Starting phenix.real_space_refine on Tue Jan 21 00:27:11 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shn_40489/01_2025/8shn_40489.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shn_40489/01_2025/8shn_40489.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8shn_40489/01_2025/8shn_40489.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shn_40489/01_2025/8shn_40489.map" model { file = "/net/cci-nas-00/data/ceres_data/8shn_40489/01_2025/8shn_40489.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shn_40489/01_2025/8shn_40489.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.043 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: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 407 5.16 5 C 41222 2.51 5 N 11486 2.21 5 O 12776 1.98 5 F 48 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 41 residue(s): 0.14s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 66003 Number of models: 1 Model: "" Number of chains: 49 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 880 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 880 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 1, 'TRANS': 114} Chain breaks: 2 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 32.20, per 1000 atoms: 0.49 Number of scatterers: 66003 At special positions: 0 Unit cell: (179.86, 177.744, 181.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 407 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12776 8.00 N 11486 7.00 C 41222 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 Atom "HETATM65782 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65590 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65654 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65526 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.22 Conformation dependent library (CDL) restraints added in 6.9 seconds 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15980 Finding SS restraints... Secondary structure from input PDB file: 358 helices and 98 sheets defined 56.6% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.82 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.584A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.597A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N GLU A 106 " --> pdb=" O LYS A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 145 through 157 Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.174A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ILE A 179 " --> pdb=" O ALA A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 281 removed outlier: 4.048A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.182A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.097A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 446 removed outlier: 3.728A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 480 through 486 removed outlier: 3.789A pdb=" N TRP A 485 " --> pdb=" O ASN A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.569A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.381A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.679A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 removed outlier: 3.564A pdb=" N SER B 212 " --> pdb=" O LEU B 209 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 284 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.687A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.116A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.722A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.505A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 127 removed outlier: 3.719A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLY D 127 " --> pdb=" O LEU D 123 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.532A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.583A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.640A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 3.916A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.935A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.990A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.642A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 50 removed outlier: 3.510A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N THR E 50 " --> pdb=" O ASN E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 73 through 80 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 125 removed outlier: 3.635A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.705A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N SER E 180 " --> pdb=" O VAL E 177 " (cutoff:3.500A) Processing helix chain 'E' and resid 181 through 196 Processing helix chain 'E' and resid 205 through 207 No H-bonds generated for 'chain 'E' and resid 205 through 207' Processing helix chain 'E' and resid 218 through 222 Processing helix chain 'E' and resid 270 through 295 removed outlier: 3.831A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.875A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.852A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.674A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.698A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 Processing helix chain 'E' and resid 500 through 505 Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.671A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.503A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.650A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 163 through 167 removed outlier: 4.234A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.692A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.537A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.630A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 removed outlier: 3.516A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.827A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.713A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.088A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.673A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.559A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.534A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.415A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 157 through 168 removed outlier: 4.223A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.435A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.810A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.882A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 430 removed outlier: 3.727A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.232A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 535 through 539 Processing helix chain 'Z' and resid 3 through 8 removed outlier: 3.838A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.724A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.650A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.823A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.033A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.650A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.675A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.737A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 removed outlier: 3.613A pdb=" N LEU Z 344 " --> pdb=" O PRO Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.512A pdb=" N ASP Z 404 " --> pdb=" O ASN Z 400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.150A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.769A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.538A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.719A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.789A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.198A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.837A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 432 through 445 removed outlier: 3.908A pdb=" N LEU a 436 " --> pdb=" O SER a 432 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.655A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.477A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.635A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 removed outlier: 3.543A pdb=" N SER b 212 " --> pdb=" O LEU b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 260 through 284 Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.867A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.508A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.808A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.838A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.595A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.711A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.347A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 194 Proline residue: d 185 - end of helix removed outlier: 3.580A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 4.017A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.840A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.954A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 25 removed outlier: 3.534A pdb=" N LYS e 25 " --> pdb=" O