Starting phenix.real_space_refine on Tue Jan 21 05:37:26 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sff_40440/01_2025/8sff_40440.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sff_40440/01_2025/8sff_40440.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sff_40440/01_2025/8sff_40440.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sff_40440/01_2025/8sff_40440.map" model { file = "/net/cci-nas-00/data/ceres_data/8sff_40440/01_2025/8sff_40440.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sff_40440/01_2025/8sff_40440.cif" } resolution = 3.2 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= 0.051 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 410 5.16 5 C 41706 2.51 5 N 11611 2.21 5 O 12911 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 57 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 66750 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: "P" Number of atoms: 1627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 205, 1627 Classifications: {'peptide': 205} Link IDs: {'PTRANS': 6, 'TRANS': 198} Chain breaks: 3 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: 32.24, per 1000 atoms: 0.48 Number of scatterers: 66750 At special positions: 0 Unit cell: (181.976, 177.744, 179.86, 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 410 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12911 8.00 N 11611 7.00 C 41706 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 "HETATM66529 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM66657 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.63 Conformation dependent library (CDL) restraints added in 6.8 seconds 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16146 Finding SS restraints... Secondary structure from input PDB file: 364 helices and 97 sheets defined 56.9% alpha, 14.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.85 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.564A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.725A 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: 3.678A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (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: 4.259A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.597A pdb=" N GLN A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) 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: 3.874A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 removed outlier: 3.565A pdb=" N MET A 344 " --> pdb=" O GLU A 341 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N LEU A 345 " --> pdb=" O ALA A 342 " (cutoff:3.500A) No H-bonds generated for '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 433 through 446 removed outlier: 3.700A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.560A pdb=" N ASN A 450 " --> pdb=" O LEU A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.880A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.296A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) 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 removed outlier: 3.557A 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: 4.421A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.630A 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 Processing helix chain 'B' and resid 260 through 284 removed outlier: 3.582A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) 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 426 Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.780A 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: 4.345A 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 126 removed outlier: 3.869A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.529A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Proline residue: D 185 - end of helix 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: 4.024A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.009A 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: 3.990A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.755A 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 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.875A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.569A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) 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: 3.664A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (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: 6.333A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.834A 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: 3.919A 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 439 removed outlier: 3.862A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.837A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 467 removed outlier: 3.836A 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: 3.699A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) 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: 3.965A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.597A 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 165 through 167 No H-bonds generated for 'chain 'G' and resid 165 through 167' 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: 3.684A 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: 3.694A 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: 3.583A 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 17 through 36 removed outlier: 3.892A pdb=" N GLN H 21 " --> pdb=" O GLN H 17 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 40 removed outlier: 3.995A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 37 through 40' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.754A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 3.947A 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: 3.662A 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 171 through 185 removed outlier: 3.670A 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 342 removed outlier: 3.532A pdb=" N VAL H 341 " --> pdb=" O SER H 338 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LEU H 342 " --> pdb=" O ALA H 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 338 through 342' 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: 4.044A 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 516 removed outlier: 3.544A pdb=" N VAL H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.086A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 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 156 through 168 removed outlier: 3.734A pdb=" N VAL Q 160 " --> pdb=" O ASP Q 156 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.226A 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 