 0.21 Number of scatterers: 33413 At special positions: 0 Unit cell: (133.3, 141.9, 175.44, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 10 26.01 S 171 16.00 P 7 15.00 O 6122 8.00 N 5696 7.00 C 21407 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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=5, symmetry=0 Number of additional bonds: simple=5, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.06 Conformation dependent library (CDL) restraints added in 1.2 seconds Enol-peptide restraints added in 953.7 nanoseconds Dynamic metal coordination Iron sulfur cluster coordination pdb=" FES C 301 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 222 " pdb="FE1 FES C 301 " - pdb=" SG CYS C 217 " pdb="FE2 FES C 301 " - pdb=" SG CYS C 238 " pdb="FE2 FES C 301 " - pdb=" ND1 HIS C 239 " pdb=" FES c 301 " pdb="FE2 FES c 301 " - pdb=" SG CYS c 222 " pdb="FE1 FES c 301 " - pdb=" ND1 HIS c 219 " pdb="FE2 FES c 301 " - pdb=" SG CYS c 238 " pdb="FE1 FES c 301 " - pdb=" SG CYS c 217 " Number of angles added : 9 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 7820 Finding SS restraints... Secondary structure from input PDB file: 189 helices and 18 sheets defined 49.0% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.86 Creating SS restraints... Processing helix chain 'A' and resid 3 through 8 Processing helix chain 'A' and resid 10 through 18 removed outlier: 3.995A pdb=" N ILE A 14 " --> pdb=" O LEU A 10 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ASN A 16 " --> pdb=" O LYS A 12 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N ALA A 17 " --> pdb=" O ILE A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 29 through 31 No H-bonds generated for 'chain 'A' and resid 29 through 31' Processing helix chain 'A' and resid 32 through 54 removed outlier: 3.518A pdb=" N ILE A 42 " --> pdb=" O GLY A 38 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N LEU A 43 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN A 44 " --> pdb=" O CYS A 40 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ILE A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N LEU A 46 " --> pdb=" O ILE A 42 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE A 50 " --> pdb=" O LEU A 46 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N LEU A 51 " --> pdb=" O THR A 47 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N ALA A 52 " --> pdb=" O GLY A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 72 removed outlier: 3.645A pdb=" N THR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ARG A 71 " --> pdb=" O THR A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 75 through 90 removed outlier: 3.923A pdb=" N ILE A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N TYR A 81 " --> pdb=" O TRP A 77 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N HIS A 83 " --> pdb=" O ILE A 79 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA A 84 " --> pdb=" O ARG A 80 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ALA A 87 " --> pdb=" O HIS A 83 " (cutoff:3.500A) removed outlier: 3.999A pdb=" N SER A 88 " --> pdb=" O ALA A 84 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N PHE A 90 " --> pdb=" O GLY A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 94 through 104 removed outlier: 3.567A pdb=" N GLY A 99 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N GLY A 101 " --> pdb=" O HIS A 97 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N LEU A 102 " --> pdb=" O VAL A 98 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N TYR A 103 " --> pdb=" O GLY A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 105 through 108 removed outlier: 3.892A pdb=" N MET A 108 " --> pdb=" O GLY A 105 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 105 through 108' Processing helix chain 'A' and resid 109 through 133 removed outlier: 3.697A pdb=" N ASN A 114 " --> pdb=" O LEU A 110 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ILE A 115 " --> pdb=" O GLU A 111 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N VAL A 117 " --> pdb=" O TRP A 113 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N VAL A 118 " --> pdb=" O ASN A 114 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LEU A 119 " --> pdb=" O ILE A 115 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N PHE A 121 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL A 123 " --> pdb=" O LEU A 119 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N MET A 124 " --> pdb=" O LEU A 120 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N THR A 126 " --> pdb=" O THR A 122 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ALA A 127 " --> pdb=" O VAL A 123 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N VAL A 132 " --> pdb=" O PHE A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 138 through 150 removed outlier: 4.840A pdb=" N VAL A 145 " --> pdb=" O TRP A 141 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 149 " --> pdb=" O VAL A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 166 removed outlier: 3.606A pdb=" N LEU A 160 " --> pdb=" O ILE A 156 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N VAL A 161 " --> pdb=" O GLY A 157 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N GLU A 162 " --> pdb=" O THR A 158 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N TRP A 163 " --> pdb=" O ASP A 159 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TRP A 165 " --> pdb=" O VAL A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 172 through 185 removed outlier: 4.150A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 190 removed outlier: 3.642A pdb=" N ILE A 189 " --> pdb=" O LEU A 185 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 245 removed outlier: 3.819A pdb=" N LEU A 230 " --> pdb=" O ILE A 226 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL A 243 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LEU A 244 " --> pdb=" O LEU A 240 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N PHE A 245 " --> pdb=" O ILE A 241 " (cutoff:3.500A) Processing helix chain 'A' and resid 246 through 250 removed outlier: 3.653A pdb=" N LEU A 249 " --> pdb=" O SER A 246 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N LEU A 250 " --> pdb=" O PRO A 247 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 246 through 250' Processing helix chain 'A' and resid 271 through 275 removed outlier: 3.584A pdb=" N LEU A 275 " --> pdb=" O TRP A 272 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 removed outlier: 3.711A pdb=" N ILE A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 286 through 301 removed outlier: 3.826A pdb=" N GLY A 290 " --> pdb=" O ASN A 286 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N VAL A 291 " --> pdb=" O LYS A 287 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N LEU A 292 " --> pdb=" O LEU A 288 " (cutoff:3.500A) removed outlier: 4.503A pdb=" N SER A 297 " --> pdb=" O ALA A 293 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N ILE A 298 " --> pdb=" O LEU A 294 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LEU A 301 " --> pdb=" O SER A 297 " (cutoff:3.500A) Processing helix chain 'A' and resid 302 through 308 Proline residue: A 305 - end of helix removed outlier: 3.736A pdb=" N HIS A 308 " --> pdb=" O PRO A 305 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 302 through 308' Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.627A pdb=" N CYS A 323 " --> pdb=" O PRO A 319 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 324 " --> pdb=" O LEU A 320 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N TRP A 326 " --> pdb=" O GLN A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 338 removed outlier: 3.666A pdb=" N TRP A 337 " --> pdb=" O ILE A 333 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ILE A 338 " --> pdb=" O THR A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 338' Processing helix chain 'A' and resid 339 through 341 No H-bonds generated for 'chain 'A' and resid 339 through 341' Processing helix chain 'A' and resid 348 through 377 removed outlier: 4.332A pdb=" N SER A 355 " --> pdb=" O GLY A 351 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE A 356 " --> pdb=" O GLN A 352 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N LEU A 357 " --> pdb=" O LEU A 353 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N TYR A 358 " --> pdb=" O ALA A 354 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N PHE A 359 " --> pdb=" O SER A 355 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N ILE A 362 " --> pdb=" O TYR A 358 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU A 363 " --> pdb=" O PHE A 359 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N MET A 366 " --> pdb=" O ILE A 362 " (cutoff:3.500A) Proline residue: A 367 - end of helix removed outlier: 3.831A pdb=" N ILE A 371 " --> pdb=" O PRO A 367 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ILE A 372 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N GLU A 373 " --> pdb=" O THR A 369 " (cutoff:3.500A) Processing helix chain 'B' and resid 114 through 120 Processing helix chain 'B' and resid 134 through 138 removed outlier: 4.125A pdb=" N VAL B 137 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 4.448A pdb=" N GLY B 138 " --> pdb=" O HIS B 135 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 134 through 138' Processing helix chain 'B' and resid 142 through 148 Processing helix chain 'B' and resid 182 through 184 No H-bonds generated for 'chain 'B' and resid 182 through 184' Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 210 through 217 removed outlier: 3.765A pdb=" N THR B 217 " --> pdb=" O PHE B 213 " (cutoff:3.500A) Processing helix chain 'B' and resid 263 through 273 removed outlier: 3.628A pdb=" N LYS B 269 " --> pdb=" O SER B 265 " (cutoff:3.500A) Processing helix chain 'B' and resid 273 through 280 removed outlier: 3.525A pdb=" N TRP B 277 " --> pdb=" O THR B 273 " (cutoff:3.500A) Processing helix chain 'B' and resid 285 through 290 removed outlier: 3.632A pdb=" N MET B 289 " --> pdb=" O HIS B 285 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 301 removed outlier: 3.853A pdb=" N MET B 296 " --> pdb=" O LYS B 292 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLY B 298 " --> pdb=" O LEU B 294 " (cutoff:3.500A) Processing helix chain 'B' and resid 303 through 310 Processing helix chain 'B' and resid 313 through 317 Processing helix chain 'C' and resid 88 through 92 Processing helix chain 'C' and resid 102 through 106 removed outlier: 4.091A pdb=" N GLU C 105 " --> pdb=" O SER C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 107 through 138 removed outlier: 3.609A pdb=" N GLY C 112 " --> pdb=" O ASP C 108 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N PHE C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER C 114 " --> pdb=" O ARG C 110 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N ILE C 117 " --> pdb=" O PHE C 113 " (cutoff:3.500A) removed outlier: 4.762A pdb=" N THR C 118 " --> pdb=" O SER C 114 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR C 122 " --> pdb=" O THR C 118 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N VAL C 123 " --> pdb=" O ALA C 119 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N GLY C 124 " --> pdb=" O THR C 120 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS C 130 " --> pdb=" O ALA C 126 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ASN C 131 " --> pdb=" O TYR C 127 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N ALA C 132 " --> pdb=" O ALA C 128 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N GLN C 135 " --> pdb=" O ASN C 131 " (cutoff:3.500A) removed outlier: 4.774A pdb=" N PHE C 136 " --> pdb=" O ALA C 132 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N SER C 138 " --> pdb=" O SER C 134 " (cutoff:3.500A) Processing helix chain 'C' and resid 143 through 152 removed outlier: 4.188A pdb=" N MET C 149 " --> pdb=" O ASP C 145 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N LYS C 151 " --> pdb=" O LEU C 147 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N ILE C 152 " --> pdb=" O ALA C 148 " (cutoff:3.500A) Processing helix chain 'C' and resid 180 through 190 removed outlier: 3.764A pdb=" N ILE C 184 " --> pdb=" O THR C 180 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N VAL C 190 " --> pdb=" O GLN C 186 " (cutoff:3.500A) Processing helix chain 'C' and resid 200 through 205 Processing helix chain 'D' and resid 37 through 43 removed outlier: 3.869A pdb=" N LEU D 42 " --> pdb=" O TYR D 38 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N GLN D 43 " --> pdb=" O ALA D 39 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 88 removed outlier: 6.089A pdb=" N GLY D 88 " --> pdb=" O LYS D 85 " (cutoff:3.500A) Processing helix chain 'D' and resid 89 through 95 removed outlier: 3.642A pdb=" N VAL D 93 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N GLU D 94 " --> pdb=" O GLY D 90 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N HIS D 95 " --> pdb=" O TYR D 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 89 through 95' Processing helix chain 'D' and resid 109 through 114 Processing helix chain 'D' and resid 139 through 153 removed outlier: 3.527A pdb=" N GLU D 145 " --> pdb=" O PRO D 141 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LEU D 146 " --> pdb=" O LYS D 142 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ILE D 150 " --> pdb=" O LEU D 146 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N GLN D 152 " --> pdb=" O ALA D 148 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASN D 153 " --> pdb=" O ASP D 149 " (cutoff:3.500A) Processing helix chain 'D' and resid 163 through 175 removed outlier: 3.717A pdb=" N VAL D 167 " --> pdb=" O LYS D 163 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N GLN D 173 " --> pdb=" O LEU D 169 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N GLU D 174 " --> pdb=" O GLN D 170 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N ASN D 175 " --> pdb=" O GLU D 171 " (cutoff:3.500A) Processing helix chain 'D' and resid 186 through 191 removed outlier: 3.617A pdb=" N ALA D 191 " --> pdb=" O LEU D 187 " (cutoff:3.500A) Processing helix chain 'D' and resid 195 through 199 removed outlier: 3.685A pdb=" N ALA D 198 " --> pdb=" O THR D 195 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N GLN D 199 " --> pdb=" O PRO D 196 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 195 through 199' Processing helix chain 'D' and resid 207 through 211 removed outlier: 3.964A pdb=" N LEU D 211 " --> pdb=" O VAL D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 215 through 223 removed outlier: 4.026A pdb=" N TYR D 219 " --> pdb=" O ASP D 215 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N VAL D 220 " --> pdb=" O LEU D 216 " (cutoff:3.500A) Processing helix chain 'D' and resid 238 through 250 Processing helix chain 'D' and resid 257 through 261 Processing helix chain 'D' and resid 301 through 312 removed outlier: 4.027A pdb=" N ALA D 307 " --> pdb=" O PRO D 303 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ASN D 308 " --> pdb=" O LEU D 304 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N ILE D 310 " --> pdb=" O VAL D 306 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE D 311 " --> pdb=" O ALA D 307 " (cutoff:3.500A) Processing helix chain 'D' and