GLN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 107 through 126 removed outlier: 3.612A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.487A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 Processing helix chain 'e' and resid 205 through 207 No H-bonds generated for 'chain 'e' and resid 205 through 207' Processing helix chain 'e' and resid 218 through 222 Processing helix chain 'e' and resid 270 through 295 removed outlier: 3.981A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 440 removed outlier: 3.896A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.892A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.563A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.669A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 41 No H-bonds generated for 'chain 'g' and resid 39 through 41' Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.686A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.581A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.862A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.543A pdb=" N ALA g 172 " --> pdb=" O TRP g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.669A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 427 removed outlier: 3.534A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.589A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.704A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 114 Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.659A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 185 removed outlier: 3.646A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 removed outlier: 3.672A pdb=" N MET h 227 " --> pdb=" O GLY h 224 " (cutoff:3.500A) Processing helix chain 'h' and resid 259 through 284 Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 removed outlier: 3.799A pdb=" N LEU h 342 " --> pdb=" O ALA h 339 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.655A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 23 through 45 removed outlier: 4.216A pdb=" N GLU q 27 " --> pdb=" O SER q 23 " (cutoff:3.500A) removed outlier: 4.310A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 157 through 168 removed outlier: 4.346A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.611A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 285 removed outlier: 4.751A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.845A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.288A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.731A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.609A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.765A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.130A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.622A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 191 Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.713A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.616A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.786A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 431 No H-bonds generated for 'chain 'z' and resid 430 through 431' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.131A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.613A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.732A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.524A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 52 through 55 removed outlier: 8.018A pdb=" N ASP A 42 " --> pdb=" O ASP G 521 " (cutoff:3.500A) removed outlier: 8.322A pdb=" N VAL G 523 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.022A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.394A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.495A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.495A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.092A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.216A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.330A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.701A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 61 through 64 removed outlier: 7.074A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.984A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.872A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB3, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.508A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.916A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.194A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.432A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.135A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB6, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB7, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.307A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.195A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.105A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.308A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.490A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.490A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 5.628A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.369A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.568A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 28 through 29 removed outlier: 7.170A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.172A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC4, first strand: chain 'E' and resid 209 through 215 removed outlier: 6.668A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.597A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.539A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.247A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.566A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.367A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.782A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.541A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.566A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.449A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.757A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.589A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC9, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.803A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.345A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.419A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD3, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD5, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.298A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.778A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AD9, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE1, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE2, first strand: chain 'Q' and resid 20 through 23 removed outlier: 4.827A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.324A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.704A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 149 through 150 removed outlier: 4.001A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.497A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE6, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AE7, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AE8, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AE9, first strand: chain 'Z' and resid 191 through 196 removed outlier: 3.581A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF2, first strand: chain 'Z' and resid 310 through 313 removed outlier: 6.252A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.922A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.752A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.429A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.503A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 8.064A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.495A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AF7, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AF8, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.346A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.866A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.175A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.736A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.736A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.154A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N LYS e 263 " --> pdb=" O ALA h 253 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG4, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.417A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.003A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.087A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.181A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.118A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG7, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.861A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.378A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 