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 3.508A pdb=" N LEU Q 265 " --> pdb=" O THR Q 261 " (cutoff:3.500A) removed outlier: 4.752A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.589A 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 429 removed outlier: 3.682A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.312A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.760A 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 removed outlier: 3.761A pdb=" N VAL Q 463 " --> pdb=" O LYS Q 459 " (cutoff:3.500A) Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.996A 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: 3.829A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.249A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.644A 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: 3.671A 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: 3.600A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 removed outlier: 3.585A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.673A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.219A 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 432 through 445 removed outlier: 4.210A 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 helix chain 'a' and resid 14 through 33 removed outlier: 3.532A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.619A 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 removed outlier: 3.570A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.999A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 135 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 144 through 157 removed outlier: 3.671A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.316A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (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: 3.810A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.955A 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 433 through 445 removed outlier: 3.859A pdb=" N ALA a 437 " --> pdb=" O ARG a 433 " (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 484 removed outlier: 3.698A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) 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: 4.414A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.662A 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 Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.534A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) 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: 3.710A 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 Processing helix chain 'd' and resid 85 through 103 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.964A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.774A 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: 3.603A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.662A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.317A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix 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: 4.332A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.806A 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 441 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.791A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.638A 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 removed outlier: 5.026A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 29 through 49 removed outlier: 3.515A pdb=" N ALA e 33 " --> pdb=" O MET e 29 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) 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 80 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 105 through 126 removed outlier: 4.160A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.527A 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: 6.595A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.873A pdb=" N SER e 180 " --> pdb=" O VAL e 177 " (cutoff:3.500A) Processing helix chain 'e' and resid 181 through 196 removed outlier: 3.564A pdb=" N VAL e 196 " --> pdb=" O ALA e 192 " (cutoff:3.500A) 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: 3.894A 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 438 Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.942A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.688A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.554A 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 37 removed outlier: 3.699A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 68 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.669A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.576A 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: 3.746A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.558A 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 306 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 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 Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.702A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 3.973A 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: 3.705A 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 186 removed outlier: 3.696A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (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 342 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: 4.057A 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 470 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: 3.537A pdb=" N ALA q 28 " --> pdb=" O GLY q 24 " (cutoff:3.500A) removed outlier: 4.622A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.917A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.454A 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 156 through 166 removed outlier: 4.386A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (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: 4.762A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.918A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.812A 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: 3.911A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N CYS q 430 " --> pdb=" O TYR q 426 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.141A 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 removed outlier: 3.551A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) 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: 3.712A 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: 3.551A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.862A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.057A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 Processing helix chain 'z' and resid 187 through 