resid 326 through 332 removed outlier: 3.779A pdb=" N VAL D 331 " --> pdb=" O THR D 327 " (cutoff:3.500A) Processing helix chain 'D' and resid 364 through 366 No H-bonds generated for 'chain 'D' and resid 364 through 366' Processing helix chain 'D' and resid 367 through 381 removed outlier: 3.580A pdb=" N PHE D 371 " --> pdb=" O ASP D 367 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N GLY D 374 " --> pdb=" O PHE D 370 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN D 375 " --> pdb=" O PHE D 371 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TRP D 376 " --> pdb=" O LEU D 372 " (cutoff:3.500A) removed outlier: 3.669A pdb=" N ARG D 378 " --> pdb=" O GLY D 374 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N LEU D 379 " --> pdb=" O GLN D 375 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N CYS D 380 " --> pdb=" O TRP D 376 " (cutoff:3.500A) Processing helix chain 'D' and resid 385 through 401 removed outlier: 3.676A pdb=" N VAL D 389 " --> pdb=" O GLU D 385 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ARG D 390 " --> pdb=" O SER D 386 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N GLY D 391 " --> pdb=" O GLU D 387 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LEU D 395 " --> pdb=" O GLY D 391 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N LEU D 399 " --> pdb=" O LEU D 395 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N VAL D 400 " --> pdb=" O ARG D 396 " (cutoff:3.500A) Processing helix chain 'D' and resid 406 through 417 removed outlier: 3.632A pdb=" N CYS D 410 " --> pdb=" O THR D 406 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N GLY D 414 " --> pdb=" O CYS D 410 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N ARG D 415 " --> pdb=" O GLU D 411 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N LEU D 417 " --> pdb=" O ILE D 413 " (cutoff:3.500A) Processing helix chain 'D' and resid 425 through 434 removed outlier: 3.583A pdb=" N GLU D 430 " --> pdb=" O LEU D 426 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N SER D 431 " --> pdb=" O ALA D 427 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ILE D 433 " --> pdb=" O TRP D 429 " (cutoff:3.500A) Processing helix chain 'D' and resid 437 through 450 removed outlier: 3.702A pdb=" N VAL D 441 " --> pdb=" O ASP D 437 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N ARG D 442 " --> pdb=" O ALA D 438 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N TYR D 448 " --> pdb=" O VAL D 444 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 472 Processing helix chain 'D' and resid 473 through 475 No H-bonds generated for 'chain 'D' and resid 473 through 475' Processing helix chain 'E' and resid 96 through 101 removed outlier: 3.752A pdb=" N THR E 100 " --> pdb=" O SER E 96 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ARG E 101 " --> pdb=" O PHE E 97 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 96 through 101' Processing helix chain 'E' and resid 126 through 130 removed outlier: 4.249A pdb=" N ILE E 130 " --> pdb=" O ARG E 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 132 through 135 removed outlier: 3.603A pdb=" N GLU E 135 " --> pdb=" O ILE E 132 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 132 through 135' Processing helix chain 'E' and resid 136 through 143 removed outlier: 3.549A pdb=" N THR E 141 " --> pdb=" O LEU E 137 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N ALA E 143 " --> pdb=" O ASN E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 147 through 152 Processing helix chain 'E' and resid 153 through 155 No H-bonds generated for 'chain 'E' and resid 153 through 155' Processing helix chain 'E' and resid 156 through 166 Processing helix chain 'E' and resid 168 through 174 removed outlier: 4.262A pdb=" N GLN E 172 " --> pdb=" O ASN E 168 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N VAL E 173 " --> pdb=" O PRO E 169 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU E 174 " --> pdb=" O GLN E 170 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 168 through 174' Processing helix chain 'E' and resid 196 through 200 removed outlier: 3.766A pdb=" N LYS E 199 " --> pdb=" O ARG E 196 " (cutoff:3.500A) removed outlier: 4.502A pdb=" N VAL E 200 " --> pdb=" O ILE E 197 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 196 through 200' Processing helix chain 'E' and resid 201 through 213 removed outlier: 3.735A pdb=" N LEU E 205 " --> pdb=" O THR E 201 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N HIS E 206 " --> pdb=" O PRO E 202 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N TYR E 207 " --> pdb=" O ASP E 203 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLN E 210 " --> pdb=" O HIS E 206 " (cutoff:3.500A) Processing helix chain 'E' and resid 226 through 235 removed outlier: 3.734A pdb=" N LEU E 230 " --> pdb=" O SER E 226 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N LYS E 231 " --> pdb=" O HIS E 227 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N GLN E 232 " --> pdb=" O PRO E 228 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N VAL E 233 " --> pdb=" O VAL E 229 " (cutoff:3.500A) Processing helix chain 'E' and resid 283 through 294 removed outlier: 3.579A pdb=" N LEU E 289 " --> pdb=" O ALA E 285 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N HIS E 291 " --> pdb=" O SER E 287 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N VAL E 292 " --> pdb=" O VAL E 288 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 315 Processing helix chain 'E' and resid 347 through 363 removed outlier: 4.096A pdb=" N ILE E 351 " --> pdb=" O ALA E 347 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN E 357 " --> pdb=" O SER E 353 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N VAL E 358 " --> pdb=" O ALA E 354 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ILE E 361 " --> pdb=" O GLN E 357 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ALA E 362 " --> pdb=" O VAL E 358 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN E 363 " --> pdb=" O LYS E 359 " (cutoff:3.500A) Processing helix chain 'E' and resid 369 through 385 removed outlier: 3.526A pdb=" N LEU E 378 " --> pdb=" O ALA E 374 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER E 385 " --> pdb=" O GLY E 381 " (cutoff:3.500A) Processing helix chain 'E' and resid 390 through 399 removed outlier: 3.890A pdb=" N ASP E 394 " --> pdb=" O GLU E 390 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU E 395 " --> pdb=" O GLY E 391 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLN E 399 " --> pdb=" O GLU E 395 " (cutoff:3.500A) Processing helix chain 'E' and resid 408 through 418 removed outlier: 3.518A pdb=" N VAL E 412 " --> pdb=" O GLN E 408 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N GLN E 414 " --> pdb=" O SER E 410 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N GLN E 415 " --> pdb=" O THR E 411 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N ILE E 416 " --> pdb=" O VAL E 412 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N ASP E 417 " --> pdb=" O LEU E 413 " (cutoff:3.500A) Processing helix chain 'E' and resid 423 through 433 removed outlier: 3.513A pdb=" N LYS E 430 " --> pdb=" O ASN E 426 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE E 431 " --> pdb=" O ALA E 427 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N VAL E 432 " --> pdb=" O ALA E 428 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N SER E 433 " --> pdb=" O LYS E 429 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 38 removed outlier: 4.554A pdb=" N GLU F 35 " --> pdb=" O THR F 31 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLN F 36 " --> pdb=" O THR F 32 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 60 removed outlier: 3.744A pdb=" N GLU F 51 " --> pdb=" O ARG F 47 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N LEU F 52 " --> pdb=" O GLU F 48 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N CYS F 53 " --> pdb=" O ARG F 49 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N ARG F 56 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ARG F 60 " --> pdb=" O ARG F 56 " (cutoff:3.500A) Processing helix chain 'F' and resid 67 through 83 removed outlier: 3.880A pdb=" N PHE F 74 " --> pdb=" O GLU F 70 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N CYS F 81 " --> pdb=" O ALA F 77 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ALA F 83 " --> pdb=" O ASP F 79 " (cutoff:3.500A) Processing helix chain 'G' and resid 10 through 25 removed outlier: 3.561A pdb=" N ASN G 23 " --> pdb=" O LYS G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 31 Processing helix chain 'G' and resid 33 through 37 Processing helix chain 'G' and resid 52 through 63 removed outlier: 3.650A pdb=" N ASP G 58 " --> pdb=" O ASN G 54 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ARG G 59 " --> pdb=" O LEU G 55 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N VAL G 60 " --> pdb=" O TYR G 56 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N PHE G 61 " --> pdb=" O ASN G 57 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ILE G 63 " --> pdb=" O ARG G 59 " (cutoff:3.500A) Processing helix chain 'G' and resid 77 through 81 removed outlier: 3.767A pdb=" N TRP G 81 " --> pdb=" O LYS G 78 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 101 removed outlier: 4.115A pdb=" N GLU G 97 " --> pdb=" O PRO G 93 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL G 98 " --> pdb=" O TYR G 94 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N ILE G 99 " --> pdb=" O LEU G 95 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N GLU G 101 " --> pdb=" O GLU G 97 " (cutoff:3.500A) Processing helix chain 'H' and resid 4 through 8 removed outlier: 4.294A pdb=" N LEU H 8 " --> pdb=" O PHE H 5 " (cutoff:3.500A) Processing helix chain 'H' and resid 33 through 45 Processing helix chain 'H' and resid 50 through 70 removed outlier: 3.834A pdb=" N VAL H 55 " --> pdb=" O PRO H 51 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N PHE H 56 " --> pdb=" O PRO H 52 " (cutoff:3.500A) removed outlier: 3.770A pdb=" N TYR H 57 " --> pdb=" O PHE H 53 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR H 64 " --> pdb=" O TYR H 60 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLN H 65 " --> pdb=" O THR H 61 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N GLU H 66 " --> pdb=" O TRP H 62 " (cutoff:3.500A) Processing helix chain 'I' and resid 7 through 15 removed outlier: 3.912A pdb=" N SER I 12 " --> pdb=" O ALA I 8 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N LEU I 13 " --> pdb=" O ARG I 9 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LEU I 14 " --> pdb=" O LEU I 10 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N PHE I 15 " --> pdb=" O TYR I 11 " (cutoff:3.500A) Processing helix chain 'I' and resid 18 through 48 removed outlier: 4.275A pdb=" N ILE I 25 " --> pdb=" O PHE I 21 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ALA I 26 " --> pdb=" O ALA I 22 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N ALA I 29 " --> pdb=" O ILE I 25 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU I 30 " --> pdb=" O ALA I 26 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N PHE I 32 " --> pdb=" O GLY I 28 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N ARG I 34 " --> pdb=" O LEU I 30 " (cutoff:3.500A) removed outlier: 5.279A pdb=" N ALA I 35 " --> pdb=" O PHE I 31 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA I 40 " --> pdb=" O PHE I 36 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N ASP I 41 " --> pdb=" O ASP I 37 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N ALA I 42 " --> pdb=" O GLN I 38 " (cutoff:3.500A) removed outlier: 5.014A pdb=" N ILE I 43 " --> pdb=" O GLY I 39 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N TYR I 44 " --> pdb=" O ALA I 40 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASN I 48 " --> pdb=" O TYR I 44 " (cutoff:3.500A) Processing helix chain 'I' and resid 53 through 58 removed outlier: 4.143A pdb=" N HIS I 58 " --> pdb=" O LYS I 54 " (cutoff:3.500A) Processing helix chain 'J' and resid 2 through 6 removed outlier: 3.901A pdb=" N PHE J 5 " --> pdb=" O LEU J 2 " (cutoff:3.500A) Processing helix chain 'J' and resid 11 through 16 removed outlier: 3.723A pdb=" N ALA J 14 " --> pdb=" O ARG J 11 " (cutoff:3.500A) Processing helix chain 'J' and resid 17 through 36 removed outlier: 3.981A pdb=" N MET J 23 " --> pdb=" O PRO J 19 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N TRP J 24 " --> pdb=" O THR J 20 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY J 25 " --> pdb=" O ALA J 21 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ALA J 26 " --> pdb=" O SER J 22 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N VAL J 27 " --> pdb=" O MET J 23 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N GLY J 28 " --> pdb=" O TRP J 24 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N VAL J 33 " --> pdb=" O ALA J 29 " (cutoff:3.500A) Processing helix chain 'K' and resid 3 through 8 Processing helix chain 'a' and resid 3 through 7 removed outlier: 3.713A pdb=" N SER a 7 " --> pdb=" O ILE a 4 " (cutoff:3.500A) Processing helix chain 'a' and resid 10 through 18 removed outlier: 3.727A pdb=" N ILE a 14 " --> pdb=" O LEU a 10 " (cutoff:3.500A) Processing helix chain 'a' and resid 28 through 31 Processing helix chain 'a' and resid 32 through 53 removed outlier: 4.044A pdb=" N LEU a 36 " --> pdb=" O ASN a 32 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N GLY a 38 " --> pdb=" O GLY a 34 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N PHE a 50 " --> pdb=" O LEU a 46 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N LEU a 51 " --> pdb=" O THR a 47 " (cutoff:3.500A) removed outlier: 3.852A pdb=" N ALA a 52 " --> pdb=" O GLY a 48 " (cutoff:3.500A) Processing helix chain 'a' and resid 61 through 73 removed outlier: 3.503A pdb=" N SER a 65 " --> pdb=" O THR a 61 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N VAL a 66 " --> pdb=" O ALA a 62 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ARG a 71 " --> pdb=" O THR a 67 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N VAL a 73 " --> pdb=" O ILE a 69 " (cutoff:3.500A) Processing helix chain 'a' and resid 75 through 86 removed outlier: 3.687A pdb=" N TYR a 81 " --> pdb=" O TRP a 77 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 100 removed outlier: 3.832A pdb=" N LEU a 94 " --> pdb=" O PHE a 90 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N PHE a 95 " --> pdb=" O PHE a 91 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N ILE a 96 " --> pdb=" O ILE a 92 " (cutoff:3.500A) Processing helix chain 'a' and resid 101 through 103 No H-bonds generated for 'chain 'a' and resid 101 through 103' Processing helix chain 'a' and resid 109 through 130 removed outlier: 3.808A pdb=" N VAL a 117 " --> pdb=" O TRP a 113 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N VAL a 118 " --> pdb=" O ASN a 114 " (cutoff:3.500A) removed outlier: 4.254A pdb=" N LEU a 119 " --> pdb=" O ILE a 115 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA a 127 " --> pdb=" O VAL a 123 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N PHE a 128 " --> pdb=" O MET a 124 " (cutoff:3.500A) Processing helix chain 'a' and resid 136 through 151 removed outlier: 3.882A pdb=" N VAL