7.050A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH2, first strand: chain 'd' and resid 208 through 214 removed outlier: 4.149A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.640A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.069A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N VAL d 297 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 5.906A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.649A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH5, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.540A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.459A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH7, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.257A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.415A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.369A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.410A pdb=" N CYS e 377 " --> pdb=" O ALA e 356 " (cutoff:3.500A) removed outlier: 7.466A pdb=" N ALA e 356 " --> pdb=" O CYS e 377 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N LEU e 358 " --> pdb=" O GLU e 244 " (cutoff:3.500A) removed outlier: 7.065A pdb=" N GLU e 244 " --> pdb=" O LEU e 358 " (cutoff:3.500A) removed outlier: 6.874A pdb=" N GLN e 360 " --> pdb=" O LYS e 242 " (cutoff:3.500A) removed outlier: 6.849A pdb=" N LYS e 242 " --> pdb=" O GLN e 360 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.309A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.659A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI2, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.792A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI4, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.428A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 407 through 409 Processing sheet with id=AI6, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AI7, first strand: chain 'h' and resid 14 through 17 removed outlier: 4.321A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.414A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 7.977A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AI9, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.765A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ2, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ3, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ4, first strand: chain 'q' and resid 20 through 22 removed outlier: 4.989A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.184A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.712A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.730A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.610A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.315A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.900A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AJ8, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AJ9, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK1, first strand: chain 'z' and resid 192 through 196 removed outlier: 6.249A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK3, first strand: chain 'z' and resid 311 through 313 removed outlier: 8.699A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 5.761A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.696A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.198A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'z' and resid 408 through 409 Processing sheet with id=AK5, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK6, first strand: chain 'N' and resid 198 through 203 removed outlier: 4.328A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N CYS N 219 " --> pdb=" O PHE N 233 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'N' and resid 240 through 245 removed outlier: 6.716A pdb=" N GLY N 257 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LEU N 243 " --> pdb=" O VAL N 255 " (cutoff:3.500A) removed outlier: 6.864A pdb=" N VAL N 255 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 5.152A pdb=" N LEU N 245 " --> pdb=" O THR N 253 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N THR N 253 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N PHE N 254 " --> pdb=" O TRP N 266 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'N' and resid 286 through 288 removed outlier: 3.647A pdb=" N SER N 286 " --> pdb=" O GLY N 299 " (cutoff:3.500A) 4035 hydrogen bonds defined for protein. 11502 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: 29.34 Time building geometry restraints manager: 14.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 22219 1.34 - 1.46: 11840 1.46 - 1.58: 31924 1.58 - 1.70: 48 1.70 - 1.81: 721 Bond restraints: 66752 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.50e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.44e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 ... (remaining 66747 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.77: 88859 1.77 - 3.53: 940 3.53 - 5.30: 234 5.30 - 7.06: 105 7.06 - 8.83: 4 Bond angle restraints: 90142 Sorted by residual: angle pdb=" N VAL e 157 " pdb=" CA VAL e 157 " pdb=" C VAL e 157 " ideal model delta sigma weight residual 111.77 106.11 5.66 1.04e+00 9.25e-01 2.97e+01 angle pdb=" N VAL q 328 " pdb=" CA VAL q 328 " pdb=" C VAL q 328 " ideal model delta sigma weight residual 112.96 109.27 3.69 1.00e+00 1.00e+00 1.36e+01 angle pdb=" N ILE g 193 " pdb=" CA ILE g 193 " pdb=" C ILE g 193 " ideal model delta sigma weight residual 111.48 108.17 3.31 9.40e-01 1.13e+00 1.24e+01 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.97 -6.43 1.91e+00 2.74e-01 1.13e+01 angle pdb=" C ALA Q 151 " pdb=" N LYS Q 152 " pdb=" CA LYS Q 152 " ideal model delta sigma weight residual 121.54 127.69 -6.15 1.91e+00 2.74e-01 1.04e+01 ... (remaining 90137 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.41: 40633 35.41 - 70.83: 570 70.83 - 106.24: 50 106.24 - 141.66: 10 141.66 - 177.07: 6 Dihedral angle restraints: 41269 sinusoidal: 16592 harmonic: 24677 Sorted by residual: dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 117.07 -177.07 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 128.88 171.12 1 2.00e+01 2.50e-03 4.77e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 110.21 -170.21 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 41266 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 8071 0.041 - 0.083: 1872 0.083 - 0.124: 764 0.124 - 0.165: 38 0.165 - 0.206: 1 Chirality restraints: 10746 Sorted by residual: chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA ILE D 70 " pdb=" N ILE D 70 " pdb=" C ILE D 70 " pdb=" CB ILE D 70 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.16e-01 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.69e-01 ... (remaining 10743 not shown) Planarity restraints: 11504 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP E 231 " -0.014 2.00e-02 2.50e+03 2.93e-02 8.60e+00 pdb=" CG ASP E 231 " 0.051 2.00e-02 2.50e+03 pdb=" OD1 ASP E 231 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP E 231 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 231 " 0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C ASP E 231 " -0.039 2.00e-02 2.50e+03 pdb=" O ASP E 231 " 0.015 2.00e-02 2.50e+03 pdb=" N LYS E 232 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.031 5.00e-02 4.00e+02 4.74e-02 3.60e+00 pdb=" N PRO e 441 " -0.082 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.026 5.00e-02 4.00e+02 ... (remaining 11501 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 556 2.53 - 3.12: 50071 3.12 - 3.71: 104006 3.71 - 4.31: 145905 4.31 - 4.90: 250765 Nonbonded interactions: 551303 Sorted by model distance: nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.936 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.973 2.120 nonbonded pdb=" O3A ADP B 601 " pdb="MG MG B 602 " model vdw 1.982 2.170 nonbonded pdb=" O2A ADP G 601 " pdb="MG MG G 602 " model vdw 1.996 2.170 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.999 2.120 ... (remaining 551298 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' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.200 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: 0.080 Extract box with map and model: 1.840 Check model and map are aligned: 0.370 Set scattering table: 0.460 Process input model: 120.260 Find NCS groups from input model: 5.860 Set up NCS constraints: 0.430 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: 0.020 Load rotamer database and sin/cos tables:11.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 141.