191 Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.956A 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 Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.732A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.327A 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: 4.179A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.584A 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 'P' and resid 58 through 61 Processing helix chain 'P' and resid 62 through 84 removed outlier: 3.701A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 139 removed outlier: 3.834A pdb=" N GLN P 139 " --> pdb=" O PHE P 136 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 136 through 139' Processing helix chain 'P' and resid 140 through 152 removed outlier: 4.206A pdb=" N ARG P 144 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 4.018A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 194 through 209 removed outlier: 3.894A pdb=" N MET P 198 " --> pdb=" O GLY P 194 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 223 Processing helix chain 'P' and resid 225 through 232 Processing helix chain 'P' and resid 251 through 256 Processing helix chain 'P' and resid 260 through 271 removed outlier: 4.139A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.789A 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: 6.357A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.480A 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: 8.208A pdb=" N ASP A 42 " --> pdb=" O ASP G 521 " (cutoff:3.500A) removed outlier: 8.548A pdb=" N VAL G 523 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 6.128A 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 196 through 199 removed outlier: 6.304A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.588A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.553A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.553A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.194A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.133A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.208A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.117A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AA9, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.390A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.316A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.514A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.520A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.453A 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: 6.915A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.915A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.885A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.798A 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: 3.808A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.424A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.497A 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: 6.268A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.376A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.401A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.272A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.431A 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: 6.160A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.160A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N VAL D 297 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.724A 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: 4.704A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 6.079A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.609A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N ARG E 534 " --> pdb=" O VAL H 50 " (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: 3.762A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.613A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N LEU E 299 " --> pdb=" O LYS E 247 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.613A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.963A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.551A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.768A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.557A 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: 7.331A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.641A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.517A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG Z 523 " --> pdb=" O GLU Z 12 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (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: 6.814A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.070A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.352A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (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 16 Processing sheet with id=AD6, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.546A pdb=" N GLY H 196 " --> pdb=" O CYS H 370 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AD8, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AD9, first strand: chain 'H' and resid 405 through 407 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: 4.922A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.377A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.631A 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: 3.989A 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: 6.462A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.394A 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 192 through 196 removed outlier: 6.457A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (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: 6.230A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.173A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.300A 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: 3.521A 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: 4.539A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.525A 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: 6.270A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 3.941A 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: 6.321A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.374A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.441A 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: 6.610A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.593A 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: 6.610A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.593A 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: 9.153A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (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: 