a 145 " --> pdb=" O TRP a 141 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N LEU a 149 " --> pdb=" O VAL a 145 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N LEU a 150 " --> pdb=" O ILE a 146 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N SER a 151 " --> pdb=" O THR a 147 " (cutoff:3.500A) Processing helix chain 'a' and resid 156 through 166 removed outlier: 3.606A pdb=" N LEU a 160 " --> pdb=" O ILE a 156 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL a 161 " --> pdb=" O GLY a 157 " (cutoff:3.500A) removed outlier: 4.216A pdb=" N GLU a 162 " --> pdb=" O THR a 158 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N TRP a 163 " --> pdb=" O ASP a 159 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE a 164 " --> pdb=" O LEU a 160 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N TRP a 165 " --> pdb=" O VAL a 161 " (cutoff:3.500A) Processing helix chain 'a' and resid 171 through 197 removed outlier: 3.608A pdb=" N LEU a 175 " --> pdb=" O ASP a 171 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N THR a 176 " --> pdb=" O LYS a 172 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ARG a 177 " --> pdb=" O ALA a 173 " (cutoff:3.500A) removed outlier: 4.380A pdb=" N PHE a 183 " --> pdb=" O PHE a 179 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N ILE a 184 " --> pdb=" O ALA a 180 " (cutoff:3.500A) Proline residue: a 186 - end of helix removed outlier: 3.703A pdb=" N THR a 190 " --> pdb=" O PRO a 186 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ALA a 191 " --> pdb=" O PHE a 187 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU a 192 " --> pdb=" O ILE a 188 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LEU a 197 " --> pdb=" O ALA a 193 " (cutoff:3.500A) Processing helix chain 'a' and resid 222 through 233 removed outlier: 3.710A pdb=" N ILE a 226 " --> pdb=" O PRO a 222 " (cutoff:3.500A) Processing helix chain 'a' and resid 234 through 246 removed outlier: 4.309A pdb=" N ILE a 238 " --> pdb=" O PHE a 234 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N LEU a 240 " --> pdb=" O MET a 236 " (cutoff:3.500A) Processing helix chain 'a' and resid 247 through 251 removed outlier: 3.823A pdb=" N LEU a 250 " --> pdb=" O PRO a 247 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N GLY a 251 " --> pdb=" O ASP a 248 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 247 through 251' Processing helix chain 'a' and resid 271 through 279 removed outlier: 3.703A pdb=" N PHE a 274 " --> pdb=" O GLU a 271 " (cutoff:3.500A) removed outlier: 5.593A pdb=" N PHE a 276 " --> pdb=" O TYR a 273 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N TYR a 278 " --> pdb=" O LEU a 275 " (cutoff:3.500A) Processing helix chain 'a' and resid 280 through 284 removed outlier: 3.510A pdb=" N ILE a 284 " --> pdb=" O LEU a 281 " (cutoff:3.500A) Processing helix chain 'a' and resid 286 through 301 removed outlier: 3.702A pdb=" N LEU a 292 " --> pdb=" O LEU a 288 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL a 295 " --> pdb=" O VAL a 291 " (cutoff:3.500A) removed outlier: 4.331A pdb=" N SER a 297 " --> pdb=" O ALA a 293 " (cutoff:3.500A) removed outlier: 5.308A pdb=" N ILE a 298 " --> pdb=" O LEU a 294 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU a 299 " --> pdb=" O VAL a 295 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N LEU a 301 " --> pdb=" O SER a 297 " (cutoff:3.500A) Processing helix chain 'a' and resid 302 through 304 No H-bonds generated for 'chain 'a' and resid 302 through 304' Processing helix chain 'a' and resid 321 through 340 removed outlier: 3.908A pdb=" N TRP a 326 " --> pdb=" O GLN a 322 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N MET a 327 " --> pdb=" O CYS a 323 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N LEU a 328 " --> pdb=" O LEU a 324 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL a 329 " --> pdb=" O PHE a 325 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N ALA a 330 " --> pdb=" O TRP a 326 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N ASP a 331 " --> pdb=" O MET a 327 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N THR a 336 " --> pdb=" O LEU a 332 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY a 339 " --> pdb=" O LEU a 335 " (cutoff:3.500A) removed outlier: 4.226A pdb=" N GLY a 340 " --> pdb=" O THR a 336 " (cutoff:3.500A) Processing helix chain 'a' and resid 344 through 363 removed outlier: 3.931A pdb=" N ILE a 348 " --> pdb=" O GLU a 344 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N ILE a 349 " --> pdb=" O HIS a 345 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N LEU a 353 " --> pdb=" O ILE a 349 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA a 354 " --> pdb=" O ILE a 350 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N PHE a 359 " --> pdb=" O SER a 355 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N ILE a 362 " --> pdb=" O TYR a 358 " (cutoff:3.500A) Processing helix chain 'a' and resid 364 through 369 Processing helix chain 'b' and resid 109 through 121 removed outlier: 3.599A pdb=" N ARG b 113 " --> pdb=" O THR b 109 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLN b 116 " --> pdb=" O ARG b 112 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N VAL b 117 " --> pdb=" O ARG b 113 " (cutoff:3.500A) Processing helix chain 'b' and resid 142 through 153 removed outlier: 4.627A pdb=" N ALA b 148 " --> pdb=" O GLU b 144 " (cutoff:3.500A) removed outlier: 4.568A pdb=" N LEU b 149 " --> pdb=" O GLU b 145 " (cutoff:3.500A) removed outlier: 3.993A pdb=" N ALA b 150 " --> pdb=" O ALA b 146 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N GLU b 151 " --> pdb=" O LYS b 147 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N GLU b 152 " --> pdb=" O ALA b 148 " (cutoff:3.500A) removed outlier: 4.475A pdb=" N VAL b 153 " --> pdb=" O LEU b 149 " (cutoff:3.500A) Processing helix chain 'b' and resid 182 through 190 Processing helix chain 'b' and resid 208 through 216 removed outlier: 3.545A pdb=" N LEU b 216 " --> pdb=" O VAL b 212 " (cutoff:3.500A) Processing helix chain 'b' and resid 263 through 280 removed outlier: 3.613A pdb=" N TRP b 277 " --> pdb=" O THR b 273 " (cutoff:3.500A) Processing helix chain 'b' and resid 282 through 293 removed outlier: 3.524A pdb=" N LYS b 287 " --> pdb=" O HIS b 283 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N ARG b 288 " --> pdb=" O ASP b 284 " (cutoff:3.500A) removed outlier: 4.287A pdb=" N MET b 289 " --> pdb=" O HIS b 285 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N LEU b 291 " --> pdb=" O LYS b 287 " (cutoff:3.500A) Processing helix chain 'b' and resid 293 through 312 removed outlier: 3.888A pdb=" N LEU b 299 " --> pdb=" O MET b 295 " (cutoff:3.500A) Proline residue: b 302 - end of helix removed outlier: 3.814A pdb=" N TYR b 305 " --> pdb=" O LEU b 301 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N ALA b 306 " --> pdb=" O PRO b 302 " (cutoff:3.500A) Processing helix chain 'c' and resid 107 through 114 removed outlier: 3.873A pdb=" N LYS c 111 " --> pdb=" O SER c 107 " (cutoff:3.500A) Processing helix chain 'c' and resid 115 through 129 removed outlier: 3.911A pdb=" N VAL c 123 " --> pdb=" O ALA c 119 " (cutoff:3.500A) Processing helix chain 'c' and resid 130 through 140 removed outlier: 4.217A pdb=" N PHE c 136 " --> pdb=" O ALA c 132 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N SER c 138 " --> pdb=" O SER c 134 " (cutoff:3.500A) removed outlier: 4.553A pdb=" N MET c 140 " --> pdb=" O PHE c 136 " (cutoff:3.500A) Processing helix chain 'c' and resid 147 through 152 removed outlier: 4.369A pdb=" N LYS c 151 " --> pdb=" O LEU c 147 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ILE c 152 " --> pdb=" O ALA c 148 " (cutoff:3.500A) No H-bonds generated for 'chain 'c' and resid 147 through 152' Processing helix chain 'c' and resid 180 through 189 Processing helix chain 'c' and resid 200 through 205 Processing helix chain 'd' and resid 78 through 82 removed outlier: 3.558A pdb=" N GLU d 82 " --> pdb=" O SER d 79 " (cutoff:3.500A) Processing helix chain 'd' and resid 89 through 94 removed outlier: 3.663A pdb=" N VAL d 93 " --> pdb=" O ALA d 89 " (cutoff:3.500A) removed outlier: 4.132A pdb=" N GLU d 94 " --> pdb=" O GLY d 90 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 89 through 94' Processing helix chain 'd' and resid 105 through 117 removed outlier: 3.580A pdb=" N MET d 116 " --> pdb=" O GLU d 112 " (cutoff:3.500A) Processing helix chain 'd' and resid 139 through 153 removed outlier: 3.564A pdb=" N LEU d 146 " --> pdb=" O LYS d 142 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N ASN d 153 " --> pdb=" O ASP d 149 " (cutoff:3.500A) Processing helix chain 'd' and resid 157 through 176 removed outlier: 4.200A pdb=" N ASP d 166 " --> pdb=" O GLU d 162 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N VAL d 167 " --> pdb=" O LYS d 163 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N GLN d 173 " --> pdb=" O LEU d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 178 through 191 removed outlier: 3.535A pdb=" N VAL d 182 " --> pdb=" O SER d 178 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N VAL d 183 " --> pdb=" O MET d 179 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N PHE d 184 " --> pdb=" O ARG d 180 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASP d 185 " --> pdb=" O ASP d 181 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N HIS d 188 " --> pdb=" O PHE d 184 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 210 removed outlier: 3.794A pdb=" N ARG d 209 " --> pdb=" O GLU d 206 " (cutoff:3.500A) removed outlier: 3.751A pdb=" N LYS d 210 " --> pdb=" O ASN d 207 " (cutoff:3.500A) Processing helix chain 'd' and resid 212 through 224 Processing helix chain 'd' and resid 238 through 251 removed outlier: 3.517A pdb=" N LYS d 248 " --> pdb=" O ASP d 244 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N HIS d 249 " --> pdb=" O LEU d 245 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N SER d 251 " --> pdb=" O GLN d 247 " (cutoff:3.500A) Processing helix chain 'd' and resid 300 through 312 removed outlier: 3.788A pdb=" N LEU d 304 " --> pdb=" O ASP d 300 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE d 310 " --> pdb=" O VAL d 306 " (cutoff:3.500A) removed outlier: 4.083A pdb=" N ILE d 311 " --> pdb=" O ALA d 307 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N GLY d 312 " --> pdb=" O ASN d 308 " (cutoff:3.500A) Processing helix chain 'd' and resid 328 through 336 removed outlier: 3.749A pdb=" N THR d 334 " --> pdb=" O SER d 330 " (cutoff:3.500A) Processing helix chain 'd' and resid 364 through 381 removed outlier: 3.629A pdb=" N MET d 368 " --> pdb=" O SER d 364 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLN d 375 " --> pdb=" O PHE d 371 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N TRP d 376 " --> pdb=" O LEU d 372 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N LEU d 379 " --> pdb=" O GLN d 375 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N THR d 381 " --> pdb=" O MET d 377 " (cutoff:3.500A) Processing helix chain 'd' and resid 388 through 402 removed outlier: 4.308A pdb=" N VAL d 400 " --> pdb=" O ARG d 396 " (cutoff:3.500A) removed outlier: 4.028A pdb=" N SER d 401 " --> pdb=" O ASN d 397 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N HIS d 402 " --> pdb=" O ALA d 398 " (cutoff:3.500A) Processing helix chain 'd' and resid 406 through 419 removed outlier: 3.728A pdb=" N CYS d 410 " --> pdb=" O THR d 406 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ARG d 415 " --> pdb=" O GLU d 411 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU d 417 " --> pdb=" O ILE d 413 " (cutoff:3.500A) Processing helix chain 'd' and resid 425 through 432 removed outlier: 3.586A pdb=" N ARG d 432 " --> pdb=" O GLU d 428 " (cutoff:3.500A) Processing helix chain 'd' and resid 437 through 450 removed outlier: 3.661A pdb=" N TYR d 450 " --> pdb=" O SER d 446 " (cutoff:3.500A) Processing helix chain 'd' and resid 467 through 473 Processing helix chain 'e' and resid 68 through 72 removed outlier: 3.928A pdb=" N GLU e 72 " --> pdb=" O SER e 69 " (cutoff:3.500A) Processing helix chain 'e' and resid 78 through 84 Processing helix chain 'e' and resid 95 through 107 removed outlier: 3.742A pdb=" N THR e 100 " --> pdb=" O SER e 96 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ARG e 101 " --> pdb=" O PHE e 97 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU e 104 " --> pdb=" O THR e 100 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N VAL e 106 " --> pdb=" O GLY e 102 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 141 removed outlier: 4.060A pdb=" N LEU e 133 " --> pdb=" O ASP e 129 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N MET e 134 " --> pdb=" O ILE e 130 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N GLU e 135 " --> pdb=" O GLU e 131 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N PHE e 136 " --> pdb=" O ILE e 132 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N ASN e 139 " --> pdb=" O GLU e 135 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N THR e 141 " --> pdb=" O LEU e 137 " (cutoff:3.500A) Processing helix chain 'e' and resid 156 through 166 removed outlier: 3.864A pdb=" N ILE e 160 " --> pdb=" O SER e 156 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N PHE e 166 " --> pdb=" O LYS e 162 " (cutoff:3.500A) Processing helix chain 'e' and resid 175 through 180 removed outlier: 3.599A pdb=" N ALA e 179 " --> pdb=" O GLU e 175 " (cutoff:3.500A) Processing helix chain 'e' and resid 193 through 200 removed outlier: 5.634A pdb=" N GLY e 198 " --> pdb=" O TYR e 195 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N VAL e 200 " --> pdb=" O ILE e 197 " (cutoff:3.500A) Processing helix chain 'e' and resid 201 through 213 removed outlier: 3.856A pdb=" N LEU e 205 " --> pdb=" O THR e 201 " (cutoff:3.500A) removed outlier: 4.165A pdb=" N HIS e 206 " --> pdb=" O PRO e 202 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 217 Processing helix chain 'e' and resid 226 through 236 removed outlier: 3.978A pdb=" N LEU e 230 " --> pdb=" O SER e 226 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N ARG e 236 " --> pdb=" O GLN e 232 " (cutoff:3.500A) Processing helix chain 'e' and resid 282 through 294 Processing helix chain 'e' and resid 307 through 314 removed outlier: 3.546A pdb=" N GLN e 311 " --> pdb=" O SER e 307 " (cutoff:3.500A) Processing helix chain 'e' and resid 346 through 352 removed outlier: 3.781A pdb=" N VAL e 350 " --> pdb=" O SER e 346 " (cutoff:3.500A) Processing helix chain 'e' and resid 353 through 362 removed outlier: 4.039A pdb=" N GLN e 357 " --> pdb=" O SER e 353 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N VAL e 358 " --> pdb=" O ALA e 354 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N LYS e 359 " --> pdb=" O TYR e 355 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ALA e 362 " --> pdb=" O VAL e 358 " (cutoff:3.500A) Processing helix chain 'e' and resid 369 through 385 removed outlier: 3.572A pdb=" N ASN e 376 " --> pdb=" O GLN e 372 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N LYS e 377 " --> pdb=" O ALA e 373 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU e 378 " --> pdb=" O ALA e 374 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N