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 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 : 0.004 0.161 66752 Z= 0.256 Angle : 0.529 8.828 90142 Z= 0.263 Chirality : 0.041 0.206 10746 Planarity : 0.003 0.047 11504 Dihedral : 13.798 177.073 25289 Min Nonbonded Distance : 1.936 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 8543 helix: 2.42 (0.08), residues: 4342 sheet: 0.34 (0.16), residues: 1137 loop : -0.42 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.013 0.001 HIS Z 161 PHE 0.029 0.001 PHE H 174 TYR 0.016 0.001 TYR z 351 ARG 0.006 0.000 ARG d 27 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 551 time to evaluate : 5.734 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 508 ILE cc_start: 0.9148 (tp) cc_final: 0.8861 (tp) REVERT: B 17 ASP cc_start: 0.8267 (t0) cc_final: 0.8041 (p0) REVERT: D 25 GLN cc_start: 0.9089 (tp-100) cc_final: 0.8875 (tp-100) REVERT: G 52 ASP cc_start: 0.8706 (t0) cc_final: 0.8429 (t0) REVERT: G 364 THR cc_start: 0.9272 (p) cc_final: 0.9060 (p) REVERT: H 14 ASP cc_start: 0.8596 (t70) cc_final: 0.8290 (t0) REVERT: H 70 ASP cc_start: 0.7533 (t70) cc_final: 0.7108 (t70) REVERT: H 81 ASP cc_start: 0.8306 (m-30) cc_final: 0.7998 (m-30) REVERT: H 440 LYS cc_start: 0.9163 (tttt) cc_final: 0.8956 (tppt) REVERT: Q 200 ASP cc_start: 0.8926 (m-30) cc_final: 0.8637 (t0) REVERT: a 51 ASP cc_start: 0.8268 (m-30) cc_final: 0.8065 (m-30) REVERT: a 156 MET cc_start: 0.8936 (mtm) cc_final: 0.8733 (mtp) REVERT: a 306 MET cc_start: 0.8258 (mmt) cc_final: 0.7980 (mpt) REVERT: e 446 TYR cc_start: 0.8859 (m-80) cc_final: 0.8657 (m-80) REVERT: g 415 GLU cc_start: 0.8498 (mp0) cc_final: 0.8150 (mp0) REVERT: g 527 LYS cc_start: 0.9059 (mmmm) cc_final: 0.8800 (mmmm) REVERT: h 194 MET cc_start: 0.8905 (mmp) cc_final: 0.8699 (mmp) REVERT: z 303 ASP cc_start: 0.8558 (t70) cc_final: 0.8287 (t0) REVERT: z 358 GLU cc_start: 0.7987 (pm20) cc_final: 0.7662 (pm20) outliers start: 0 outliers final: 2 residues processed: 551 average time/residue: 1.5715 time to fit residues: 1114.8296 Evaluate side-chains 434 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 432 time to evaluate : 5.792 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain Q residue 208 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 717 optimal weight: 9.9990 chunk 644 optimal weight: 6.9990 chunk 357 optimal weight: 2.9990 chunk 220 optimal weight: 9.9990 chunk 434 optimal weight: 1.9990 chunk 344 optimal weight: 0.8980 chunk 666 optimal weight: 7.9990 chunk 257 optimal weight: 7.9990 chunk 405 optimal weight: 3.9990 chunk 495 optimal weight: 7.9990 chunk 771 optimal weight: 7.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN E 435 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN Z 84 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 347 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN e 435 GLN h 331 GLN q 303 HIS q 316 ASN z 23 ASN z 84 GLN N 275 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.064307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2664 r_free = 0.2664 target = 0.052564 restraints weight = 205263.045| |-----------------------------------------------------------------------------| r_work (start): 0.2673 rms_B_bonded: 3.25 r_work: 0.2529 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.0840 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 66752 Z= 0.310 Angle : 0.589 11.332 90142 Z= 0.294 Chirality : 0.043 0.175 10746 Planarity : 0.004 0.056 11504 Dihedral : 7.457 177.627 9284 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.62 % Allowed : 5.85 % Favored : 93.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.63 (0.09), residues: 8543 helix: 2.37 (0.08), residues: 4405 sheet: 0.24 (0.16), residues: 1140 loop : -0.53 (0.11), residues: 2998 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.012 0.001 HIS Z 161 PHE 0.022 0.001 PHE H 174 TYR 0.020 0.001 TYR z 351 ARG 0.009 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 494 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 450 time to evaluate : 5.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.8193 (m-30) cc_final: 0.7728 (m-30) REVERT: A 306 MET cc_start: 0.8988 (mtp) cc_final: 0.8520 (mtm) REVERT: A 386 ASP cc_start: 0.9074 (m-30) cc_final: 0.8794 (m-30) REVERT: A 508 ILE cc_start: 0.8909 (tp) cc_final: 0.8626 (tp) REVERT: D 25 GLN cc_start: 0.9276 (tp-100) cc_final: 0.8912 (tp-100) REVERT: D 28 ASP cc_start: 0.8460 (t0) cc_final: 0.8092 (t0) REVERT: D 57 MET cc_start: 0.9201 (mmm) cc_final: 0.8973 (mmm) REVERT: E 468 MET cc_start: 0.8717 (mtt) cc_final: 0.8252 (mtt) REVERT: G 47 MET cc_start: 0.8863 (OUTLIER) cc_final: 0.8354 (mtp) REVERT: G 52 ASP cc_start: 0.8820 (t0) cc_final: 0.8589 (t0) REVERT: G 364 THR cc_start: 0.9057 (p) cc_final: 0.8849 (p) REVERT: H 14 ASP cc_start: 0.8788 (t70) cc_final: 0.8457 (t0) REVERT: H 70 ASP cc_start: 0.8247 (t70) cc_final: 0.7622 (t70) REVERT: H 81 ASP cc_start: 0.8803 (m-30) cc_final: 0.8478 (m-30) REVERT: Q 200 ASP cc_start: 0.9385 (m-30) cc_final: 0.8741 (t0) REVERT: Q 357 ASP cc_start: 0.9031 (t0) cc_final: 0.8757 (t0) REVERT: Z 161 HIS cc_start: 0.6249 (OUTLIER) cc_final: 0.5887 (t-170) REVERT: Z 337 ASP cc_start: 0.8655 (m-30) cc_final: 0.8431 (m-30) REVERT: a 51 ASP cc_start: 0.8852 (m-30) cc_final: 0.8434 (m-30) REVERT: a 306 MET cc_start: 0.8480 (mmt) cc_final: 0.8127 (mpt) REVERT: b 415 MET cc_start: 0.9404 (mmm) cc_final: 0.9124 (mmp) REVERT: g 15 LYS cc_start: 0.8474 (OUTLIER) cc_final: 0.8239 (mmmt) REVERT: g 47 MET cc_start: 0.9032 (OUTLIER) cc_final: 0.8245 (mtp) REVERT: g 415 GLU cc_start: 0.9131 (mp0) cc_final: 0.8693 (mp0) REVERT: g 527 LYS cc_start: 0.9001 (mmmm) cc_final: 0.8678 (mmmm) REVERT: h 7 ILE cc_start: 0.8257 (OUTLIER) cc_final: 0.7989 (pp) REVERT: h 194 MET cc_start: 0.9175 (mmp) cc_final: 0.8910 (mmp) REVERT: z 358 GLU cc_start: 0.8138 (pm20) cc_final: 0.7699 (pm20) REVERT: N 267 ASP cc_start: 0.7828 (t0) cc_final: 0.7612 (t0) REVERT: N 272 GLN cc_start: 0.7615 (mm110) cc_final: 0.7050 (mm110) outliers start: 44 outliers final: 20 residues processed: 470 average time/residue: 1.5001 time to fit residues: 918.6828 Evaluate side-chains 442 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 417 time to evaluate : 5.783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 77 ASP Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain e residue 368 LYS Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain N residue 264 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 296 optimal weight: 9.9990 chunk 726 optimal weight: 8.9990 chunk 382 optimal weight: 7.9990 chunk 733 optimal weight: 4.9990 chunk 743 optimal weight: 9.9990 chunk 589 optimal weight: 4.9990 chunk 586 optimal weight: 4.9990 chunk 134 optimal weight: 0.9990 chunk 451 optimal weight: 10.0000 chunk 606 optimal weight: 2.9990 chunk 780 optimal weight: 0.7980 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 347 HIS h 459 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2911 r_free = 0.2911 target = 0.064187 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2668 r_free = 0.2668 target = 0.052652 restraints weight = 187494.059| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 3.07 r_work: 0.2540 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2540 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 66752 Z= 0.274 Angle : 0.561 10.402 90142 Z= 0.278 Chirality : 0.042 0.166 10746 Planarity : 0.003 0.058 11504 Dihedral : 7.250 178.561 9280 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.20 % Favored : 96.80 % Rotamer: Outliers : 0.87 % Allowed : 7.57 % Favored : 91.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 8543 helix: 2.41 (0.08), residues: 4395 sheet: 0.22 (0.16), residues: 1124 loop : -0.54 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.012 0.001 HIS Z 161 PHE 0.021 0.001 PHE H 174 TYR 0.020 0.001 TYR z 351 ARG 0.007 0.000 ARG d 27 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 450 time to evaluate : 5.694 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8257 (OUTLIER) cc_final: 0.8034 (p) REVERT: A 306 MET cc_start: 0.8996 (mtp) cc_final: 0.8522 (mtm) REVERT: A 386 ASP cc_start: 0.9069 (m-30) cc_final: 0.8815 (m-30) REVERT: A 508 ILE cc_start: 0.8889 (tp) cc_final: 0.8599 (tp) REVERT: B 17 ASP cc_start: 0.8547 (t0) cc_final: 0.7505 (p0) REVERT: D 25 GLN cc_start: 0.9259 (tp-100) cc_final: 0.8892 (tp-100) REVERT: D 28 ASP cc_start: 0.8378 (t0) cc_final: 0.7948 (t70) REVERT: D 57 MET cc_start: 0.9130 (mmm) cc_final: 0.8847 (mmm) REVERT: D 93 GLU cc_start: 0.9153 (mm-30) cc_final: 0.8656 (mm-30) REVERT: E 468 MET cc_start: 0.8754 (mtt) cc_final: 0.8471 (mtp) REVERT: G 47 MET cc_start: 0.8826 (OUTLIER) cc_final: 0.8259 (mtp) REVERT: G 52 ASP cc_start: 0.8895 (t0) cc_final: 0.8433 (t0) REVERT: G 54 MET cc_start: 0.8780 (mmm) cc_final: 0.8315 (mpm) REVERT: H 14 ASP cc_start: 0.8820 (t70) cc_final: 0.8477 (t0) REVERT: H 70 ASP cc_start: 0.8273 (t70) cc_final: 0.7571 (t70) REVERT: H 81 ASP cc_start: 0.8837 (m-30) cc_final: 0.8520 (m-30) REVERT: H 524 ARG cc_start: 0.7207 (mmm160) cc_final: 0.7002 (mmm160) REVERT: Q 200 ASP cc_start: 0.9384 (m-30) cc_final: 0.8734 (t0) REVERT: Q 357 ASP cc_start: 0.9012 (t0) cc_final: 0.8648 (t0) REVERT: Z 67 MET cc_start: 0.8663 (mtm) cc_final: 0.8347 (mtp) REVERT: Z 161 HIS cc_start: 0.6290 (OUTLIER) cc_final: 0.5967 (t-170) REVERT: Z 337 ASP cc_start: 0.8681 (m-30) cc_final: 0.8382 (m-30) REVERT: a 156 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8618 (mtp) REVERT: a 306 MET cc_start: 0.8604 (mmt) cc_final: 0.8378 (mmt) REVERT: d 27 ARG cc_start: 0.8406 (mmm-85) cc_final: 0.8199 (mmm-85) REVERT: g 15 LYS cc_start: 0.8513 (OUTLIER) cc_final: 0.8269 (mmmt) REVERT: g 47 MET cc_start: 0.9078 (mtp) cc_final: 0.8410 (mtp) REVERT: g 415 GLU cc_start: 0.9142 (mp0) cc_final: 0.8667 (mp0) REVERT: g 527 LYS cc_start: 0.9011 (mmmm) cc_final: 0.8695 (mmmm) REVERT: h 14 ASP cc_start: 0.8498 (t0) cc_final: 0.8202 (t0) REVERT: h 194 MET cc_start: 0.9162 (mmp) cc_final: 0.8937 (mmp) REVERT: z 244 VAL cc_start: 0.8527 (OUTLIER) cc_final: 0.8231 (t) REVERT: z 358 GLU cc_start: 0.8138 (pm20) cc_final: 0.7690 (pm20) REVERT: N 267 ASP cc_start: 0.7941 (t0) cc_final: 0.7717 (t0) REVERT: N 272 GLN cc_start: 0.7713 (mm110) cc_final: 0.7070 (mm110) outliers start: 62 outliers final: 21 residues processed: 482 average time/residue: 1.5280 time to fit residues: 956.7246 Evaluate side-chains 454 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 427 time to evaluate : 5.