4.478A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.096A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.592A 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: 6.996A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.033A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.963A 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: 6.535A pdb=" N HIS b 200 " --> pdb=" O ILE b 373 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N LEU b 375 " --> pdb=" O HIS b 200 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N ILE b 202 " --> pdb=" O LEU b 375 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N GLY b 377 " --> pdb=" O ILE b 202 " (cutoff:3.500A) removed outlier: 7.244A pdb=" N LYS b 204 " --> pdb=" O GLY b 377 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.313A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.278A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (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: 6.499A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.528A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) removed outlier: 8.427A pdb=" N GLY d 392 " --> pdb=" O VAL d 211 " (cutoff:3.500A) removed outlier: 7.448A pdb=" N LYS d 213 " --> pdb=" O GLY d 392 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH2 Processing sheet with id=AH3, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.968A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.968A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.777A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.766A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.858A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.844A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH6, first strand: chain 'e' and resid 26 through 28 removed outlier: 4.553A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.475A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH8, first strand: chain 'e' and resid 209 through 215 removed outlier: 3.747A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 228 through 230 removed outlier: 3.513A pdb=" N VAL e 230 " --> pdb=" O LEU e 372 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 7.338A pdb=" N LEU e 299 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 5.664A pdb=" N LYS e 247 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 7.243A pdb=" N ILE e 301 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'g' and resid 57 through 60 removed outlier: 6.352A pdb=" N MET g 47 " --> pdb=" O VAL z 518 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU z 520 " --> pdb=" O MET g 47 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI3, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI4, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.847A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) removed outlier: 4.141A pdb=" N THR g 373 " --> pdb=" O LEU g 215 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI6, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.421A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 6.188A pdb=" N VAL g 290 " --> pdb=" O ILE g 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI6 Processing sheet with id=AI7, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AI8, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.410A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AJ1, first strand: chain 'h' and resid 195 through 201 removed outlier: 4.241A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ3, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ4, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ5, first strand: chain 'q' and resid 20 through 22 removed outlier: 4.751A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.653A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.889A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.550A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.877A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AJ9, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK1, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK2, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK3, first strand: chain 'z' and resid 192 through 196 Processing sheet with id=AK4, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK5, first strand: chain 'z' and resid 310 through 313 removed outlier: 8.957A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.925A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.284A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK7, first strand: chain 'P' and resid 162 through 163 removed outlier: 6.095A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.946A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 8.200A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.663A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.865A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N PHE P 248 " --> pdb=" O LEU P 236 " (cutoff:3.500A) 4095 hydrogen bonds defined for protein. 11691 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: 32.98 Time building geometry restraints manager: 15.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 22425 1.34 - 1.46: 8685 1.46 - 1.58: 35620 1.58 - 1.70: 48 1.70 - 1.81: 728 Bond restraints: 67506 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 6.48e+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 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 6.39e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.35e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 67501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.83: 89840 1.83 - 3.66: 968 3.66 - 5.50: 245 5.50 - 7.33: 82 7.33 - 9.16: 8 Bond angle restraints: 91143 Sorted by residual: angle pdb=" N ILE P 245 " pdb=" CA ILE P 245 " pdb=" C ILE P 245 " ideal model delta sigma weight residual 113.10 106.66 6.44 9.70e-01 1.06e+00 4.40e+01 angle pdb=" C ALA q 530 " pdb=" CA ALA q 530 " pdb=" CB ALA q 530 " ideal model delta sigma weight residual 116.54 110.27 6.27 1.15e+00 7.56e-01 2.97e+01 angle pdb=" C CYS E 181 " pdb=" N HIS E 182 " pdb=" CA HIS E 182 " ideal model delta sigma weight residual 121.19 127.67 -6.48 1.59e+00 3.96e-01 1.66e+01 angle pdb=" C CYS e 181 " pdb=" N HIS e 182 " pdb=" CA HIS e 182 " ideal model delta sigma weight residual 121.19 127.04 -5.85 1.59e+00 3.96e-01 1.35e+01 angle pdb=" N VAL q 328 " pdb=" CA VAL q 328 " pdb=" C VAL q 328 " ideal model delta sigma weight residual 112.96 109.36 3.60 1.00e+00 1.00e+00 1.30e+01 ... (remaining 91138 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 41017 35.49 - 70.97: 663 70.97 - 106.46: 62 106.46 - 141.94: 11 141.94 - 177.43: 