LYS e 379 " --> pdb=" O LYS e 375 " (cutoff:3.500A) Processing helix chain 'e' and resid 390 through 400 removed outlier: 3.577A pdb=" N ASP e 394 " --> pdb=" O GLU e 390 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLN e 399 " --> pdb=" O GLU e 395 " (cutoff:3.500A) Processing helix chain 'e' and resid 408 through 417 removed outlier: 3.586A pdb=" N VAL e 412 " --> pdb=" O GLN e 408 " (cutoff:3.500A) Processing helix chain 'e' and resid 420 through 433 removed outlier: 4.219A pdb=" N VAL e 424 " --> pdb=" O ALA e 420 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N ILE e 425 " --> pdb=" O ASP e 421 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ALA e 428 " --> pdb=" O VAL e 424 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LYS e 429 " --> pdb=" O ILE e 425 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LYS e 430 " --> pdb=" O ASN e 426 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N PHE e 431 " --> pdb=" O ALA e 427 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N VAL e 432 " --> pdb=" O ALA e 428 " (cutoff:3.500A) Processing helix chain 'f' and resid 29 through 39 removed outlier: 3.898A pdb=" N GLN f 39 " --> pdb=" O GLU f 35 " (cutoff:3.500A) Processing helix chain 'f' and resid 40 through 59 removed outlier: 3.805A pdb=" N SER f 59 " --> pdb=" O GLN f 55 " (cutoff:3.500A) Processing helix chain 'f' and resid 69 through 86 removed outlier: 4.049A pdb=" N CYS f 81 " --> pdb=" O ALA f 77 " (cutoff:3.500A) removed outlier: 4.464A pdb=" N HIS f 84 " --> pdb=" O HIS f 80 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N LYS f 85 " --> pdb=" O CYS f 81 " (cutoff:3.500A) Processing helix chain 'f' and resid 87 through 90 removed outlier: 3.508A pdb=" N LEU f 90 " --> pdb=" O PHE f 87 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 87 through 90' Processing helix chain 'g' and resid 10 through 25 removed outlier: 3.523A pdb=" N GLY g 16 " --> pdb=" O LYS g 12 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N TYR g 22 " --> pdb=" O ARG g 18 " (cutoff:3.500A) Processing helix chain 'g' and resid 33 through 37 Processing helix chain 'g' and resid 55 through 66 removed outlier: 3.617A pdb=" N ARG g 59 " --> pdb=" O LEU g 55 " (cutoff:3.500A) Processing helix chain 'g' and resid 77 through 81 Processing helix chain 'g' and resid 91 through 96 Processing helix chain 'g' and resid 97 through 111 removed outlier: 4.068A pdb=" N GLU g 104 " --> pdb=" O ARG g 100 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG g 105 " --> pdb=" O GLU g 101 " (cutoff:3.500A) Processing helix chain 'h' and resid 30 through 73 removed outlier: 4.237A pdb=" N ILE h 35 " --> pdb=" O PHE h 31 " (cutoff:3.500A) Proline residue: h 36 - end of helix removed outlier: 3.988A pdb=" N ARG h 43 " --> pdb=" O LEU h 39 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N ALA h 44 " --> pdb=" O ARG h 40 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU h 47 " --> pdb=" O ARG h 43 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ARG h 48 " --> pdb=" O ALA h 44 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ALA h 50 " --> pdb=" O ILE h 46 " (cutoff:3.500A) Proline residue: h 51 - end of helix removed outlier: 3.683A pdb=" N VAL h 55 " --> pdb=" O PRO h 51 " (cutoff:3.500A) removed outlier: 4.897A pdb=" N PHE h 56 " --> pdb=" O PRO h 52 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N TYR h 57 " --> pdb=" O PHE h 53 " (cutoff:3.500A) removed outlier: 4.062A pdb=" N LEU h 58 " --> pdb=" O VAL h 54 " (cutoff:3.500A) removed outlier: 5.992A pdb=" N VAL h 59 " --> pdb=" O VAL h 55 " (cutoff:3.500A) Processing helix chain 'h' and resid 74 through 77 Processing helix chain 'i' and resid 5 through 15 removed outlier: 3.904A pdb=" N ARG i 9 " --> pdb=" O THR i 5 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N PHE i 15 " --> pdb=" O TYR i 11 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 48 removed outlier: 3.593A pdb=" N THR i 24 " --> pdb=" O THR i 20 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE i 25 " --> pdb=" O PHE i 21 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY i 28 " --> pdb=" O THR i 24 " (cutoff:3.500A) removed outlier: 4.217A pdb=" N ALA i 29 " --> pdb=" O ILE i 25 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU i 30 " --> pdb=" O ALA i 26 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N ASP i 37 " --> pdb=" O GLU i 33 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N GLN i 38 " --> pdb=" O ARG i 34 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY i 39 " --> pdb=" O ALA i 35 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE i 43 " --> pdb=" O GLY i 39 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N ASN i 48 " --> pdb=" O TYR i 44 " (cutoff:3.500A) Processing helix chain 'i' and resid 52 through 57 Processing helix chain 'i' and resid 58 through 60 No H-bonds generated for 'chain 'i' and resid 58 through 60' Processing helix chain 'j' and resid 7 through 36 removed outlier: 4.035A pdb=" N ARG j 11 " --> pdb=" O GLY j 7 " (cutoff:3.500A) Proline residue: j 19 - end of helix removed outlier: 3.522A pdb=" N TRP j 34 " --> pdb=" O VAL j 30 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N THR j 36 " --> pdb=" O LEU j 32 " (cutoff:3.500A) Processing helix chain 'j' and resid 38 through 43 Processing helix chain 'k' and resid 30 through 34 Processing sheet with id=AA1, first strand: chain 'A' and resid 23 through 24 Processing sheet with id=AA2, first strand: chain 'B' and resid 233 through 234 Processing sheet with id=AA3, first strand: chain 'C' and resid 174 through 178 removed outlier: 3.703A pdb=" N ARG C 177 " --> pdb=" O VAL C 211 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N VAL C 211 " --> pdb=" O ARG C 177 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 234 through 235 Processing sheet with id=AA5, first strand: chain 'D' and resid 49 through 52 removed outlier: 4.119A pdb=" N GLN D 49 " --> pdb=" O SER D 61 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER D 61 " --> pdb=" O GLN D 49 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N GLY D 72 " --> pdb=" O ALA D 232 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N CYS D 69 " --> pdb=" O ALA D 135 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ALA D 135 " --> pdb=" O CYS D 69 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THR D 129 " --> pdb=" O ILE D 75 " (cutoff:3.500A) removed outlier: 3.830A pdb=" N LYS D 134 " --> pdb=" O HIS D 119 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 276 through 277 removed outlier: 3.525A pdb=" N ARG D 276 " --> pdb=" O THR H 16 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 314 through 315 removed outlier: 7.048A pdb=" N VAL D 359 " --> pdb=" O GLN D 339 " (cutoff:3.500A) removed outlier: 4.407A pdb=" N PHE D 341 " --> pdb=" O HIS D 357 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N HIS D 357 " --> pdb=" O PHE D 341 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 48 through 51 removed outlier: 6.222A pdb=" N VAL E 48 " --> pdb=" O LEU E 220 " (cutoff:3.500A) removed outlier: 7.632A pdb=" N GLY E 222 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N ALA E 50 " --> pdb=" O GLY E 222 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N CYS E 125 " --> pdb=" O SER E 59 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLU E 124 " --> pdb=" O LYS E 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.781A pdb=" N ILE E 258 " --> pdb=" O ALA E 440 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLY E 442 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP E 260 " --> pdb=" O GLY E 442 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 437 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA E 439 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 270 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS E 268 " --> pdb=" O SER E 441 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 271 " --> pdb=" O ILE E 338 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 258 through 261 removed outlier: 6.781A pdb=" N ILE E 258 " --> pdb=" O ALA E 440 " (cutoff:3.500A) removed outlier: 8.586A pdb=" N GLY E 442 " --> pdb=" O ILE E 258 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N ASP E 260 " --> pdb=" O GLY E 442 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N SER E 437 " --> pdb=" O VAL E 272 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N ALA E 439 " --> pdb=" O ALA E 270 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N ALA E 270 " --> pdb=" O ALA E 439 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N HIS E 268 " --> pdb=" O SER E 441 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N LEU E 271 " --> pdb=" O ILE E 338 " (cutoff:3.500A) removed outlier: 3.668A pdb=" N LEU E 335 " --> pdb=" O ALA E 328 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N ALA E 328 " --> pdb=" O LEU E 335 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'b' and resid 155 through 156 removed outlier: 3.806A pdb=" N VAL b 155 " --> pdb=" O ARG b 168 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N ARG b 168 " --> pdb=" O VAL b 155 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'b' and resid 233 through 234 removed outlier: 3.561A pdb=" N TYR b 233 " --> pdb=" O ILE b 243 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'b' and resid 321 through 322 removed outlier: 3.626A pdb=" N GLY d 458 " --> pdb=" O ILE d 275 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N HIS d 277 " --> pdb=" O GLY d 458 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N PHE d 344 " --> pdb=" O GLY d 355 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER d 340 " --> pdb=" O VAL d 359 " (cutoff:3.500A) removed outlier: 3.709A pdb=" N TYR d 314 " --> pdb=" O PHE d 341 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'c' and resid 174 through 178 Processing sheet with id=AB6, first strand: chain 'c' and resid 234 through 236 Processing sheet with id=AB7, first strand: chain 'd' and resid 49 through 52 removed outlier: 3.550A pdb=" N GLN d 49 " --> pdb=" O SER d 61 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N SER d 61 " --> pdb=" O GLN d 49 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL d 59 " --> pdb=" O SER d 51 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N ARG d 58 " --> pdb=" O LEU d 231 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N ALA d 233 " --> pdb=" O ARG d 58 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N ALA d 60 " --> pdb=" O ALA d 233 " (cutoff:3.500A) removed outlier: 8.739A pdb=" N GLY d 235 " --> pdb=" O ALA d 60 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N GLU d 62 " --> pdb=" O GLY d 235 " (cutoff:3.500A) removed outlier: 3.957A pdb=" N CYS d 69 " --> pdb=" O ALA d 135 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N ALA d 135 " --> pdb=" O CYS d 69 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N THR d 129 " --> pdb=" O ILE d 75 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'e' and resid 48 through 51 removed outlier: 6.550A pdb=" N VAL e 48 " --> pdb=" O LEU e 220 " (cutoff:3.500A) removed outlier: 8.063A pdb=" N GLY e 222 " --> pdb=" O VAL e 48 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ALA e 50 " --> pdb=" O GLY e 222 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'e' and resid 322 through 328 removed outlier: 3.854A pdb=" N GLY e 334 " --> pdb=" O SER e 275 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N HIS e 268 " --> pdb=" O SER e 441 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N SER e 441 " --> pdb=" O HIS e 268 " (cutoff:3.500A) 1032 hydrogen bonds defined for protein. 2865 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: 4.92 Time building geometry restraints manager: 2.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.05 - 1.29: 5399 1.29 - 1.53: 24059 1.53 - 1.76: 4494 1.76 - 2.00: 257 2.00 - 2.24: 29 Bond restraints: 34238 Sorted by residual: bond pdb=" C LYS B 311 " pdb=" O LYS B 311 " ideal model delta sigma weight residual 1.236 1.053 0.183 1.32e-02 5.74e+03 1.93e+02 bond pdb=" C LYS B 308 " pdb=" O LYS B 308 " ideal model delta sigma weight residual 1.237 1.074 0.163 1.19e-02 7.06e+03 1.87e+02 bond pdb=" C HIS a 196 " pdb=" O HIS a 196 " ideal model delta sigma weight residual 1.237 1.097 0.139 1.17e-02 7.31e+03 1.42e+02 bond pdb=" CA MET e 438 " pdb=" C MET e 438 " ideal model delta sigma weight residual 1.524 1.673 -0.148 1.35e-02 5.49e+03 1.21e+02 bond pdb=" C VAL a 195 " pdb=" O VAL a 195 " ideal model delta sigma weight residual 1.240 1.117 0.123 1.18e-02 7.18e+03 1.08e+02 ... (remaining 34233 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.94: 46024 5.94 - 11.88: 394 11.88 - 17.82: 54 17.82 - 23.76: 8 23.76 - 29.70: 1 Bond angle restraints: 46481 Sorted by residual: angle pdb=" N ALA e 440 " pdb=" CA ALA e 440 " pdb=" C ALA e 440 " ideal model delta sigma weight residual 107.88 86.76 21.12 1.41e+00 5.03e-01 2.24e+02 angle pdb=" N SER a 297 " pdb=" CA SER a 297 " pdb=" C SER a 297 " ideal model delta sigma weight residual 111.14 126.70 -15.56 1.08e+00 8.57e-01 2.08e+02 angle pdb=" N GLY e 245 " pdb=" CA GLY e 245 " pdb=" C GLY e 245 " ideal model delta sigma weight residual 112.50 129.01 -16.51 1.16e+00 7.43e-01 2.03e+02 angle pdb=" N MET A 304 " pdb=" CA MET A 304 " pdb=" C MET A 304 " ideal model delta sigma weight residual 112.55 130.66 -18.11 1.35e+00 5.49e-01 1.80e+02 angle pdb=" N GLY e 242 " pdb=" CA GLY e 242 " pdb=" C GLY e 242 " ideal model delta sigma weight residual 112.77 129.62 -16.85 1.28e+00 6.10e-01 1.73e+02 ... (remaining 46476 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.23: 19681 34.23 - 68.47: 644 68.47 - 102.70: 37 102.70 - 136.93: 10 136.93 - 171.16: 1 Dihedral angle restraints: 20373 sinusoidal: 8225 harmonic: 12148 Sorted by residual: dihedral pdb=" CA HIS a 221 " pdb=" C HIS a 221 " pdb=" N PRO a 222 " pdb=" CA PRO a 222 " ideal model delta harmonic sigma weight residual -180.00 -116.41 -63.59 0 5.00e+00 4.00e-02 1.62e+02 dihedral pdb=" C ILE a 184 " pdb=" N ILE a 184 " pdb=" CA ILE a 184 " pdb=" CB ILE a 184 " ideal model delta harmonic sigma weight residual -122.00 -147.20 25.20 0 2.50e+00 1.60e-01 1.02e+02 dihedral pdb=" C PHE a 187 " pdb=" N PHE a 187 " pdb=" CA PHE a 187 " pdb=" CB PHE a 187 " ideal model delta harmonic sigma weight residual -122.60 -146.97 24.37 0 2.50e+00 1.60e-01 9.50e+01 ... (remaining 20370 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.188: 4865 0.188 - 0.375: 146 0.375 - 0.563: 31 0.563 - 0.750: 12 0.750 - 0.938: 6 Chirality restraints: 5060 Sorted by residual: chirality pdb=" CA PHE a 187 " pdb=" N PHE a 187 " pdb=" C PHE a 187 " pdb=" CB PHE a 187 " both_signs ideal model delta sigma weight residual False 2.51 1.57 0.94 2.00e-01 2.50e+01 2.20e+01 chirality pdb=" CA TRP A 326 " pdb=" N TRP A 326 " pdb=" C TRP A 326 " pdb=" CB TRP A 326 " both_signs ideal model delta sigma weight residual False 2.51 1.62 0.89 2.00e-01 2.50e+01 1.99e+01 chirality pdb=" CA ILE a 184 " pdb=" N ILE a 184 " pdb=" C ILE a 184 " pdb=" CB ILE a 184 " both_signs ideal model delta sigma weight residual False 2.43 1.56 0.87 2.00e-01 2.50e+01 1.89e+01 ... (remaining 5057 not shown) Planarity restraints: 5915 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN d 66 " 0.103 5.00e-02 