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 553 optimal weight: 2.9990 chunk 452 optimal weight: 0.3980 chunk 532 optimal weight: 10.0000 chunk 607 optimal weight: 10.0000 chunk 398 optimal weight: 5.9990 chunk 171 optimal weight: 7.9990 chunk 581 optimal weight: 6.9990 chunk 135 optimal weight: 4.9990 chunk 843 optimal weight: 4.9990 chunk 664 optimal weight: 3.9990 chunk 41 optimal weight: 1.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 352 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.064259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2665 r_free = 0.2665 target = 0.052693 restraints weight = 186853.049| |-----------------------------------------------------------------------------| r_work (start): 0.2679 rms_B_bonded: 3.11 r_work: 0.2539 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2539 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2522 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2522 r_free = 0.2522 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2522 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.1106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 66752 Z= 0.268 Angle : 0.558 11.140 90142 Z= 0.275 Chirality : 0.042 0.178 10746 Planarity : 0.003 0.058 11504 Dihedral : 7.069 172.030 9280 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 0.87 % Allowed : 8.86 % Favored : 90.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.09), residues: 8543 helix: 2.43 (0.08), residues: 4398 sheet: 0.16 (0.16), residues: 1133 loop : -0.53 (0.11), residues: 3012 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.014 0.001 HIS z 161 PHE 0.022 0.001 PHE H 174 TYR 0.022 0.001 TYR z 351 ARG 0.010 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 510 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 448 time to evaluate : 5.830 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8250 (OUTLIER) cc_final: 0.8021 (p) REVERT: A 306 MET cc_start: 0.8988 (mtp) cc_final: 0.8521 (mtm) REVERT: A 386 ASP cc_start: 0.9066 (m-30) cc_final: 0.8827 (m-30) REVERT: A 508 ILE cc_start: 0.8878 (tp) cc_final: 0.8594 (tp) REVERT: B 353 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9173 (tpt) REVERT: B 480 MET cc_start: 0.9351 (OUTLIER) cc_final: 0.8801 (mmp) REVERT: D 25 GLN cc_start: 0.9262 (tp-100) cc_final: 0.8904 (tp-100) REVERT: D 57 MET cc_start: 0.9043 (mmm) cc_final: 0.8755 (mmm) REVERT: D 93 GLU cc_start: 0.9133 (mm-30) cc_final: 0.8613 (mm-30) REVERT: E 468 MET cc_start: 0.8779 (mtt) cc_final: 0.8421 (mtp) REVERT: G 47 MET cc_start: 0.8821 (OUTLIER) cc_final: 0.8273 (mtp) REVERT: G 52 ASP cc_start: 0.8898 (t0) cc_final: 0.8688 (t0) REVERT: H 14 ASP cc_start: 0.8808 (t70) cc_final: 0.8457 (t0) REVERT: H 70 ASP cc_start: 0.8341 (t70) cc_final: 0.7643 (t70) REVERT: H 81 ASP cc_start: 0.8845 (m-30) cc_final: 0.8526 (m-30) REVERT: H 185 MET cc_start: 0.8743 (mtp) cc_final: 0.8522 (mtp) REVERT: H 524 ARG cc_start: 0.7252 (mmm160) cc_final: 0.7036 (mmm160) REVERT: Q 200 ASP cc_start: 0.9383 (m-30) cc_final: 0.8735 (t0) REVERT: Q 357 ASP cc_start: 0.9009 (t0) cc_final: 0.8629 (t0) REVERT: Z 337 ASP cc_start: 0.8727 (m-30) cc_final: 0.8419 (m-30) REVERT: a 51 ASP cc_start: 0.8861 (m-30) cc_final: 0.8464 (m-30) REVERT: a 156 MET cc_start: 0.8965 (OUTLIER) cc_final: 0.8530 (mtp) REVERT: a 306 MET cc_start: 0.8647 (mmt) cc_final: 0.8382 (mmt) REVERT: b 19 GLU cc_start: 0.8302 (OUTLIER) cc_final: 0.8035 (mt-10) REVERT: d 27 ARG cc_start: 0.8492 (mmm-85) cc_final: 0.8204 (mmm-85) REVERT: e 4 MET cc_start: 0.5394 (tmm) cc_final: 0.5144 (tmm) REVERT: g 15 LYS cc_start: 0.8508 (OUTLIER) cc_final: 0.8284 (mmmt) REVERT: g 47 MET cc_start: 0.9020 (OUTLIER) cc_final: 0.8218 (mtp) REVERT: g 415 GLU cc_start: 0.9153 (mp0) cc_final: 0.8660 (mp0) REVERT: g 527 LYS cc_start: 0.9006 (mmmm) cc_final: 0.8689 (mmmm) REVERT: h 7 ILE cc_start: 0.8319 (OUTLIER) cc_final: 0.8097 (pp) REVERT: h 14 ASP cc_start: 0.8505 (t0) cc_final: 0.8143 (t0) REVERT: h 194 MET cc_start: 0.9159 (mmp) cc_final: 0.8942 (mmp) REVERT: z 358 GLU cc_start: 0.8196 (pm20) cc_final: 0.7710 (pm20) REVERT: N 267 ASP cc_start: 0.8051 (t0) cc_final: 0.7808 (t0) outliers start: 62 outliers final: 25 residues processed: 484 average time/residue: 1.5018 time to fit residues: 952.8020 Evaluate side-chains 459 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 425 time to evaluate : 5.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 31 ILE Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 289 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 280 optimal weight: 7.9990 chunk 690 optimal weight: 3.9990 chunk 154 optimal weight: 2.9990 chunk 389 optimal weight: 8.9990 chunk 528 optimal weight: 7.9990 chunk 308 optimal weight: 7.9990 chunk 401 optimal weight: 8.9990 chunk 813 optimal weight: 1.9990 chunk 293 optimal weight: 3.9990 chunk 352 optimal weight: 1.9990 chunk 557 optimal weight: 0.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN H 119 GLN Z 161 HIS g 302 HIS z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2917 r_free = 0.2917 target = 0.064624 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2680 r_free = 0.2680 target = 0.053334 restraints weight = 166979.345| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.92 r_work: 0.2558 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2558 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8524 moved from start: 0.1154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 66752 Z= 0.234 Angle : 0.548 12.380 90142 Z= 0.269 Chirality : 0.042 0.179 10746 Planarity : 0.003 0.058 11504 Dihedral : 6.923 170.662 9280 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 1.04 % Allowed : 9.69 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8543 helix: 2.47 (0.08), residues: 4400 sheet: 0.16 (0.16), residues: 1127 loop : -0.51 (0.11), residues: 3016 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.013 0.001 HIS Z 161 PHE 0.023 0.001 PHE H 174 TYR 0.022 0.001 TYR z 351 ARG 0.009 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 521 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 447 time to evaluate : 6.380 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8016 (p) REVERT: A 306 MET cc_start: 0.8982 (mtp) cc_final: 0.8540 (mtm) REVERT: A 386 ASP cc_start: 0.9055 (m-30) cc_final: 0.8820 (m-30) REVERT: A 430 MET cc_start: 0.8762 (tpp) cc_final: 0.8470 (ttp) REVERT: A 508 ILE cc_start: 0.8858 (tp) cc_final: 0.8583 (tp) REVERT: B 480 MET cc_start: 0.9318 (OUTLIER) cc_final: 0.8674 (mmp) REVERT: D 25 GLN cc_start: 0.9249 (tp-100) cc_final: 0.8820 (tp-100) REVERT: D 57 MET cc_start: 0.8968 (mmm) cc_final: 0.8723 (mmm) REVERT: D 65 LYS cc_start: 0.9145 (OUTLIER) cc_final: 0.8898 (mmmt) REVERT: D 93 GLU cc_start: 0.9120 (mm-30) cc_final: 0.8576 (mm-30) REVERT: E 468 MET cc_start: 0.8749 (mtt) cc_final: 0.8442 (mtp) REVERT: G 46 MET cc_start: 0.9192 (mmm) cc_final: 0.8980 (mmm) REVERT: G 47 MET cc_start: 0.8787 (OUTLIER) cc_final: 0.8244 (mtp) REVERT: G 52 ASP cc_start: 0.8867 (t0) cc_final: 0.8660 (t0) REVERT: H 14 ASP cc_start: 0.8766 (t70) cc_final: 0.8410 (t0) REVERT: H 70 ASP cc_start: 0.8301 (t70) cc_final: 0.7537 (t70) REVERT: H 81 ASP cc_start: 0.8824 (m-30) cc_final: 0.8501 (m-30) REVERT: H 185 MET cc_start: 0.8797 (mtp) cc_final: 0.8551 (mtp) REVERT: Q 200 ASP cc_start: 0.9374 (m-30) cc_final: 0.8725 (t0) REVERT: Q 276 MET cc_start: 0.9194 (tpp) cc_final: 0.8987 (tpt) REVERT: Q 357 ASP cc_start: 0.8997 (t0) cc_final: 0.8542 (t0) REVERT: Q 492 MET cc_start: 0.8186 (OUTLIER) cc_final: 0.7367 (mtt) REVERT: Z 337 ASP cc_start: 0.8737 (m-30) cc_final: 0.8395 (m-30) REVERT: a 51 ASP cc_start: 0.8834 (m-30) cc_final: 0.8415 (m-30) REVERT: a 156 MET cc_start: 0.8906 (OUTLIER) cc_final: 0.8638 (mtp) REVERT: a 306 MET cc_start: 0.8612 (mmt) cc_final: 0.8396 (mmt) REVERT: a 416 GLU cc_start: 0.8842 (mp0) cc_final: 0.8403 (mp0) REVERT: b 19 