4.00e+02 1.61e-01 4.13e+01 pdb=" N PRO d 67 " -0.278 5.00e-02 4.00e+02 pdb=" CA PRO d 67 " 0.099 5.00e-02 4.00e+02 pdb=" CD PRO d 67 " 0.075 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER i 19 " 0.028 2.00e-02 2.50e+03 5.76e-02 3.31e+01 pdb=" C SER i 19 " -0.100 2.00e-02 2.50e+03 pdb=" O SER i 19 " 0.038 2.00e-02 2.50e+03 pdb=" N THR i 20 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA k 12 " 0.089 5.00e-02 4.00e+02 1.33e-01 2.83e+01 pdb=" N PRO k 13 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO k 13 " 0.072 5.00e-02 4.00e+02 pdb=" CD PRO k 13 " 0.069 5.00e-02 4.00e+02 ... (remaining 5912 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 487 2.62 - 3.19: 28848 3.19 - 3.76: 45365 3.76 - 4.33: 63553 4.33 - 4.90: 104839 Nonbonded interactions: 243092 Sorted by model distance: nonbonded pdb=" O ASP c 82 " pdb=" CG2 ILE c 83 " model vdw 2.053 3.460 nonbonded pdb=" O HIS d 323 " pdb=" ND1 HIS d 323 " model vdw 2.109 3.120 nonbonded pdb=" OD1 ASP E 421 " pdb=" N ALA E 422 " model vdw 2.112 3.120 nonbonded pdb=" O HIS B 310 " pdb=" ND1 HIS B 310 " model vdw 2.140 3.120 nonbonded pdb=" O LEU K 2 " pdb=" OG SER K 3 " model vdw 2.159 3.040 ... (remaining 243087 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 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'a' and (resid 2 through 402 or (resid 403 and (name N or name C1 or name \ C10 or name C11 or name C12 or name C13 or name C14 or name C15 or name C16 or \ name C17 or name C18 or name C19 or name C2 or name C20 or name C21 or name C22 \ or name C23 or name C24 or name C25 or name C26 or name C27 or name C3 or name C \ 30 or name C31 or name C32 or name C33 or name C34 or name C35 or name C36 or na \ me C37 or name C38 or name C39 or name C4 or name C40 or name C41 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or \ name O5 or name P )))) } ncs_group { reference = (chain 'B' and (resid 86 through 324 or resid 401)) selection = chain 'b' } ncs_group { reference = chain 'C' selection = (chain 'c' and resid 81 through 301) } ncs_group { reference = (chain 'D' and resid 36 through 480) selection = (chain 'd' and resid 36 through 480) } ncs_group { reference = chain 'E' selection = chain 'e' } ncs_group { reference = chain 'F' selection = chain 'f' } ncs_group { reference = chain 'G' selection = chain 'g' } ncs_group { reference = chain 'H' selection = (chain 'h' and resid 3 through 73) } ncs_group { reference = chain 'I' selection = chain 'i' } ncs_group { reference = (chain 'J' and resid 2 through 49) selection = (chain 'j' and resid 2 through 49) } ncs_group { reference = chain 'K' selection = chain 'k' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.680 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.370 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 27.950 Find NCS groups from input model: 0.550 Set up NCS constraints: 0.090 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.250 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7163 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 : 0.017 0.991 34251 Z= 0.770 Angle : 1.535 68.943 46490 Z= 0.869 Chirality : 0.090 0.938 5060 Planarity : 0.008 0.161 5915 Dihedral : 16.625 171.164 12553 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.39 Ramachandran Plot: Outliers : 0.41 % Allowed : 8.63 % Favored : 90.96 % Rotamer: Outliers : 4.18 % Allowed : 3.24 % Favored : 92.57 % Cbeta Deviations : 0.79 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 1.50 % Twisted General : 0.28 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.39 (0.12), residues: 4137 helix: -2.37 (0.11), residues: 1670 sheet: -1.16 (0.30), residues: 288 loop : -2.29 (0.12), residues: 2179 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.021 0.001 ARG E 84 TYR 0.033 0.003 TYR a 224 PHE 0.053 0.003 PHE K 11 TRP 0.055 0.003 TRP A 135 HIS 0.017 0.002 HIS e 81 Details of bonding type rmsd covalent geometry : bond 0.01229 (34238) covalent geometry : angle 1.46422 (46481) hydrogen bonds : bond 0.28313 ( 1021) hydrogen bonds : angle 8.24966 ( 2865) metal coordination : bond 0.74410 ( 8) metal coordination : angle 33.22879 ( 9) Misc. bond : bond 0.34906 ( 5) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 548 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 147 poor density : 401 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 63 PHE cc_start: 0.6576 (t80) cc_final: 0.6302 (t80) REVERT: A 306 MET cc_start: 0.8108 (mtt) cc_final: 0.7837 (mtt) REVERT: A 327 MET cc_start: 0.7552 (OUTLIER) cc_final: 0.7221 (ttm) REVERT: B 212 VAL cc_start: 0.7405 (t) cc_final: 0.7127 (p) REVERT: B 264 MET cc_start: 0.7143 (ttp) cc_final: 0.6909 (ttt) REVERT: B 296 MET cc_start: 0.7059 (mtt) cc_final: 0.6715 (mtp) REVERT: C 84 ARG cc_start: 0.5596 (mmp-170) cc_final: 0.4963 (ttm170) REVERT: D 43 GLN cc_start: 0.6988 (pp30) cc_final: 0.6555 (pp30) REVERT: D 176 ASP cc_start: 0.7672 (t70) cc_final: 0.7360 (t0) REVERT: D 323 HIS cc_start: 0.8756 (OUTLIER) cc_final: 0.8548 (m90) REVERT: D 369 MET cc_start: 0.8145 (mmt) cc_final: 0.7825 (mmt) REVERT: E 110 LEU cc_start: 0.8801 (OUTLIER) cc_final: 0.8240 (tt) REVERT: E 138 LEU cc_start: 0.7877 (tt) cc_final: 0.7631 (tt) REVERT: E 236 ARG cc_start: 0.6396 (mtm180) cc_final: 0.6030 (mtp180) REVERT: E 301 ARG cc_start: 0.7033 (mtm180) cc_final: 0.6191 (ptp-110) REVERT: G 86 GLU cc_start: 0.7346 (mt-10) cc_final: 0.7097 (pt0) REVERT: H 65 GLN cc_start: 0.7154 (tt0) cc_final: 0.6950 (tt0) REVERT: a 21 LEU cc_start: 0.7410 (pp) cc_final: 0.7169 (tp) REVERT: a 121 PHE cc_start: 0.6793 (OUTLIER) cc_final: 0.6421 (m-80) REVERT: a 177 ARG cc_start: 0.5043 (ptp-170) cc_final: 0.4477 (ptm160) REVERT: a 306 MET cc_start: 0.6536 (OUTLIER) cc_final: 0.5981 (mtp) REVERT: a 363 LEU cc_start: 0.8301 (mm) cc_final: 0.7851 (mm) REVERT: b 128 MET cc_start: 0.3693 (mmt) cc_final: 0.3357 (mpt) REVERT: b 129 ASP cc_start: 0.3875 (OUTLIER) cc_final: 0.2315 (t0) REVERT: b 297 MET cc_start: 0.6201 (OUTLIER) cc_final: 0.4995 (tmm) REVERT: b 307 MET cc_start: 0.6362 (OUTLIER) cc_final: 0.5259 (tpt) REVERT: c 147 LEU cc_start: 0.2815 (OUTLIER) cc_final: 0.2445 (mt) REVERT: d 324 MET cc_start: 0.7726 (OUTLIER) cc_final: 0.7490 (mtm) REVERT: e 318 HIS cc_start: 0.6075 (m170) cc_final: 0.5808 (m-70) REVERT: e 441 SER cc_start: 0.8839 (OUTLIER) cc_final: 0.8390 (m) REVERT: g 103 LYS cc_start: 0.6866 (OUTLIER) cc_final: 0.6160 (mttt) REVERT: g 107 GLU cc_start: 0.6573 (OUTLIER) cc_final: 0.6134 (mp0) REVERT: k 20 ARG cc_start: 0.6693 (mtt180) cc_final: 0.6458 (mtt180) outliers start: 147 outliers final: 59 residues processed: 530 average time/residue: 0.6320 time to fit residues: 400.8274 Evaluate side-chains 368 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 296 time to evaluate : 1.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 47 THR Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 138 MET Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 300 ILE Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 307 LEU Chi-restraints excluded: chain A residue 327 MET Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 349 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 352 GLN Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 140 CYS Chi-restraints excluded: chain B residue 280 GLU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 309 ARG Chi-restraints excluded: chain B residue 310 HIS Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 154 ILE Chi-restraints excluded: chain D residue 61 SER Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 75 ILE Chi-restraints excluded: chain D residue 323 HIS Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 336 LYS Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 SER Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain E residue 438 MET Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain a residue 26 ASN Chi-restraints excluded: chain a residue 121 PHE Chi-restraints excluded: chain a residue 186 PRO Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain a residue 233 LEU Chi-restraints excluded: chain a residue 275 LEU Chi-restraints excluded: chain a residue 276 PHE Chi-restraints excluded: chain a residue 297 SER Chi-restraints excluded: chain a residue 302 ILE Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain a residue 350 ILE Chi-restraints excluded: chain b residue 129 ASP Chi-restraints excluded: chain b residue 297 MET Chi-restraints excluded: chain b residue 307 MET Chi-restraints excluded: chain c residue 147 LEU Chi-restraints excluded: chain c residue 156 LEU Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain d residue 64 SER Chi-restraints excluded: chain d residue 65 SER Chi-restraints excluded: chain d residue 322 THR Chi-restraints excluded: chain d residue 324 MET Chi-restraints excluded: chain d residue 406 THR Chi-restraints excluded: chain e residue 241 ARG Chi-restraints excluded: chain e residue 244 LEU Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain e residue 275 SER Chi-restraints excluded: chain e residue 441 SER Chi-restraints excluded: chain g residue 103 LYS Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain i residue 20 THR Chi-restraints excluded: chain i residue 24 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 197 optimal weight: 10.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 3.9990 chunk 20 optimal weight: 7.9990 chunk 132 optimal weight: 2.9990 chunk 261 optimal weight: 3.9990 chunk 248 optimal weight: 6.9990 chunk 207 optimal weight: 3.9990 chunk 401 optimal weight: 2.9990 chunk 155 optimal weight: 3.9990 chunk 244 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 ASN ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 341 GLN B 108 HIS B 182 ASN D 95 HIS D 241 GLN D 323 HIS D 345 ASN E 168 ASN E 206 HIS E 232 GLN E 261 GLN E 311 GLN a 201 HIS b 116 GLN b 190 ASN ** c 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 239 HIS ** d 286 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** e 357 GLN e 446 HIS i 38 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.241239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4427 r_free = 0.4427 target = 0.197730 restraints weight = 37730.489| |-----------------------------------------------------------------------------| r_work (start): 0.4362 rms_B_bonded: 3.10 r_work: 0.3989 rms_B_bonded: 3.90 restraints_weight: 0.5000 r_work (final): 0.3989 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.1656 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.327 34251 Z= 0.199 Angle : 0.933 52.078 46490 Z= 0.429 Chirality : 0.048 0.271 5060 Planarity : 0.007 0.099 5915 Dihedral : 12.304 169.421 5016 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.30 % Favored : 92.60 % Rotamer: Outliers : 3.53 % Allowed : 12.09 % Favored : 84.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.13 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.09 (0.12), residues: 4137 helix: -1.92 (0.11), residues: 1779 sheet: -0.72 (0.28), residues: 334 loop : -2.39 (0.13), residues: 2024 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.001 ARG K 27 TYR 0.024 0.002 TYR B 175 PHE 0.022 0.002 PHE d 92 TRP 0.031 0.002 TRP A 135 HIS 0.011 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00455 (34238) covalent geometry : angle 0.84011 (46481) hydrogen bonds : bond 0.06872 ( 1021) hydrogen bonds : angle 5.39833 ( 2865) metal coordination : bond 0.05324 ( 8) metal coordination : angle 29.13311 ( 9) Misc. bond : bond 0.18441 ( 5) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 124 poor density : 340 time to evaluate : 1.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 139 SER cc_start: 0.7199 (OUTLIER) cc_final: 0.6902 (p) REVERT: A 315 MET cc_start: 0.7059 (mtt) cc_final: 0.6820 (mtp) REVERT: B 212 VAL cc_start: 0.7296 (t) cc_final: 0.6958 (p) REVERT: B 320 LEU cc_start: 0.7824 (OUTLIER) cc_final: 0.7577 (pp) REVERT: C 84 ARG cc_start: 0.6061 (mmp-170) cc_final: 0.5081 (ttm170) REVERT: C 99 SER cc_start: 0.5702 (p) cc_final: 0.5449 (p) REVERT: D 43 GLN cc_start: 0.7232 (pp30) cc_final: 0.6822 (pp30) REVERT: D 215 ASP cc_start: 0.7384 (m-30) cc_final: 0.7114 (m-30) REVERT: E 186 LEU cc_start: 0.8211 (OUTLIER) cc_final: 0.7816 (mp) REVERT: E 236 ARG cc_start: 0.6424 (mtm180) cc_final: 0.5925 (mtp180) REVERT: E 252 LYS cc_start: 0.7867 (ptpp) cc_final: 0.7283 (ptmm) REVERT: E 261 GLN cc_start: 0.8492 (OUTLIER) cc_final: 0.7990 (tt0) REVERT: E 306 THR cc_start: 0.6108 (OUTLIER) cc_final: 0.5702 (p) REVERT: E 388 SER cc_start: 0.7520 (OUTLIER) cc_final: 0.6975 (t) REVERT: H 4 GLU cc_start: 0.7146 (OUTLIER) cc_final: 0.6811 (mp0) REVERT: J 23 MET cc_start: 0.2423 (OUTLIER) cc_final: 0.2152 (pp-130) REVERT: b 243 ILE cc_start: 0.5396 (tp) cc_final: 0.5092 (tt) REVERT: b 276 ARG cc_start: 0.6902 (ttt-90) cc_final: 0.6447 (tmt170) REVERT: b 293 MET cc_start: 0.7016 (OUTLIER) cc_final: 0.6765 (ptm) REVERT: c 147 LEU cc_start: 0.1314 (OUTLIER) cc_final: 0.0434 (tp) REVERT: e 124 GLU cc_start: 0.7986 (tm-30) cc_final: 0.7621 (tt0) REVERT: g 74 GLN cc_start: 0.7535 (OUTLIER) cc_final: 0.6741 (mp10) REVERT: g 80 GLN cc_start: 0.6825 (tp-100) cc_final: 0.6594 (mm-40) REVERT: i 32 PHE cc_start: 0.2329 (OUTLIER) cc_final: 0.1123 (t80) outliers start: 124 outliers final: 50 residues processed: 430 average time/residue: 0.5958 time to fit residues: 312.1118 Evaluate side-chains 363 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 301 time to evaluate : 1.249 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 40 CYS Chi-restraints excluded: chain A residue 49 LEU Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 230 LEU Chi-restraints excluded: chain A residue 284 ILE Chi-restraints excluded: chain A residue 297 SER Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 302 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 353 LEU Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain B residue 320 LEU Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain D residue 63 GLN Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 325 SER Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain E residue 73 ASP Chi-restraints excluded: chain E residue 74 SER Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 186 LEU Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 261 GLN Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain E residue 388 SER Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain J residue 23 MET Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 183 PHE Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain b residue 131 VAL Chi-restraints excluded: chain b residue 214 SER Chi-restraints excluded: chain b residue 293 MET Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 147 LEU Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 136 LEU Chi-restraints excluded: chain d residue 177 SER Chi-restraints excluded: chain d residue 231 LEU Chi-restraints excluded: chain d residue 406 THR Chi-restraints excluded: chain e residue 172 GLN Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain h residue 8 LEU Chi-restraints excluded: chain i residue 24 THR Chi-restraints excluded: chain i residue 32 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 355 optimal weight: 5.9990 chunk 391 optimal weight: 7.9990 chunk 33 optimal weight: 0.0670 chunk 123 optimal weight: 6.9990 chunk 208 optimal weight: 10.0000 chunk 281 optimal weight: 0.7980 chunk 196 optimal weight: 8.9990 chunk 117 optimal weight: 0.0170 chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 overall best weight: 1.3358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 HIS ** B 182 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 87 ASN D 95 HIS E 168 ASN E 399 GLN a 267 HIS ** c 200 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 286 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4770 r_free = 0.4770 target = 0.246113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.197705 restraints weight = 38003.756| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 4.03 r_work: 0.4079 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.4079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7429 moved from start: 0.2240 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.264 34251 Z= 0.127 Angle : 0.769 42.883 46490 Z= 0.341 Chirality : 0.042 0.195 5060 Planarity : 0.005 0.077 5915 Dihedral : 10.815 177.873 4917 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 6.31 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.57 % Favored : 93.35 % Rotamer: Outliers : 2.93 % Allowed : 16.05 % Favored : 81.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.53 (0.12), residues: 4137 helix: -1.34 (0.12), residues: 1794 sheet: -0.38 (0.28), residues: 339 loop : -2.22 (0.13), residues: 2004 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG K 27 TYR 0.024 0.001 TYR B 175 PHE 0.019 0.001 PHE E 321 TRP 0.016 0.001 TRP A 135 HIS 0.007 0.001 HIS b 283 Details of bonding type rmsd covalent geometry : bond 0.00273 (34238) covalent geometry : angle 0.67403 (46481) hydrogen bonds : bond 0.04858 ( 1021) hydrogen bonds : angle 4.74252 ( 2865) metal coordination : bond 0.05254 ( 8) metal coordination : angle 26.68150 ( 9) Misc. bond : bond 0.15151 ( 5) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 436 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 103 poor density : 333 time to evaluate : 1.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7145 (mtt) cc_final: 0.6929 (mtp) REVERT: B 102 LEU cc_start: 0.8010 (mt) cc_final: 0.7654 (mt) REVERT: B 178 LYS cc_start: 0.7631 (tmmt) cc_final: 0.7340 (tmmt) REVERT: B 282 GLU cc_start: 0.7206 (pt0) cc_final: 0.6975 (pm20) REVERT: C 84 ARG cc_start: 0.6070 (mmp-170) cc_final: 0.5738 (mmp-170) REVERT: C 99 SER cc_start: 0.5758 (OUTLIER) cc_final: 0.5472 (p) REVERT: C 161 GLU cc_start: -0.0907 (OUTLIER) cc_final: -0.1663 (tp30) REVERT: D 43 GLN cc_start: 0.7271 (pp30) cc_final: 0.6766 (pp30) REVERT: D 112 GLU cc_start: 0.8377 (tt0) cc_final: 0.8103 (tm-30) REVERT: D 209 ARG cc_start: 0.7528 (OUTLIER) cc_final: 0.7107 (mtm-85) REVERT: D 215 ASP cc_start: 0.7439 (m-30) cc_final: 0.7148 (m-30) REVERT: E 252 LYS cc_start: 0.7649 (ptpp) cc_final: 0.7101 (ptmm) REVERT: E 272 VAL cc_start: 0.8390 (m) cc_final: 0.8189 (p) REVERT: E 306 THR cc_start: 0.6476 (OUTLIER) cc_final: 0.6251 (p) REVERT: G 86 GLU cc_start: 0.7708 (mt-10) cc_final: 0.7202 (pt0) REVERT: H 4 GLU cc_start: 0.6978 (OUTLIER) cc_final: 0.6716 (mp0) REVERT: I 47 ILE cc_start: 0.7551 (tt) cc_final: 0.7308 (pt) REVERT: J 23 MET cc_start: 0.2656 (pp-130) cc_final: 0.2406 (pp-130) REVERT: a 42 ILE cc_start: 0.7168 (mp) cc_final: 0.6967 (mp) REVERT: b 276 ARG cc_start: 0.6721 (ttt-90) cc_final: 0.6283 (tmt170) REVERT: b 297 MET cc_start: 0.6275 (ttm) cc_final: 0.5802 (ttp) REVERT: c 147 LEU cc_start: 0.0683 (OUTLIER) cc_final: -0.0228 (tp) REVERT: d 279 ASP cc_start: 0.6209 (t0) cc_final: 0.5873 (t0) REVERT: e 124 GLU cc_start: 0.7834 (tm-30) cc_final: 0.7565 (tt0) REVERT: g 74 GLN cc_start: 0.7464 (OUTLIER) cc_final: 0.6805 (mt0) REVERT: g 80 GLN cc_start: 0.6827 (tp-100) cc_final: 0.6523 (mm-40) REVERT: i 32 PHE cc_start: 0.2413 (OUTLIER) cc_final: 0.1119 (t80) REVERT: k 20 ARG cc_start: 0.6685 (mtt180) cc_final: 0.6253 (mtt180) outliers start: 103 outliers final: 44 residues processed: 409 average time/residue: 0.6479 time to fit residues: 319.1777 Evaluate side-chains 350 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 298 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 SER Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 299 LEU Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain D residue 407 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 306 THR Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 38 VAL Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain a residue 20 ASP Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 175 LEU Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 268 ILE Chi-restraints excluded: chain b residue 131 VAL Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 147 LEU Chi-restraints excluded: chain c residue 157 SER Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 136 LEU Chi-restraints excluded: chain d residue 151 VAL Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 231 LEU Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 359 VAL Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 348 optimal weight: 2.9990 chunk 219 optimal weight: 7.9990 chunk 381 optimal weight: 1.9990 chunk 10 optimal weight: 4.9990 chunk 220 optimal weight: 0.0980 chunk 356 optimal weight: 4.9990 chunk 104 optimal weight: 5.9990 chunk 285 optimal weight: 9.9990 chunk 299 optimal weight: 0.4980 chunk 76 optimal weight: 0.0870 chunk 155 optimal weight: 10.0000 overall best weight: 1.1362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN D 193 GLN D 305 GLN E 168 ASN b 99 HIS c 200 HIS d 95 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.247268 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 94)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.197522 restraints weight = 37823.124| |-----------------------------------------------------------------------------| r_work (start): 0.4361 rms_B_bonded: 4.30 r_work: 0.4078 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7407 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.321 34251 Z= 0.118 Angle : 0.729 39.560 46490 Z= 0.321 Chirality : 0.041 0.178 5060 Planarity : 0.005 0.077 5915 Dihedral : 9.954 175.244 4892 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.24 % Favored : 93.72 % Rotamer: Outliers : 3.19 % Allowed : 17.39 % Favored : 79.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.17 (0.13), residues: 4137 helix: -1.01 (0.12), residues: 1830 sheet: -0.17 (0.28), residues: 340 loop : -2.07 (0.13), residues: 1967 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG d 213 TYR 0.023 0.001 TYR B 175 PHE 0.016 0.001 PHE a 121 TRP 0.012 0.001 TRP A 326 HIS 0.006 0.001 HIS b 283 Details of bonding type rmsd covalent geometry : bond 0.00256 (34238) covalent geometry : angle 0.63484 (46481) hydrogen bonds : bond 0.04313 ( 1021) hydrogen bonds : angle 4.48922 ( 2865) metal coordination : bond 0.04701 ( 8) metal coordination : angle 25.70062 ( 9) Misc. bond : bond 0.16882 ( 5) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 437 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 325 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7165 (mtt) cc_final: 0.6945 (mtp) REVERT: B 264 MET cc_start: 0.7361 (ttt) cc_final: 0.7158 (ttt) REVERT: B 282 GLU cc_start: 0.7107 (pt0) cc_final: 0.6865 (pm20) REVERT: C 90 ASP cc_start: 0.6543 (OUTLIER) cc_final: 0.6337 (m-30) REVERT: C 99 SER cc_start: 0.5469 (OUTLIER) cc_final: 0.5220 (p) REVERT: C 161 GLU cc_start: -0.1112 (OUTLIER) cc_final: -0.1665 (tp30) REVERT: D 43 GLN cc_start: 0.7213 (pp30) cc_final: 0.6705 (pp30) REVERT: D 112 GLU cc_start: 0.8400 (tt0) cc_final: 0.8088 (tm-30) REVERT: D 209 ARG cc_start: 0.7520 (OUTLIER) cc_final: 0.7073 (mtm-85) REVERT: D 215 ASP cc_start: 0.7514 (m-30) cc_final: 0.7213 (m-30) REVERT: D 241 GLN cc_start: 0.7932 (tt0) cc_final: 0.7535 (tp40) REVERT: E 43 LEU cc_start: 0.6191 (mt) cc_final: 0.5787 (tp) REVERT: a 42 ILE cc_start: 0.7169 (OUTLIER) cc_final: 0.6914 (mp) REVERT: a 171 ASP cc_start: 0.6347 (m-30) cc_final: 0.6018 (m-30) REVERT: b 276 ARG cc_start: 0.6599 (ttt-90) cc_final: 0.6288 (tmt170) REVERT: b 297 MET cc_start: 0.6230 (ttm) cc_final: 0.5849 (ttt) REVERT: c 147 LEU cc_start: 0.0437 (OUTLIER) cc_final: -0.0456 (tp) REVERT: e 240 MET cc_start: 0.5986 (OUTLIER) cc_final: 0.4852 (ppp) REVERT: g 74 GLN cc_start: 0.7412 (OUTLIER) cc_final: 0.6868 (mt0) REVERT: g 80 GLN cc_start: 0.6737 (tp-100) cc_final: 0.6352 (mm-40) REVERT: i 32 PHE cc_start: 0.2280 (OUTLIER) cc_final: 0.1015 (t80) outliers start: 112 outliers final: 49 residues processed: 409 average time/residue: 0.6262 time to fit residues: 307.6630 Evaluate side-chains 352 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 294 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 90 ASP Chi-restraints excluded: chain C residue 99 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain D residue 406 THR Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 42 ILE Chi-restraints excluded: chain a residue 60 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain b residue 131 VAL Chi-restraints excluded: chain b residue 214 SER Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 147 LEU Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 136 LEU Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 351 THR Chi-restraints excluded: chain d residue 359 VAL Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 241 ARG Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain g residue 71 MET Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 8 LEU Chi-restraints excluded: chain i residue 32 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 169 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 chunk 369 optimal weight: 9.9990 chunk 278 optimal weight: 5.9990 chunk 143 optimal weight: 3.9990 chunk 29 optimal weight: 9.9990 chunk 19 optimal weight: 0.5980 chunk 86 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 132 optimal weight: 3.9990 chunk 79 optimal weight: 30.0000 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS E 168 ASN b 120 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4739 r_free = 0.4739 target = 0.242682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.199008 restraints weight = 37876.920| |-----------------------------------------------------------------------------| r_work (start): 0.4370 rms_B_bonded: 2.94 r_work: 0.4012 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.345 34251 Z= 0.160 Angle : 0.791 40.437 46490 Z= 0.354 Chirality : 0.044 0.228 5060 Planarity : 0.005 0.084 5915 Dihedral : 9.897 170.120 4888 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.32 % Favored : 92.60 % Rotamer: Outliers : 4.04 % Allowed : 17.96 % Favored : 78.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.23 (0.12), residues: 4137 helix: -1.09 (0.12), residues: 1820 sheet: -0.18 (0.28), residues: 328 loop : -2.07 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 213 TYR 0.024 0.002 TYR a 55 PHE 0.020 0.002 PHE E 321 TRP 0.014 0.001 TRP A 326 HIS 0.009 0.001 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00366 (34238) covalent geometry : angle 0.70851 (46481) hydrogen bonds : bond 0.05460 ( 1021) hydrogen bonds : angle 4.57066 ( 2865) metal coordination : bond 0.04132 ( 8) metal coordination : angle 25.29217 ( 9) Misc. bond : bond 0.18502 ( 5) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 451 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 142 poor density : 309 time to evaluate : 1.062 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 315 MET cc_start: 0.7292 (mtt) cc_final: 0.7057 (mtt) REVERT: B 282 GLU cc_start: 0.7259 (pt0) cc_final: 0.6955 (pm20) REVERT: C 161 GLU cc_start: -0.1048 (OUTLIER) cc_final: -0.1690 (tp30) REVERT: D 43 GLN cc_start: 0.7199 (pp30) cc_final: 0.6723 (pp30) REVERT: D 112 GLU cc_start: 0.8409 (tt0) cc_final: 0.8081 (tm-30) REVERT: D 209 ARG cc_start: 0.7627 (OUTLIER) cc_final: 0.7199 (mtm-85) REVERT: D 215 ASP cc_start: 0.7571 (m-30) cc_final: 0.7278 (m-30) REVERT: D 241 GLN cc_start: 0.7974 (tt0) cc_final: 0.7520 (tp-100) REVERT: E 114 SER cc_start: 0.8612 (OUTLIER) cc_final: 0.8403 (m) REVERT: E 161 ASP cc_start: 0.8062 (OUTLIER) cc_final: 0.7739 (t0) REVERT: E 241 ARG cc_start: 0.6512 (ttm170) cc_final: 0.6296 (ttp-170) REVERT: H 43 ARG cc_start: 0.6028 (tmm160) cc_final: 0.5169 (tmm-80) REVERT: a 42 ILE cc_start: 0.7163 (OUTLIER) cc_final: 0.6902 (mp) REVERT: a 171 ASP cc_start: 0.6256 (m-30) cc_final: 0.5917 (m-30) REVERT: a 181 PHE cc_start: 0.6182 (OUTLIER) cc_final: 0.5538 (t80) REVERT: a 363 LEU cc_start: 0.7935 (mm) cc_final: 0.7403 (mm) REVERT: b 297 MET cc_start: 0.6179 (ttm) cc_final: 0.4537 (tmm) REVERT: c 147 LEU cc_start: 0.0343 (OUTLIER) cc_final: -0.0494 (tp) REVERT: e 240 MET cc_start: 0.5935 (OUTLIER) cc_final: 0.4772 (ppp) REVERT: g 74 GLN cc_start: 0.7472 (OUTLIER) cc_final: 0.6960 (mt0) REVERT: g 80 GLN cc_start: 0.6657 (tp-100) cc_final: 0.6213 (mm-40) REVERT: i 32 PHE cc_start: 0.2391 (OUTLIER) cc_final: 0.1061 (t80) outliers start: 142 outliers final: 70 residues processed: 410 average time/residue: 0.6061 time to fit residues: 300.8123 Evaluate side-chains 373 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 80 poor density : 293 time to evaluate : 1.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 129 MET Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 42 ILE Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 94 LEU Chi-restraints excluded: chain a residue 115 ILE Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 268 ILE Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 362 ILE Chi-restraints excluded: chain b residue 131 VAL Chi-restraints excluded: chain b residue 214 SER Chi-restraints excluded: chain b residue 226 VAL Chi-restraints excluded: chain b residue 320 LEU Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 147 LEU Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 136 LEU Chi-restraints excluded: chain d residue 164 GLU Chi-restraints excluded: chain d residue 177 SER Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 231 LEU Chi-restraints excluded: chain d residue 327 THR Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 351 THR Chi-restraints excluded: chain d residue 359 VAL Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 241 ARG Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain g residue 33 MET Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain h residue 8 LEU Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain k residue 15 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 376 optimal weight: 7.9990 chunk 267 optimal weight: 10.0000 chunk 309 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 203 optimal weight: 7.9990 chunk 326 optimal weight: 7.9990 chunk 254 optimal weight: 5.9990 chunk 364 optimal weight: 8.9990 chunk 97 optimal weight: 10.0000 chunk 321 optimal weight: 1.