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.7966 (mt-10) REVERT: d 27 ARG cc_start: 0.8586 (mmm-85) cc_final: 0.8270 (mmm-85) REVERT: e 4 MET cc_start: 0.5313 (tmm) cc_final: 0.4919 (tmm) REVERT: g 15 LYS cc_start: 0.8500 (OUTLIER) cc_final: 0.8262 (mmmt) REVERT: g 47 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8207 (mtp) REVERT: g 219 MET cc_start: 0.9529 (ttt) cc_final: 0.9215 (tmm) REVERT: g 415 GLU cc_start: 0.9132 (mp0) cc_final: 0.8644 (mp0) REVERT: g 527 LYS cc_start: 0.8989 (mmmm) cc_final: 0.8681 (mmmm) REVERT: h 14 ASP cc_start: 0.8422 (t0) cc_final: 0.7996 (t0) REVERT: z 244 VAL cc_start: 0.8495 (OUTLIER) cc_final: 0.8214 (t) REVERT: z 358 GLU cc_start: 0.8228 (pm20) cc_final: 0.7788 (pm20) REVERT: N 267 ASP cc_start: 0.8082 (t0) cc_final: 0.7856 (t0) outliers start: 74 outliers final: 30 residues processed: 489 average time/residue: 1.4996 time to fit residues: 958.0163 Evaluate side-chains 468 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 428 time to evaluate : 5.774 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 713 optimal weight: 0.0020 chunk 651 optimal weight: 1.9990 chunk 402 optimal weight: 6.9990 chunk 823 optimal weight: 6.9990 chunk 388 optimal weight: 7.9990 chunk 10 optimal weight: 7.9990 chunk 748 optimal weight: 0.0470 chunk 88 optimal weight: 0.9980 chunk 658 optimal weight: 6.9990 chunk 771 optimal weight: 10.0000 chunk 200 optimal weight: 5.9990 overall best weight: 1.8090 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN Z 161 HIS q 53 ASN z 161 HIS z 497 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2935 r_free = 0.2935 target = 0.065460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.053963 restraints weight = 183309.788| |-----------------------------------------------------------------------------| r_work (start): 0.2707 rms_B_bonded: 3.04 r_work: 0.2569 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8517 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 66752 Z= 0.194 Angle : 0.536 10.941 90142 Z= 0.262 Chirality : 0.041 0.178 10746 Planarity : 0.003 0.103 11504 Dihedral : 6.757 167.749 9280 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 0.88 % Allowed : 10.40 % Favored : 88.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.09), residues: 8543 helix: 2.51 (0.08), residues: 4410 sheet: 0.20 (0.16), residues: 1118 loop : -0.49 (0.11), residues: 3015 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.015 0.001 HIS z 161 PHE 0.022 0.001 PHE H 174 TYR 0.024 0.001 TYR z 351 ARG 0.013 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 527 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 464 time to evaluate : 5.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8016 (p) REVERT: A 306 MET cc_start: 0.8963 (mtp) cc_final: 0.8529 (mtm) REVERT: A 386 ASP cc_start: 0.9050 (m-30) cc_final: 0.8815 (m-30) REVERT: A 430 MET cc_start: 0.8784 (tpp) cc_final: 0.8469 (ttp) REVERT: A 508 ILE cc_start: 0.8842 (tp) cc_final: 0.8616 (tp) REVERT: B 17 ASP cc_start: 0.8502 (t0) cc_final: 0.7473 (p0) REVERT: B 480 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8669 (mmp) REVERT: D 25 GLN cc_start: 0.9238 (tp-100) cc_final: 0.8867 (tp-100) REVERT: D 57 MET cc_start: 0.8970 (mmm) cc_final: 0.8704 (mmm) REVERT: D 93 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8592 (mm-30) REVERT: E 468 MET cc_start: 0.8752 (mtt) cc_final: 0.8486 (mtp) REVERT: E 532 ASP cc_start: 0.8678 (OUTLIER) cc_final: 0.8436 (m-30) REVERT: G 46 MET cc_start: 0.9210 (mmm) cc_final: 0.9001 (mmm) REVERT: G 47 MET cc_start: 0.8756 (mtm) cc_final: 0.8149 (mtp) REVERT: H 14 ASP cc_start: 0.8804 (t70) cc_final: 0.8440 (t0) REVERT: H 70 ASP cc_start: 0.8318 (t70) cc_final: 0.7551 (t70) REVERT: H 81 ASP cc_start: 0.8844 (m-30) cc_final: 0.8523 (m-30) REVERT: H 185 MET cc_start: 0.8852 (mtp) cc_final: 0.8614 (mtp) REVERT: H 440 LYS cc_start: 0.9197 (tttt) cc_final: 0.8872 (tppt) REVERT: Q 200 ASP cc_start: 0.9378 (m-30) cc_final: 0.8732 (t0) REVERT: Q 357 ASP cc_start: 0.8968 (t0) cc_final: 0.8537 (t0) REVERT: Q 492 MET cc_start: 0.8117 (OUTLIER) cc_final: 0.7302 (mtt) REVERT: Z 337 ASP cc_start: 0.8780 (m-30) cc_final: 0.8448 (m-30) REVERT: a 51 ASP cc_start: 0.8838 (m-30) cc_final: 0.8443 (m-30) REVERT: a 156 MET cc_start: 0.8846 (OUTLIER) cc_final: 0.8591 (mtp) REVERT: a 416 GLU cc_start: 0.8830 (mp0) cc_final: 0.8407 (mp0) REVERT: b 19 GLU cc_start: 0.8274 (OUTLIER) cc_final: 0.7990 (mt-10) REVERT: d 27 ARG cc_start: 0.8583 (mmm-85) cc_final: 0.8257 (mmm-85) REVERT: e 4 MET cc_start: 0.5411 (tmm) cc_final: 0.4980 (tmm) REVERT: g 15 LYS cc_start: 0.8512 (OUTLIER) cc_final: 0.8278 (mmmt) REVERT: g 47 MET cc_start: 0.9037 (OUTLIER) cc_final: 0.8217 (mtp) REVERT: g 219 MET cc_start: 0.9513 (OUTLIER) cc_final: 0.9183 (tmm) REVERT: g 415 GLU cc_start: 0.9145 (mp0) cc_final: 0.8646 (mp0) REVERT: g 527 LYS cc_start: 0.8998 (mmmm) cc_final: 0.8673 (mmmm) REVERT: h 14 ASP cc_start: 0.8457 (t0) cc_final: 0.8020 (t0) REVERT: z 244 VAL cc_start: 0.8451 (OUTLIER) cc_final: 0.8158 (t) REVERT: z 358 GLU cc_start: 0.8267 (pm20) cc_final: 0.7824 (pm20) REVERT: N 267 ASP cc_start: 0.8077 (t0) cc_final: 0.7823 (t0) outliers start: 63 outliers final: 30 residues processed: 501 average time/residue: 1.4610 time to fit residues: 964.7553 Evaluate side-chains 475 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 435 time to evaluate : 5.798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 532 ASP Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 844 optimal weight: 40.0000 chunk 33 optimal weight: 8.9990 chunk 294 optimal weight: 1.9990 chunk 176 optimal weight: 6.9990 chunk 623 optimal weight: 3.9990 chunk 771 optimal weight: 10.0000 chunk 680 optimal weight: 7.9990 chunk 613 optimal weight: 10.0000 chunk 446 optimal weight: 6.9990 chunk 329 optimal weight: 10.0000 chunk 144 optimal weight: 0.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 400 ASN h 501 ASN z 161 HIS N 275 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.063260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2642 r_free = 0.2642 target = 0.051612 restraints weight = 198353.905| |-----------------------------------------------------------------------------| r_work (start): 0.2652 rms_B_bonded: 3.16 r_work: 0.2507 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2495 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2495 r_free = 0.2495 target_work(ls_wunit_k1) = 0.046 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2495 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.1300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 66752 Z= 0.370 Angle : 0.602 15.696 90142 Z= 0.295 Chirality : 0.043 0.174 10746 Planarity : 0.003 0.065 11504 Dihedral : 6.811 167.615 9280 Min Nonbonded Distance : 1.831 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 1.06 % Allowed : 10.71 % Favored : 88.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.09), residues: 8543 helix: 2.41 (0.08), residues: 4407 sheet: 0.09 (0.16), residues: 1128 loop : -0.52 (0.11), residues: 3008 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP e 304 HIS 0.013 0.001 HIS z 161 PHE 0.024 0.002 PHE H 174 TYR 0.024 0.001 TYR z 351 ARG 0.014 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 507 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 431 time to evaluate : 5.840 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8233 (OUTLIER) cc_final: 0.7967 (p) REVERT: A 306 MET cc_start: 0.9021 (mtp) cc_final: 0.8564 (mtm) REVERT: A 386 ASP cc_start: 0.9061 (m-30) cc_final: 0.8843 (m-30) REVERT: A 430 MET cc_start: 0.8874 (tpp) cc_final: 0.8525 (ttp) REVERT: A 508 ILE cc_start: 0.8902 (tp) cc_final: 0.8621 (tp) REVERT: B 310 MET cc_start: 0.8980 (ttm) cc_final: 0.8743 (ttp) REVERT: B 480 MET cc_start: 0.9359 (OUTLIER) cc_final: 0.8772 (mmp) REVERT: D 25 GLN cc_start: 0.9255 (tp-100) cc_final: 0.8921 (tp-100) REVERT: D 57 MET cc_start: 0.8908 (mmm) cc_final: 0.8621 (mmm) REVERT: D 65 LYS cc_start: 0.9140 (OUTLIER) cc_final: 0.8882 (mmmt) REVERT: D 93 GLU cc_start: 0.9168 (mm-30) cc_final: 0.8570 (mm-30) REVERT: E 23 ASP cc_start: 0.9281 (m-30) cc_final: 0.8988 (p0) REVERT: E 468 MET cc_start: 0.8778 (mtt) cc_final: 0.8531 (mtp) REVERT: G 47 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8326 (mtp) REVERT: G 52 ASP cc_start: 0.8573 (t0) cc_final: 0.7878 (t0) REVERT: G 54 MET cc_start: 0.8689 (mmm) cc_final: 0.8455 (mpm) REVERT: G 442 GLN cc_start: 0.8672 (OUTLIER) cc_final: 0.8376 (mp10) REVERT: H 14 ASP cc_start: 0.8786 (t70) cc_final: 0.8432 (t0) REVERT: H 70 ASP cc_start: 0.8322 (t70) cc_final: 0.7535 (t70) REVERT: H 81 ASP cc_start: 0.8833 (m-30) cc_final: 0.8510 (m-30) REVERT: H 185 MET cc_start: 0.8902 (mtp) cc_final: 0.8689 (mtm) REVERT: Q 200 ASP cc_start: 0.9390 (m-30) cc_final: 0.8739 (t0) REVERT: Q 357 ASP cc_start: 0.8993 (t0) cc_final: 0.8619 (t0) REVERT: Q 492 MET cc_start: 0.8239 (OUTLIER) cc_final: 0.7401 (mtt) REVERT: Z 67 MET cc_start: 0.8622 (OUTLIER) cc_final: 0.8267 (mtp) REVERT: Z 161 HIS cc_start: 0.6273 (OUTLIER) cc_final: 0.5962 (t-170) REVERT: Z 196 MET cc_start: 0.8371 (mtp) cc_final: 0.8151 (mtm) REVERT: Z 337 ASP cc_start: 0.8788 (m-30) cc_final: 0.8465 (m-30) REVERT: a 51 ASP cc_start: 0.8840 (m-30) cc_final: 0.8425 (m-30) REVERT: a 156 MET cc_start: 0.8962 (OUTLIER) cc_final: 0.8547 (mtp) REVERT: a 416 GLU cc_start: 0.8880 (mp0) cc_final: 0.8454 (mp0) REVERT: b 19 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.8051 (mt-10) REVERT: e 4 MET cc_start: 0.5495 (tmm) cc_final: 0.5064 (tmm) REVERT: g 15 LYS cc_start: 0.8507 (OUTLIER) cc_final: 0.8275 (mmmt) REVERT: g 47 MET cc_start: 0.9007 (OUTLIER) cc_final: 0.8215 (mtp) REVERT: g 219 MET cc_start: 0.9534 (OUTLIER) cc_final: 0.8926 (tmm) REVERT: g 415 GLU cc_start: 0.9140 (mp0) cc_final: 0.8692 (mp0) REVERT: g 527 LYS cc_start: 0.8986 (mmmm) cc_final: 0.8664 (mmmm) REVERT: h 14 ASP cc_start: 0.8449 (t0) cc_final: 0.8006 (t0) REVERT: q 335 ARG cc_start: 0.8467 (mmt180) cc_final: 0.8113 (mtt90) REVERT: z 10 LYS cc_start: 0.8602 (pttm) cc_final: 0.8369 (pmtt) REVERT: z 244 VAL cc_start: 0.8512 (OUTLIER) cc_final: 0.8250 (t) REVERT: z 358 GLU cc_start: 0.8330 (pm20) cc_final: 0.7834 (pm20) REVERT: N 267 ASP cc_start: 0.8154 (t0) cc_final: 0.7902 (t0) outliers start: 76 outliers final: 38 residues processed: 478 average time/residue: 1.5106 time to fit residues: 942.7182 Evaluate side-chains 474 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 422 time to evaluate : 5.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain G residue 442 GLN Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 311 MET Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 67 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 246 SER Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 41 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 669 optimal weight: 2.9990 chunk 447 optimal weight: 5.9990 chunk 296 optimal weight: 9.9990 chunk 1 optimal weight: 0.8980 chunk 92 optimal weight: 3.9990 chunk 763 optimal weight: 9.9990 chunk 484 optimal weight: 0.8980 chunk 556 optimal weight: 7.9990 chunk 272 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 chunk 673 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS h 501 ASN z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2934 r_free = 0.2934 target = 0.065429 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2694 r_free = 0.2694 target = 0.053904 restraints weight = 186209.868| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 3.07 r_work: 0.2568 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2568 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 66752 Z= 0.181 Angle : 0.545 13.626 90142 Z= 0.266 Chirality : 0.041 0.177 10746 Planarity : 0.003 0.072 11504 Dihedral : 6.632 163.318 9280 Min Nonbonded Distance : 1.904 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.90 % Allowed : 11.25 % Favored : 87.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.09), residues: 8543 helix: 2.51 (0.08), residues: 4411 sheet: 0.17 (0.16), residues: 1108 loop : -0.49 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.017 0.001 HIS z 161 PHE 0.024 0.001 PHE H 174 TYR 0.022 0.001 TYR z 351 ARG 0.017 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 512 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 64 poor density : 448 time to evaluate : 5.788 Fit side-chains revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8256 (OUTLIER) cc_final: 0.8006 (p) REVERT: A 306 MET cc_start: 0.8978 (mtp) cc_final: 0.8527 (mtm) REVERT: A 386 ASP cc_start: 0.9039 (m-30) cc_final: 0.8801 (m-30) REVERT: A 430 MET cc_start: 0.8826 (tpp) cc_final: 0.8489 (ttp) REVERT: A 508 ILE cc_start: 0.8834 (tp) cc_final: 0.8554 (tp) REVERT: B 480 MET cc_start: 0.9338 (OUTLIER) cc_final: 0.8680 (mmp) REVERT: D 25 GLN cc_start: 0.9226 (tp-100) cc_final: 0.8813 (tp-100) REVERT: D 57 MET cc_start: 0.8941 (mmm) cc_final: 0.8651 (mmm) REVERT: D 65 LYS cc_start: 0.9170 (OUTLIER) cc_final: 0.8913 (mmmt) REVERT: D 93 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8567 (mm-30) REVERT: E 23 ASP cc_start: 0.9275 (m-30) cc_final: 0.8968 (p0) REVERT: E 468 MET cc_start: 0.8766 (mtt) cc_final: 0.8474 (mtp) REVERT: G 47 MET cc_start: 0.8773 (OUTLIER) cc_final: 0.8204 (mtp) REVERT: G 52 ASP cc_start: 0.8623 (t0) cc_final: 0.7854 (t0) REVERT: H 14 ASP cc_start: 0.8804 (t70) cc_final: 0.8441 (t0) REVERT: H 70 ASP cc_start: 0.8325 (t70) cc_final: 0.7552 (t70) REVERT: H 81 ASP cc_start: 0.8844 (m-30) cc_final: 0.8523 (m-30) REVERT: H 185 MET cc_start: 0.8903 (mtp) cc_final: 0.8651 (mtm) REVERT: Q 200 ASP cc_start: 0.9374 (m-30) cc_final: 0.8728 (t0) REVERT: Q 357 ASP cc_start: 0.8880 (t0) cc_final: 0.8478 (t0) REVERT: Z 67 MET cc_start: 0.8569 (mtm) cc_final: 0.8196 (mtp) REVERT: Z 337 ASP cc_start: 0.8787 (m-30) cc_final: 0.8450 (m-30) REVERT: a 51 ASP cc_start: 0.8842 (m-30) cc_final: 0.8443 (m-30) REVERT: a 156 MET cc_start: 0.8822 (OUTLIER) cc_final: 0.8510 (mtp) REVERT: a 416 GLU cc_start: 0.8823 (mp0) cc_final: 0.8397 (mp0) REVERT: b 19 GLU cc_start: 0.8296 (OUTLIER) cc_final: 0.8006 (mt-10) REVERT: d 27 ARG cc_start: 0.8574 (mmm-85) cc_final: 0.8303 (mmm-85) REVERT: e 4 MET cc_start: 0.5554 (tmm) cc_final: 0.5138 (tmm) REVERT: g 15 LYS cc_start: 0.8525 (OUTLIER) cc_final: 0.8294 (mmmt) REVERT: g 47 MET cc_start: 0.8979 (OUTLIER) cc_final: 0.8138 (mtp) REVERT: g 219 MET cc_start: 0.9513 (OUTLIER) cc_final: 0.9244 (tmm) REVERT: g 415 GLU cc_start: 0.9163 (mp0) cc_final: 0.8706 (mp0) REVERT: g 527 LYS cc_start: 0.8999 (mmmm) cc_final: 0.8688 (mmmm) REVERT: h 14 ASP cc_start: 0.8456 (t0) cc_final: 0.8037 (t0) REVERT: h 524 ARG cc_start: 0.8031 (tmt170) cc_final: 0.7548 (tmm160) REVERT: z 10 LYS cc_start: 0.8603 (pttm) cc_final: 0.8385 (pmtt) REVERT: z 244 VAL cc_start: 0.8459 (OUTLIER) cc_final: 0.8184 (t) REVERT: z 358 GLU cc_start: 0.8318 (pm20) cc_final: 0.7819 (pm20) REVERT: N 267 ASP cc_start: 0.8092 (t0) cc_final: 0.7868 (t0) outliers start: 64 outliers final: 30 residues processed: 490 average time/residue: 1.4701 time to fit residues: 947.2046 Evaluate side-chains 472 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 432 time to evaluate : 5.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 468 MET Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 572 optimal weight: 10.0000 chunk 320 optimal weight: 7.9990 chunk 590 optimal weight: 5.9990 chunk 678 optimal weight: 7.9990 chunk 169 optimal weight: 3.9990 chunk 422 optimal weight: 0.0870 chunk 771 optimal weight: 7.9990 chunk 377 optimal weight: 5.9990 chunk 181 optimal weight: 6.9990 chunk 350 optimal weight: 5.9990 chunk 397 optimal weight: 1.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2904 r_free = 0.2904 target = 0.063907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2660 r_free = 0.2660 target = 0.052385 restraints weight = 188524.573| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 3.07 r_work: 0.2533 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2533 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2515 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2515 r_free = 0.2515 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2515 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 66752 Z= 0.321 Angle : 0.585 13.916 90142 Z= 0.286 Chirality : 0.043 0.174 10746 Planarity : 0.003 0.079 11504 Dihedral : 6.664 164.256 9280 Min Nonbonded Distance : 1.847 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 0.85 % Allowed : 11.73 % Favored : 87.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 8543 helix: 2.46 (0.08), residues: 4404 sheet: 0.12 (0.16), residues: 1111 loop : -0.52 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.015 0.001 HIS z 161 PHE 0.024 0.001 PHE H 174 TYR 0.024 0.001 TYR z 351 ARG 0.018 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 490 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 429 time to evaluate : 6.009 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8234 (OUTLIER) cc_final: 0.7970 (p) REVERT: A 306 MET cc_start: 0.9007 (mtp) cc_final: 0.8573 (mtm) REVERT: A 386 ASP cc_start: 0.9045 (m-30) cc_final: 0.8818 (m-30) REVERT: A 430 MET cc_start: 0.8872 (tpp) cc_final: 0.8503 (ttp) REVERT: A 508 ILE cc_start: 0.8886 (tp) cc_final: 0.8612 (tp) REVERT: B 480 MET cc_start: 0.9337 (OUTLIER) cc_final: 0.8749 (mmp) REVERT: D 25 GLN cc_start: 0.9242 (tp-100) cc_final: 0.8828 (tp-100) REVERT: D 57 MET cc_start: 0.8905 (mmm) cc_final: 0.8601 (mmm) REVERT: D 65 LYS cc_start: 0.9137 (OUTLIER) cc_final: 0.8883 (mmmt) REVERT: D 93 GLU cc_start: 0.9157 (mm-30) cc_final: 0.8563 (mm-30) REVERT: E 23 ASP cc_start: 0.9271 (m-30) cc_final: 0.8973 (p0) REVERT: E 468 MET cc_start: 0.8781 (mtt) cc_final: 0.8496 (mtp) REVERT: G 47 MET cc_start: 0.8815 (OUTLIER) cc_final: 0.8292 (mtp) REVERT: G 52 ASP cc_start: 0.8407 (t0) cc_final: 0.8098 (t0) REVERT: H 14 ASP cc_start: 0.8778 (t70) cc_final: 0.8423 (t0) REVERT: H 70 ASP cc_start: 0.8310 (t70) cc_final: 0.7534 (t70) REVERT: H 81 ASP cc_start: 0.8831 (m-30) cc_final: 0.8507 (m-30) REVERT: Q 200 ASP cc_start: 0.9390 (m-30) cc_final: 0.8746 (t0) REVERT: Q 357 ASP cc_start: 0.8923 (t0) cc_final: 0.8525 (t0) REVERT: Z 67 MET cc_start: 0.8612 (mtm) cc_final: 0.8236 (mtp) REVERT: Z 337 ASP cc_start: 0.8806 (m-30) cc_final: 0.8469 (m-30) REVERT: a 51 ASP cc_start: 0.8836 (m-30) cc_final: 0.8419 (m-30) REVERT: a 156 MET cc_start: 0.8930 (OUTLIER) cc_final: 0.8467 (mtp) REVERT: a 344 MET cc_start: 0.9040 (mmm) cc_final: 0.8458 (mmm) REVERT: a 416 GLU cc_start: 0.8852 (mp0) cc_final: 0.8430 (mp0) REVERT: b 19 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: b 310 MET cc_start: 0.8858 (ttm) cc_final: 0.8648 (ttp) REVERT: e 4 MET cc_start: 0.5514 (tmm) cc_final: 0.5104 (tmm) REVERT: e 61 MET cc_start: 0.9282 (mmm) cc_final: 0.8755 (mmm) REVERT: e 212 GLU cc_start: 0.8199 (mm-30) cc_final: 0.7933 (mm-30) REVERT: g 13 ASN cc_start: 0.8610 (OUTLIER) cc_final: 0.8161 (p0) REVERT: g 15 LYS cc_start: 0.8497 (OUTLIER) cc_final: 0.8281 (mmmt) REVERT: g 47 MET cc_start: 0.9001 (OUTLIER) cc_final: 0.8179 (mtp) REVERT: g 219 MET cc_start: 0.9539 (OUTLIER) cc_final: 0.9070 (tmm) REVERT: g 415 GLU cc_start: 0.9160 (mp0) cc_final: 0.8708 (mp0) REVERT: g 527 LYS cc_start: 0.8977 (mmmm) cc_final: 0.8650 (mmmm) REVERT: h 14 ASP cc_start: 0.8444 (t0) cc_final: 0.8030 (t0) REVERT: z 10 LYS cc_start: 0.8582 (pttm) cc_final: 0.8372 (pmtt) REVERT: z 244 VAL cc_start: 0.8528 (OUTLIER) cc_final: 0.8262 (t) REVERT: z 358 GLU cc_start: 0.8339 (pm20) cc_final: 0.7826 (pm20) REVERT: N 267 ASP cc_start: 0.8129 (t0) cc_final: 0.7842 (t0) outliers start: 61 outliers final: 36 residues processed: 471 average time/residue: 1.5367 time to fit residues: 944.9584 Evaluate side-chains 471 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 424 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 13 ASN Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 805 optimal weight: 10.0000 chunk 763 optimal weight: 9.9990 chunk 412 optimal weight: 4.9990 chunk 698 optimal weight: 1.9990 chunk 759 optimal weight: 4.9990 chunk 112 optimal weight: 6.9990 chunk 588 optimal weight: 1.9990 chunk 237 optimal weight: 7.9990 chunk 318 optimal weight: 3.9990 chunk 464 optimal weight: 10.0000 chunk 680 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS z 161 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.064172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2663 r_free = 0.2663 target = 0.052498 restraints weight = 202382.047| |-----------------------------------------------------------------------------| r_work (start): 0.2675 rms_B_bonded: 3.18 r_work: 0.2531 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2531 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2517 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2517 r_free = 0.2517 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2517 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8540 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 66752 Z= 0.278 Angle : 0.577 13.009 90142 Z= 0.282 Chirality : 0.042 0.174 10746 Planarity : 0.003 0.084 11504 Dihedral : 6.649 163.402 9280 Min Nonbonded Distance : 1.852 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 0.78 % Allowed : 11.78 % Favored : 87.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 8543 helix: 2.46 (0.08), residues: 4403 sheet: 0.09 (0.16), residues: 1121 loop : -0.52 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP e 304 HIS 0.017 0.001 HIS z 161 PHE 0.027 0.001 PHE H 174 TYR 0.023 0.001 TYR z 351 ARG 0.020 0.000 ARG H 524 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17086 Ramachandran restraints generated. 8543 Oldfield, 0 Emsley, 8543 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 487 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 431 time to evaluate : 6.578 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 230 VAL cc_start: 0.8260 (OUTLIER) cc_final: 0.8007 (p) REVERT: A 306 MET cc_start: 0.8997 (mtp) cc_final: 0.8564 (mtm) REVERT: A 386 ASP cc_start: 0.9040 (m-30) cc_final: 0.8813 (m-30) REVERT: A 430 MET cc_start: 0.8900 (tpp) cc_final: 0.8544 (ttp) REVERT: A 508 ILE cc_start: 0.8877 (tp) cc_final: 0.8603 (tp) REVERT: B 480 MET cc_start: 0.9334 (OUTLIER) cc_final: 0.8749 (mmp) REVERT: D 25 GLN cc_start: 0.9237 (tp-100) cc_final: 0.8820 (tp-100) REVERT: D 57 MET cc_start: 0.8934 (mmm) cc_final: 0.8624 (mmm) REVERT: D 65 LYS cc_start: 0.9134 (OUTLIER) cc_final: 0.8886 (mmmt) REVERT: D 93 GLU cc_start: 0.9160 (mm-30) cc_final: 0.8568 (mm-30) REVERT: E 23 ASP cc_start: 0.9255 (m-30) cc_final: 0.8976 (p0) REVERT: E 468 MET cc_start: 0.8771 (mtt) cc_final: 0.8487 (mtp) REVERT: G 47 MET cc_start: 0.8798 (OUTLIER) cc_final: 0.8186 (mtp) REVERT: G 52 ASP cc_start: 0.8392 (t0) cc_final: 0.7746 (t0) REVERT: G 54 MET cc_start: 0.8843 (mpp) cc_final: 0.8484 (mpp) REVERT: H 14 ASP cc_start: 0.8783 (t70) cc_final: 0.8433 (t0) REVERT: H 70 ASP cc_start: 0.8310 (t70) cc_final: 0.7530 (t70) REVERT: H 81 ASP cc_start: 0.8839 (m-30) cc_final: 0.8515 (m-30) REVERT: Q 200 ASP cc_start: 0.9394 (m-30) cc_final: 0.8750 (t0) REVERT: Q 357 ASP cc_start: 0.8903 (t0) cc_final: 0.8612 (t0) REVERT: Z 337 ASP cc_start: 0.8802 (m-30) cc_final: 0.8468 (m-30) REVERT: a 51 ASP cc_start: 0.8836 (m-30) cc_final: 0.8416 (m-30) REVERT: a 156 MET cc_start: 0.8927 (OUTLIER) cc_final: 0.8657 (mtp) REVERT: a 344 MET cc_start: 0.8993 (mmm) cc_final: 0.8435 (mmm) REVERT: a 416 GLU cc_start: 0.8849 (mp0) cc_final: 0.8427 (mp0) REVERT: b 19 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.8024 (mt-10) REVERT: e 4 MET cc_start: 0.5510 (tmm) cc_final: 0.5112 (tmm) REVERT: e 61 MET cc_start: 0.9276 (mmm) cc_final: 0.8899 (mmm) REVERT: g 13 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8169 (p0) REVERT: g 15 LYS cc_start: 0.8515 (OUTLIER) cc_final: 0.8282 (mmmt) REVERT: g 47 MET cc_start: 0.9002 (OUTLIER) cc_final: 0.8193 (mtp) REVERT: g 219 MET cc_start: 0.9523 (OUTLIER) cc_final: 0.9052 (tmm) REVERT: g 415 GLU cc_start: 0.9161 (mp0) cc_final: 0.8708 (mp0) REVERT: g 527 LYS cc_start: 0.8976 (mmmm) cc_final: 0.8649 (mmmm) REVERT: h 14 ASP cc_start: 0.8424 (t0) cc_final: 0.8073 (t0) REVERT: z 10 LYS cc_start: 0.8587 (pttm) cc_final: 0.8377 (pmtt) REVERT: z 244 VAL cc_start: 0.8511 (OUTLIER) cc_final: 0.8247 (t) REVERT: z 358 GLU cc_start: 0.8351 (pm20) cc_final: 0.7841 (pm20) REVERT: N 267 ASP cc_start: 0.8120 (t0) cc_final: 0.7824 (t0) outliers start: 56 outliers final: 35 residues processed: 471 average time/residue: 1.5111 time to fit residues: 935.0776 Evaluate side-chains 472 residues out of total 7145 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 426 time to evaluate : 5.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 320 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 254 THR Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 379 GLU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Z residue 44 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 19 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain g residue 13 ASN Chi-restraints excluded: chain g residue 15 LYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 219 MET Chi-restraints excluded: chain g residue 254 THR Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 143 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain N residue 240 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 850 random chunks: chunk 214 optimal weight: 4.9990 chunk 35 optimal weight: 0.9990 chunk 501 optimal weight: 0.9980 chunk 608 optimal weight: 7.9990 chunk 691 optimal weight: 0.9990 chunk 821 optimal weight: 4.9990 chunk 72 optimal weight: 0.0050 chunk 460 optimal weight: 2.9990 chunk 664 optimal weight: 5.9990 chunk 605 optimal weight: 0.7980 chunk 147 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS Z 382 HIS z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.066749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.055520 restraints weight = 164790.643| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.88 r_work: 0.2610 rms_B_bonded: 3.28 restraints_weight: 0.5000 r_work (final): 0.2610 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8491 moved from start: 0.1390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 66752 Z= 0.146 Angle : 0.540 13.905 90142 Z= 0.263 Chirality : 0.041 0.186 10746 Planarity : 0.003 0.080 11504 Dihedral : 6.453 159.843 9280 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.69 % Allowed : 12.01 % Favored : 87.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.09), residues: 8543 helix: 2.56 (0.08), residues: 4404 sheet: 0.20 (0.16), residues: 1115 loop : -0.47 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.018 0.001 HIS z 161 PHE 0.027 0.001 PHE H 174 TYR 0.023 0.001 TYR z 351 ARG 0.019 0.000 ARG H 524 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 29885.96 seconds wall clock time: 515 minutes 37.70 seconds (30937.70 seconds total)