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 95 HIS D 305 GLN E 168 ASN ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** J 16 ASN b 120 GLN d 55 ASN d 95 HIS d 160 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.239045 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4397 r_free = 0.4397 target = 0.194539 restraints weight = 37624.271| |-----------------------------------------------------------------------------| r_work (start): 0.4338 rms_B_bonded: 3.30 r_work: 0.3970 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.3970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7578 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.398 34251 Z= 0.218 Angle : 0.870 41.035 46490 Z= 0.398 Chirality : 0.047 0.254 5060 Planarity : 0.006 0.087 5915 Dihedral : 10.194 166.859 4887 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.10 % Allowed : 7.95 % Favored : 91.95 % Rotamer: Outliers : 4.70 % Allowed : 18.53 % Favored : 76.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.49 (0.12), residues: 4137 helix: -1.26 (0.12), residues: 1819 sheet: -0.58 (0.28), residues: 332 loop : -2.20 (0.13), residues: 1986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 196 TYR 0.026 0.002 TYR a 55 PHE 0.027 0.002 PHE D 344 TRP 0.018 0.002 TRP A 135 HIS 0.012 0.002 HIS A 196 Details of bonding type rmsd covalent geometry : bond 0.00519 (34238) covalent geometry : angle 0.79542 (46481) hydrogen bonds : bond 0.06507 ( 1021) hydrogen bonds : angle 4.81584 ( 2865) metal coordination : bond 0.03818 ( 8) metal coordination : angle 25.26659 ( 9) Misc. bond : bond 0.20673 ( 5) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 464 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 165 poor density : 299 time to evaluate : 0.990 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 161 GLU cc_start: -0.0877 (OUTLIER) cc_final: -0.1647 (tp30) REVERT: D 43 GLN cc_start: 0.7209 (pp30) cc_final: 0.6720 (pp30) REVERT: D 112 GLU cc_start: 0.8388 (tt0) cc_final: 0.8056 (tm-30) REVERT: D 209 ARG cc_start: 0.7666 (OUTLIER) cc_final: 0.7275 (mtm-85) REVERT: D 211 LEU cc_start: 0.6778 (mt) cc_final: 0.6130 (mp) REVERT: D 215 ASP cc_start: 0.7545 (m-30) cc_final: 0.7306 (m-30) REVERT: D 241 GLN cc_start: 0.8023 (tt0) cc_final: 0.7531 (tp-100) REVERT: E 161 ASP cc_start: 0.8108 (OUTLIER) cc_final: 0.7766 (t0) REVERT: E 241 ARG cc_start: 0.6682 (OUTLIER) cc_final: 0.6385 (ttp-170) REVERT: F 79 ASP cc_start: 0.6825 (m-30) cc_final: 0.6623 (m-30) REVERT: G 86 GLU cc_start: 0.7617 (mt-10) cc_final: 0.7148 (pt0) REVERT: H 43 ARG cc_start: 0.5925 (tmm160) cc_final: 0.5391 (tpp80) REVERT: a 20 ASP cc_start: 0.7373 (OUTLIER) cc_final: 0.7077 (m-30) REVERT: a 61 THR cc_start: 0.4197 (OUTLIER) cc_final: 0.3170 (t) REVERT: a 124 MET cc_start: 0.7302 (ttp) cc_final: 0.7092 (mtt) REVERT: a 171 ASP cc_start: 0.6244 (m-30) cc_final: 0.5886 (m-30) REVERT: a 181 PHE cc_start: 0.6408 (OUTLIER) cc_final: 0.5696 (t80) REVERT: a 214 ASP cc_start: 0.7190 (OUTLIER) cc_final: 0.6556 (m-30) REVERT: a 274 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: a 363 LEU cc_start: 0.8051 (OUTLIER) cc_final: 0.7542 (mm) REVERT: b 297 MET cc_start: 0.6236 (ttm) cc_final: 0.4499 (tmm) REVERT: c 147 LEU cc_start: 0.0060 (OUTLIER) cc_final: -0.0624 (tp) REVERT: c 149 MET cc_start: 0.0062 (OUTLIER) cc_final: -0.0157 (mpt) REVERT: d 170 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7664 (mp10) REVERT: d 274 GLU cc_start: 0.7418 (OUTLIER) cc_final: 0.6324 (tt0) REVERT: e 138 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.8028 (tp) REVERT: e 240 MET cc_start: 0.5994 (OUTLIER) cc_final: 0.4903 (ppp) REVERT: g 74 GLN cc_start: 0.7559 (OUTLIER) cc_final: 0.6976 (mt0) REVERT: g 80 GLN cc_start: 0.6659 (tp-100) cc_final: 0.6111 (mm-40) REVERT: i 32 PHE cc_start: 0.2595 (OUTLIER) cc_final: 0.1232 (t80) outliers start: 165 outliers final: 86 residues processed: 414 average time/residue: 0.5852 time to fit residues: 294.8296 Evaluate side-chains 397 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 293 time to evaluate : 1.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 115 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 173 SER Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain B residue 313 SER Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 245 LEU Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 114 SER Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 226 SER Chi-restraints excluded: chain E residue 241 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 317 VAL Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 4 GLU Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 32 THR Chi-restraints excluded: chain H residue 42 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 66 GLU Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 20 ASP Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 59 THR Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 133 LEU Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 195 VAL Chi-restraints excluded: chain a residue 201 HIS Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain a residue 274 PHE Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain a residue 336 THR Chi-restraints excluded: chain a residue 362 ILE Chi-restraints excluded: chain a residue 363 LEU Chi-restraints excluded: chain b residue 131 VAL Chi-restraints excluded: chain b residue 142 THR Chi-restraints excluded: chain b residue 214 SER Chi-restraints excluded: chain b residue 226 VAL Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 121 THR Chi-restraints excluded: chain c residue 147 LEU Chi-restraints excluded: chain c residue 149 MET Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 136 LEU Chi-restraints excluded: chain d residue 170 GLN Chi-restraints excluded: chain d residue 177 SER Chi-restraints excluded: chain d residue 182 VAL Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 231 LEU Chi-restraints excluded: chain d residue 274 GLU Chi-restraints excluded: chain d residue 327 THR Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 351 THR Chi-restraints excluded: chain d residue 359 VAL Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 197 ILE Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain e residue 315 LYS Chi-restraints excluded: chain e residue 416 ILE Chi-restraints excluded: chain g residue 33 MET Chi-restraints excluded: chain g residue 71 MET Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain g residue 107 GLU Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain h residue 8 LEU Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain k residue 15 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 228 optimal weight: 0.4980 chunk 246 optimal weight: 30.0000 chunk 272 optimal weight: 10.0000 chunk 342 optimal weight: 1.9990 chunk 208 optimal weight: 5.9990 chunk 144 optimal weight: 0.3980 chunk 163 optimal weight: 4.9990 chunk 169 optimal weight: 7.9990 chunk 227 optimal weight: 0.0870 chunk 173 optimal weight: 0.0870 chunk 127 optimal weight: 10.0000 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 308 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 182 ASN D 95 HIS D 305 GLN E 139 ASN E 168 ASN H 13 HIS ** a 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 196 HIS b 120 GLN ** d 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4780 r_free = 0.4780 target = 0.247360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.204560 restraints weight = 38145.007| |-----------------------------------------------------------------------------| r_work (start): 0.4412 rms_B_bonded: 2.96 r_work: 0.4069 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.3005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.399 34251 Z= 0.110 Angle : 0.706 38.851 46490 Z= 0.311 Chirality : 0.041 0.184 5060 Planarity : 0.005 0.084 5915 Dihedral : 9.403 162.313 4887 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.12 % Favored : 93.84 % Rotamer: Outliers : 2.85 % Allowed : 20.66 % Favored : 76.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.01 (0.13), residues: 4137 helix: -0.83 (0.12), residues: 1837 sheet: -0.24 (0.28), residues: 345 loop : -2.03 (0.13), residues: 1955 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG d 213 TYR 0.014 0.001 TYR g 56 PHE 0.022 0.001 PHE E 321 TRP 0.018 0.001 TRP a 379 HIS 0.005 0.001 HIS b 283 Details of bonding type rmsd covalent geometry : bond 0.00242 (34238) covalent geometry : angle 0.61797 (46481) hydrogen bonds : bond 0.03753 ( 1021) hydrogen bonds : angle 4.38423 ( 2865) metal coordination : bond 0.03215 ( 8) metal coordination : angle 24.52491 ( 9) Misc. bond : bond 0.19830 ( 5) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 426 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 100 poor density : 326 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 282 GLU cc_start: 0.7266 (pt0) cc_final: 0.7029 (pm20) REVERT: C 161 GLU cc_start: -0.0927 (OUTLIER) cc_final: -0.1533 (tp30) REVERT: D 43 GLN cc_start: 0.7203 (pp30) cc_final: 0.6743 (pp30) REVERT: D 112 GLU cc_start: 0.8415 (tt0) cc_final: 0.8176 (tm-30) REVERT: D 209 ARG cc_start: 0.7555 (OUTLIER) cc_final: 0.7144 (mtm-85) REVERT: D 211 LEU cc_start: 0.6551 (mt) cc_final: 0.5959 (mp) REVERT: D 215 ASP cc_start: 0.7578 (m-30) cc_final: 0.7301 (m-30) REVERT: D 241 GLN cc_start: 0.7857 (tt0) cc_final: 0.7565 (tp-100) REVERT: D 377 MET cc_start: 0.7933 (mmp) cc_final: 0.7342 (mmp) REVERT: E 43 LEU cc_start: 0.6170 (mt) cc_final: 0.5735 (tp) REVERT: E 49 ILE cc_start: 0.7672 (pt) cc_final: 0.7360 (mt) REVERT: E 241 ARG cc_start: 0.6522 (OUTLIER) cc_final: 0.6270 (ttp-170) REVERT: a 61 THR cc_start: 0.3815 (OUTLIER) cc_final: 0.2887 (t) REVERT: a 171 ASP cc_start: 0.6265 (m-30) cc_final: 0.5899 (m-30) REVERT: a 274 PHE cc_start: 0.7797 (OUTLIER) cc_final: 0.6919 (m-10) REVERT: b 297 MET cc_start: 0.6155 (ttm) cc_final: 0.4395 (tmm) REVERT: c 149 MET cc_start: 0.0662 (OUTLIER) cc_final: 0.0382 (mmt) REVERT: e 138 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7861 (tp) REVERT: e 170 GLN cc_start: 0.8669 (OUTLIER) cc_final: 0.8133 (pt0) REVERT: e 240 MET cc_start: 0.5973 (OUTLIER) cc_final: 0.4842 (ppp) REVERT: g 74 GLN cc_start: 0.7194 (OUTLIER) cc_final: 0.6842 (mt0) REVERT: g 80 GLN cc_start: 0.6716 (tp-100) cc_final: 0.6088 (mm-40) REVERT: i 32 PHE cc_start: 0.2512 (OUTLIER) cc_final: 0.1148 (t80) outliers start: 100 outliers final: 40 residues processed: 403 average time/residue: 0.5685 time to fit residues: 278.3107 Evaluate side-chains 350 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 299 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 268 ILE Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 241 ARG Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 384 MET Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 274 PHE Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 149 MET Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 170 GLN Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 146 optimal weight: 5.9990 chunk 61 optimal weight: 5.9990 chunk 184 optimal weight: 2.9990 chunk 145 optimal weight: 6.9990 chunk 111 optimal weight: 2.9990 chunk 322 optimal weight: 0.9980 chunk 294 optimal weight: 7.9990 chunk 257 optimal weight: 0.7980 chunk 396 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 125 optimal weight: 10.0000 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 308 HIS D 95 HIS E 168 ASN b 120 GLN d 95 HIS ** d 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4747 r_free = 0.4747 target = 0.243247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.191853 restraints weight = 37806.706| |-----------------------------------------------------------------------------| r_work (start): 0.4301 rms_B_bonded: 4.86 r_work: 0.4005 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.4005 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.400 34251 Z= 0.151 Angle : 0.771 39.060 46490 Z= 0.344 Chirality : 0.043 0.231 5060 Planarity : 0.005 0.089 5915 Dihedral : 9.442 162.868 4884 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.20 % Favored : 92.72 % Rotamer: Outliers : 3.16 % Allowed : 20.83 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.08 (0.13), residues: 4137 helix: -0.90 (0.12), residues: 1836 sheet: -0.23 (0.29), residues: 324 loop : -2.04 (0.13), residues: 1977 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 313 TYR 0.019 0.001 TYR a 55 PHE 0.019 0.001 PHE G 27 TRP 0.012 0.001 TRP a 379 HIS 0.014 0.001 HIS d 323 Details of bonding type rmsd covalent geometry : bond 0.00351 (34238) covalent geometry : angle 0.69173 (46481) hydrogen bonds : bond 0.05087 ( 1021) hydrogen bonds : angle 4.47122 ( 2865) metal coordination : bond 0.03074 ( 8) metal coordination : angle 24.55761 ( 9) Misc. bond : bond 0.20074 ( 5) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 301 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 68 HIS cc_start: 0.6013 (OUTLIER) cc_final: 0.5701 (t70) REVERT: A 141 TRP cc_start: 0.5691 (OUTLIER) cc_final: 0.5476 (m-90) REVERT: C 161 GLU cc_start: -0.1163 (OUTLIER) cc_final: -0.1675 (tp30) REVERT: D 43 GLN cc_start: 0.7055 (pp30) cc_final: 0.6581 (pp30) REVERT: D 112 GLU cc_start: 0.8409 (tt0) cc_final: 0.8048 (tm-30) REVERT: D 209 ARG cc_start: 0.7604 (OUTLIER) cc_final: 0.7178 (mtm-85) REVERT: D 211 LEU cc_start: 0.6617 (mt) cc_final: 0.5951 (mp) REVERT: D 215 ASP cc_start: 0.7550 (m-30) cc_final: 0.7280 (m-30) REVERT: D 241 GLN cc_start: 0.7847 (tt0) cc_final: 0.7486 (tp-100) REVERT: E 161 ASP cc_start: 0.8185 (OUTLIER) cc_final: 0.7819 (t0) REVERT: F 79 ASP cc_start: 0.6361 (m-30) cc_final: 0.6159 (m-30) REVERT: a 61 THR cc_start: 0.4004 (OUTLIER) cc_final: 0.3035 (t) REVERT: a 171 ASP cc_start: 0.6220 (m-30) cc_final: 0.5829 (m-30) REVERT: a 181 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5527 (t80) REVERT: b 264 MET cc_start: 0.5291 (OUTLIER) cc_final: 0.4669 (mtp) REVERT: b 297 MET cc_start: 0.6130 (ttm) cc_final: 0.4245 (tmm) REVERT: c 149 MET cc_start: 0.0116 (OUTLIER) cc_final: -0.0117 (mmt) REVERT: d 274 GLU cc_start: 0.7439 (OUTLIER) cc_final: 0.6348 (tt0) REVERT: e 138 LEU cc_start: 0.8025 (OUTLIER) cc_final: 0.7767 (tp) REVERT: e 170 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.8146 (pt0) REVERT: e 240 MET cc_start: 0.5930 (OUTLIER) cc_final: 0.4766 (ppp) REVERT: e 309 LEU cc_start: 0.7277 (pp) cc_final: 0.6984 (pt) REVERT: g 74 GLN cc_start: 0.7253 (OUTLIER) cc_final: 0.6890 (mt0) REVERT: g 80 GLN cc_start: 0.6638 (tp-100) cc_final: 0.5918 (mm-40) REVERT: i 32 PHE cc_start: 0.2190 (OUTLIER) cc_final: 0.0896 (t80) outliers start: 111 outliers final: 59 residues processed: 384 average time/residue: 0.5586 time to fit residues: 259.1828 Evaluate side-chains 369 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 295 time to evaluate : 1.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 141 TRP Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 299 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 115 ILE Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 201 HIS Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 241 ILE Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain b residue 155 VAL Chi-restraints excluded: chain b residue 226 VAL Chi-restraints excluded: chain b residue 264 MET Chi-restraints excluded: chain c residue 80 HIS Chi-restraints excluded: chain c residue 149 MET Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 274 GLU Chi-restraints excluded: chain d residue 279 ASP Chi-restraints excluded: chain d residue 327 THR Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 170 GLN Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain e residue 315 LYS Chi-restraints excluded: chain e residue 416 ILE Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain k residue 15 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 15 optimal weight: 0.0670 chunk 171 optimal weight: 0.0970 chunk 135 optimal weight: 4.9990 chunk 375 optimal weight: 2.9990 chunk 265 optimal weight: 6.9990 chunk 53 optimal weight: 10.0000 chunk 253 optimal weight: 20.0000 chunk 41 optimal weight: 9.9990 chunk 362 optimal weight: 9.9990 chunk 277 optimal weight: 5.9990 chunk 316 optimal weight: 9.9990 overall best weight: 2.8322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS E 168 ASN E 170 GLN ** H 13 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 120 GLN ** d 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4745 r_free = 0.4745 target = 0.242999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4449 r_free = 0.4449 target = 0.200460 restraints weight = 37618.212| |-----------------------------------------------------------------------------| r_work (start): 0.4380 rms_B_bonded: 3.17 r_work: 0.4006 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2984 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.410 34251 Z= 0.152 Angle : 0.770 38.537 46490 Z= 0.345 Chirality : 0.043 0.234 5060 Planarity : 0.005 0.088 5915 Dihedral : 9.420 162.020 4884 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 7.08 % Favored : 92.85 % Rotamer: Outliers : 3.16 % Allowed : 21.09 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.05 (0.13), residues: 4137 helix: -0.84 (0.12), residues: 1795 sheet: -0.29 (0.29), residues: 324 loop : -2.02 (0.13), residues: 2018 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG b 168 TYR 0.020 0.001 TYR a 55 PHE 0.025 0.002 PHE E 321 TRP 0.014 0.001 TRP A 135 HIS 0.014 0.001 HIS d 323 Details of bonding type rmsd covalent geometry : bond 0.00355 (34238) covalent geometry : angle 0.69132 (46481) hydrogen bonds : bond 0.05069 ( 1021) hydrogen bonds : angle 4.49062 ( 2865) metal coordination : bond 0.03007 ( 8) metal coordination : angle 24.41720 ( 9) Misc. bond : bond 0.20314 ( 5) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 111 poor density : 300 time to evaluate : 1.295 Fit side-chains revert: symmetry clash REVERT: A 68 HIS cc_start: 0.6174 (OUTLIER) cc_final: 0.5916 (t70) REVERT: B 254 LEU cc_start: 0.6940 (OUTLIER) cc_final: 0.6506 (tt) REVERT: C 161 GLU cc_start: -0.0848 (OUTLIER) cc_final: -0.1525 (tp30) REVERT: D 43 GLN cc_start: 0.7118 (pp30) cc_final: 0.6648 (pp30) REVERT: D 112 GLU cc_start: 0.8428 (tt0) cc_final: 0.8139 (tm-30) REVERT: D 209 ARG cc_start: 0.7651 (OUTLIER) cc_final: 0.7247 (mtm-85) REVERT: D 211 LEU cc_start: 0.6662 (mt) cc_final: 0.5999 (mp) REVERT: D 215 ASP cc_start: 0.7559 (m-30) cc_final: 0.7314 (m-30) REVERT: D 241 GLN cc_start: 0.7891 (tt0) cc_final: 0.7583 (tp-100) REVERT: E 161 ASP cc_start: 0.8096 (OUTLIER) cc_final: 0.7787 (t0) REVERT: a 61 THR cc_start: 0.4226 (OUTLIER) cc_final: 0.3246 (t) REVERT: a 171 ASP cc_start: 0.6306 (m-30) cc_final: 0.5934 (m-30) REVERT: a 181 PHE cc_start: 0.5865 (OUTLIER) cc_final: 0.5514 (t80) REVERT: a 214 ASP cc_start: 0.7161 (OUTLIER) cc_final: 0.6506 (m-30) REVERT: b 297 MET cc_start: 0.6261 (ttm) cc_final: 0.4467 (tmm) REVERT: c 149 MET cc_start: 0.0784 (OUTLIER) cc_final: 0.0514 (mmt) REVERT: d 274 GLU cc_start: 0.7416 (OUTLIER) cc_final: 0.6380 (tt0) REVERT: e 138 LEU cc_start: 0.8164 (OUTLIER) cc_final: 0.7924 (tp) REVERT: e 170 GLN cc_start: 0.8731 (OUTLIER) cc_final: 0.8127 (pt0) REVERT: e 240 MET cc_start: 0.5972 (OUTLIER) cc_final: 0.4804 (ppp) REVERT: e 309 LEU cc_start: 0.7493 (pp) cc_final: 0.7141 (pt) REVERT: g 74 GLN cc_start: 0.7285 (OUTLIER) cc_final: 0.6913 (mt0) REVERT: g 80 GLN cc_start: 0.6621 (tp-100) cc_final: 0.6002 (mm-40) REVERT: i 32 PHE cc_start: 0.2608 (OUTLIER) cc_final: 0.1154 (t80) outliers start: 111 outliers final: 69 residues processed: 384 average time/residue: 0.5554 time to fit residues: 257.5385 Evaluate side-chains 374 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 290 time to evaluate : 1.042 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 291 LEU Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 217 CYS Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 275 ILE Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 13 HIS Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 115 ILE Chi-restraints excluded: chain a residue 151 SER Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 201 HIS Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 241 ILE Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain b residue 226 VAL Chi-restraints excluded: chain c residue 149 MET Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 136 LEU Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain d residue 177 SER Chi-restraints excluded: chain d residue 190 THR Chi-restraints excluded: chain d residue 274 GLU Chi-restraints excluded: chain d residue 279 ASP Chi-restraints excluded: chain d residue 327 THR Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 359 VAL Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 170 GLN Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain e residue 315 LYS Chi-restraints excluded: chain e residue 416 ILE Chi-restraints excluded: chain g residue 74 GLN Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain k residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 36 optimal weight: 2.9990 chunk 65 optimal weight: 0.8980 chunk 247 optimal weight: 20.0000 chunk 84 optimal weight: 5.9990 chunk 301 optimal weight: 20.0000 chunk 151 optimal weight: 9.9990 chunk 328 optimal weight: 0.6980 chunk 335 optimal weight: 9.9990 chunk 224 optimal weight: 6.9990 chunk 154 optimal weight: 10.0000 chunk 45 optimal weight: 0.0570 overall best weight: 2.1302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS E 168 ASN H 13 HIS b 120 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4757 r_free = 0.4757 target = 0.244328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4461 r_free = 0.4461 target = 0.202291 restraints weight = 37952.254| |-----------------------------------------------------------------------------| r_work (start): 0.4390 rms_B_bonded: 3.00 r_work: 0.4017 rms_B_bonded: 3.89 restraints_weight: 0.5000 r_work (final): 0.4017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.417 34251 Z= 0.134 Angle : 0.743 37.092 46490 Z= 0.332 Chirality : 0.042 0.216 5060 Planarity : 0.005 0.088 5915 Dihedral : 9.184 160.554 4880 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.05 % Allowed : 7.11 % Favored : 92.85 % Rotamer: Outliers : 2.70 % Allowed : 21.71 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.97 (0.13), residues: 4137 helix: -0.75 (0.12), residues: 1818 sheet: -0.29 (0.29), residues: 330 loop : -2.02 (0.13), residues: 1989 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 80 TYR 0.018 0.001 TYR a 55 PHE 0.026 0.001 PHE A 18 TRP 0.014 0.001 TRP a 379 HIS 0.023 0.001 HIS d 323 Details of bonding type rmsd covalent geometry : bond 0.00309 (34238) covalent geometry : angle 0.66238 (46481) hydrogen bonds : bond 0.04612 ( 1021) hydrogen bonds : angle 4.43410 ( 2865) metal coordination : bond 0.02833 ( 8) metal coordination : angle 24.21344 ( 9) Misc. bond : bond 0.20444 ( 5) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8274 Ramachandran restraints generated. 4137 Oldfield, 0 Emsley, 4137 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 390 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 295 time to evaluate : 0.847 Fit side-chains revert: symmetry clash REVERT: A 68 HIS cc_start: 0.6145 (OUTLIER) cc_final: 0.5801 (t70) REVERT: A 141 TRP cc_start: 0.5931 (m-90) cc_final: 0.5708 (m-90) REVERT: B 254 LEU cc_start: 0.6961 (OUTLIER) cc_final: 0.6541 (tt) REVERT: C 161 GLU cc_start: -0.0879 (OUTLIER) cc_final: -0.1448 (tp30) REVERT: D 43 GLN cc_start: 0.7063 (pp30) cc_final: 0.6607 (pp30) REVERT: D 112 GLU cc_start: 0.8456 (tt0) cc_final: 0.8169 (tm-30) REVERT: D 209 ARG cc_start: 0.7652 (OUTLIER) cc_final: 0.7259 (mtm-85) REVERT: D 211 LEU cc_start: 0.6642 (mt) cc_final: 0.6030 (mp) REVERT: D 215 ASP cc_start: 0.7548 (m-30) cc_final: 0.7297 (m-30) REVERT: D 241 GLN cc_start: 0.7877 (tt0) cc_final: 0.7605 (tp-100) REVERT: E 161 ASP cc_start: 0.8069 (OUTLIER) cc_final: 0.7761 (t0) REVERT: G 43 ASP cc_start: 0.7468 (t0) cc_final: 0.7233 (t0) REVERT: a 61 THR cc_start: 0.4256 (OUTLIER) cc_final: 0.3314 (t) REVERT: a 171 ASP cc_start: 0.6259 (m-30) cc_final: 0.5888 (m-30) REVERT: a 181 PHE cc_start: 0.5792 (OUTLIER) cc_final: 0.5426 (t80) REVERT: a 214 ASP cc_start: 0.7129 (OUTLIER) cc_final: 0.6486 (m-30) REVERT: b 297 MET cc_start: 0.6202 (ttm) cc_final: 0.4425 (tmm) REVERT: c 149 MET cc_start: 0.0822 (OUTLIER) cc_final: 0.0560 (mmt) REVERT: d 274 GLU cc_start: 0.7367 (OUTLIER) cc_final: 0.6337 (tt0) REVERT: e 138 LEU cc_start: 0.8056 (OUTLIER) cc_final: 0.7813 (tp) REVERT: e 170 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8199 (pt0) REVERT: e 240 MET cc_start: 0.5971 (OUTLIER) cc_final: 0.4749 (ppp) REVERT: e 309 LEU cc_start: 0.7563 (pp) cc_final: 0.7194 (pt) REVERT: g 80 GLN cc_start: 0.6630 (tp-100) cc_final: 0.6022 (mm-40) REVERT: i 32 PHE cc_start: 0.2704 (OUTLIER) cc_final: 0.1217 (t80) outliers start: 95 outliers final: 63 residues processed: 363 average time/residue: 0.5512 time to fit residues: 242.1860 Evaluate side-chains 367 residues out of total 3517 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 77 poor density : 290 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 42 ILE Chi-restraints excluded: chain A residue 68 HIS Chi-restraints excluded: chain A residue 264 THR Chi-restraints excluded: chain A residue 291 VAL Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain B residue 105 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 165 MET Chi-restraints excluded: chain B residue 254 LEU Chi-restraints excluded: chain B residue 263 THR Chi-restraints excluded: chain B residue 311 LYS Chi-restraints excluded: chain C residue 149 MET Chi-restraints excluded: chain C residue 161 GLU Chi-restraints excluded: chain C residue 238 CYS Chi-restraints excluded: chain D residue 57 LEU Chi-restraints excluded: chain D residue 116 MET Chi-restraints excluded: chain D residue 145 GLU Chi-restraints excluded: chain D residue 156 LEU Chi-restraints excluded: chain D residue 190 THR Chi-restraints excluded: chain D residue 209 ARG Chi-restraints excluded: chain D residue 237 VAL Chi-restraints excluded: chain D residue 271 THR Chi-restraints excluded: chain D residue 351 THR Chi-restraints excluded: chain D residue 359 VAL Chi-restraints excluded: chain E residue 124 GLU Chi-restraints excluded: chain E residue 132 ILE Chi-restraints excluded: chain E residue 161 ASP Chi-restraints excluded: chain E residue 236 ARG Chi-restraints excluded: chain E residue 272 VAL Chi-restraints excluded: chain E residue 292 VAL Chi-restraints excluded: chain E residue 435 ARG Chi-restraints excluded: chain F residue 33 VAL Chi-restraints excluded: chain G residue 67 LEU Chi-restraints excluded: chain H residue 12 ARG Chi-restraints excluded: chain H residue 16 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain I residue 5 THR Chi-restraints excluded: chain K residue 11 PHE Chi-restraints excluded: chain K residue 15 LEU Chi-restraints excluded: chain a residue 11 MET Chi-restraints excluded: chain a residue 35 SER Chi-restraints excluded: chain a residue 61 THR Chi-restraints excluded: chain a residue 73 VAL Chi-restraints excluded: chain a residue 115 ILE Chi-restraints excluded: chain a residue 181 PHE Chi-restraints excluded: chain a residue 182 HIS Chi-restraints excluded: chain a residue 201 HIS Chi-restraints excluded: chain a residue 214 ASP Chi-restraints excluded: chain a residue 238 ILE Chi-restraints excluded: chain a residue 241 ILE Chi-restraints excluded: chain a residue 294 LEU Chi-restraints excluded: chain a residue 329 VAL Chi-restraints excluded: chain b residue 226 VAL Chi-restraints excluded: chain c residue 83 ILE Chi-restraints excluded: chain c residue 149 MET Chi-restraints excluded: chain c residue 154 ILE Chi-restraints excluded: chain c residue 184 ILE Chi-restraints excluded: chain d residue 133 ILE Chi-restraints excluded: chain d residue 152 GLN Chi-restraints excluded: chain d residue 274 GLU Chi-restraints excluded: chain d residue 279 ASP Chi-restraints excluded: chain d residue 327 THR Chi-restraints excluded: chain d residue 338 CYS Chi-restraints excluded: chain d residue 359 VAL Chi-restraints excluded: chain d residue 420 TYR Chi-restraints excluded: chain e residue 52 LEU Chi-restraints excluded: chain e residue 113 THR Chi-restraints excluded: chain e residue 138 LEU Chi-restraints excluded: chain e residue 170 GLN Chi-restraints excluded: chain e residue 240 MET Chi-restraints excluded: chain e residue 257 GLU Chi-restraints excluded: chain e residue 315 LYS Chi-restraints excluded: chain g residue 98 VAL Chi-restraints excluded: chain g residue 111 LYS Chi-restraints excluded: chain i residue 32 PHE Chi-restraints excluded: chain j residue 45 VAL Chi-restraints excluded: chain k residue 15 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 406 random chunks: chunk 123 optimal weight: 0.9990 chunk 71 optimal weight: 0.5980 chunk 169 optimal weight: 6.9990 chunk 238 optimal weight: 5.9990 chunk 173 optimal weight: 0.8980 chunk 176 optimal weight: 0.0970 chunk 261 optimal weight: 4.9990 chunk 217 optimal weight: 10.0000 chunk 189 optimal weight: 4.9990 chunk 369 optimal weight: 7.9990 chunk 101 optimal weight: 5.9990 overall best weight: 1.5182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 HIS E 168 ASN H 13 HIS b 120 GLN d 66 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4765 r_free = 0.4765 target = 0.245594 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4473 r_free = 0.4473 target = 0.202732 restraints weight = 37965.547| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 3.06 r_work: 0.4035 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.4035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.3238 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.411 34251 Z= 0.119 Angle : 0.719 36.936 46490 Z= 0.319 Chirality : 0.042 0.205 5060 Planarity : 0.005 0.087 5915 Dihedral : 8.961 159.126 4880 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.05 % Allowed : 6.70 % Favored : 93.26 % Rotamer: Outliers : 2.62 % Allowed : 21.94 % Favored : 75.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.50 % Cis-general : 0.00 % Twisted Proline : 2.00 % Twisted General : 0.03 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.83 (0.13), residues: 4137 helix: -0.61 (0.12), residues: 1813 sheet: -0.32 (0.28), residues: 341 loop : -1.94 (0.13), residues: 1983 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG K 20 TYR 0.017 0.001 TYR b 118 PHE 0.030 0.001 PHE A 18 TRP 0.014 0.001 TRP a 379 HIS 0.022 0.001 HIS d 323 Details of bonding type rmsd covalent geometry : bond 0.00272 (34238) covalent geometry : angle 0.63712 (46481) hydrogen bonds : bond 0.04132 ( 1021) hydrogen bonds : angle 4.30997 ( 2865) metal coordination : bond 0.02685 ( 8) metal coordination : angle 23.99072 ( 9) Misc. bond : bond 0.20125 ( 5) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10018.07 seconds wall clock time: 171 minutes 26.72 seconds (10286.72 seconds total)