6 Dihedral angle restraints: 41759 sinusoidal: 16828 harmonic: 24931 Sorted by residual: 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 300.00 122.57 177.43 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 -60.00 116.90 -176.90 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" C5' ADP q 601 " pdb=" O5' ADP q 601 " pdb=" PA ADP q 601 " pdb=" O2A ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 131.86 168.14 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 41756 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 7985 0.040 - 0.080: 2032 0.080 - 0.120: 769 0.120 - 0.160: 67 0.160 - 0.200: 2 Chirality restraints: 10855 Sorted by residual: chirality pdb=" CB ILE P 88 " pdb=" CA ILE P 88 " pdb=" CG1 ILE P 88 " pdb=" CG2 ILE P 88 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.00e+00 chirality pdb=" CB VAL P 62 " pdb=" CA VAL P 62 " pdb=" CG1 VAL P 62 " pdb=" CG2 VAL P 62 " both_signs ideal model delta sigma weight residual False -2.63 -2.47 -0.16 2.00e-01 2.50e+01 6.66e-01 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.58e-01 ... (remaining 10852 not shown) Planarity restraints: 11637 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.038 5.00e-02 4.00e+02 5.83e-02 5.44e+00 pdb=" N PRO e 441 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA B 7 " -0.038 5.00e-02 4.00e+02 5.82e-02 5.43e+00 pdb=" N PRO B 8 " 0.101 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CG GLU B 22 " -0.011 2.00e-02 2.50e+03 2.24e-02 5.01e+00 pdb=" CD GLU B 22 " 0.039 2.00e-02 2.50e+03 pdb=" OE1 GLU B 22 " -0.014 2.00e-02 2.50e+03 pdb=" OE2 GLU B 22 " -0.014 2.00e-02 2.50e+03 ... (remaining 11634 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.26: 120 2.26 - 2.92: 27091 2.92 - 3.58: 99859 3.58 - 4.24: 155472 4.24 - 4.90: 273293 Nonbonded interactions: 555835 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb=" F3 AF3 B 603 " model vdw 1.599 2.990 nonbonded pdb=" O2B ADP B 601 " pdb="AL AF3 B 603 " model vdw 1.693 2.760 nonbonded pdb=" O3A ADP b 601 " pdb="MG MG b 602 " model vdw 1.957 2.170 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.957 2.120 nonbonded pdb=" OD1 ASP B 97 " pdb="MG MG B 602 " model vdw 1.960 2.170 ... (remaining 555830 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: 0.010 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.820 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: 0.060 Extract box with map and model: 2.080 Check model and map are aligned: 0.370 Set scattering table: 0.470 Process input model: 125.930 Find NCS groups from input model: 5.640 Set up NCS constraints: 0.410 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 139.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 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 67506 Z= 0.292 Angle : 0.546 9.161 91143 Z= 0.269 Chirality : 0.041 0.200 10855 Planarity : 0.003 0.058 11637 Dihedral : 14.504 177.430 25613 Min Nonbonded Distance : 1.599 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.15 % Favored : 96.84 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: 8630 helix: 2.37 (0.08), residues: 4456 sheet: 0.30 (0.16), residues: 1136 loop : -0.38 (0.11), residues: 3038 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.007 0.001 HIS E 182 PHE 0.024 0.001 PHE E 386 TYR 0.020 0.001 TYR b 297 ARG 0.007 0.000 ARG P 86 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 573 time to evaluate : 5.885 Fit side-chains REVERT: A 10 ASP cc_start: 0.8342 (m-30) cc_final: 0.8140 (m-30) REVERT: D 320 MET cc_start: 0.8620 (mtp) cc_final: 0.8238 (mtp) REVERT: E 96 LYS cc_start: 0.8506 (tptp) cc_final: 0.8206 (tptt) REVERT: E 121 GLU cc_start: 0.8304 (tm-30) cc_final: 0.8080 (tp30) REVERT: G 182 MET cc_start: 0.8733 (ttm) cc_final: 0.8446 (ttp) REVERT: H 316 GLU cc_start: 0.8079 (tm-30) cc_final: 0.7814 (tp30) REVERT: d 27 ARG cc_start: 0.7673 (mtm-85) cc_final: 0.7334 (mmm-85) REVERT: d 458 MET cc_start: 0.8351 (tpp) cc_final: 0.8138 (mmm) REVERT: g 52 ASP cc_start: 0.7837 (t70) cc_final: 0.6912 (t70) REVERT: g 54 MET cc_start: 0.8034 (mpp) cc_final: 0.7612 (mpp) REVERT: q 318 LYS cc_start: 0.8581 (pttp) cc_final: 0.8211 (pttp) REVERT: z 389 ASP cc_start: 0.8440 (m-30) cc_final: 0.8220 (m-30) REVERT: P 63 ILE cc_start: 0.8230 (pt) cc_final: 0.7959 (mm) REVERT: P 85 GLU cc_start: 0.8563 (tt0) cc_final: 0.8145 (tt0) REVERT: P 148 MET cc_start: 0.8368 (mpp) cc_final: 0.8091 (mpp) REVERT: P 273 LEU cc_start: 0.5209 (mm) cc_final: 0.4893 (mm) outliers start: 0 outliers final: 0 residues processed: 573 average time/residue: 0.6136 time to fit residues: 610.8313 Evaluate side-chains 499 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 5.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 725 optimal weight: 5.9990 chunk 651 optimal weight: 9.9990 chunk 361 optimal weight: 9.9990 chunk 222 optimal weight: 4.9990 chunk 439 optimal weight: 7.9990 chunk 347 optimal weight: 0.0670 chunk 673 optimal weight: 1.9990 chunk 260 optimal weight: 0.8980 chunk 409 optimal weight: 0.5980 chunk 501 optimal weight: 0.9990 chunk 780 optimal weight: 3.9990 overall best weight: 0.9122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN B 73 ASN B 302 GLN H 119 GLN Q 316 ASN Z 84 GLN ** Z 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 103 ASN ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 25 GLN e 122 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 516 GLN z 23 ASN z 84 GLN ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.078894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2746 r_free = 0.2746 target = 0.064565 restraints weight = 176263.396| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 2.95 r_work: 0.2596 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2603 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.0730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 67506 Z= 0.155 Angle : 0.541 9.365 91143 Z= 0.270 Chirality : 0.041 0.189 10855 Planarity : 0.003 0.061 11637 Dihedral : 7.510 174.392 9375 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.08 % Favored : 96.91 % Rotamer: Outliers : 0.29 % Allowed : 4.44 % Favored : 95.27 % 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: 1.77 (0.09), residues: 8630 helix: 2.43 (0.08), residues: 4505 sheet: 0.25 (0.16), residues: 1124 loop : -0.41 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.007 0.001 HIS G 111 PHE 0.023 0.001 PHE P 170 TYR 0.013 0.001 TYR G 437 ARG 0.005 0.000 ARG Z 264 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 577 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 556 time to evaluate : 5.835 Fit side-chains REVERT: A 246 MET cc_start: 0.9143 (mmm) cc_final: 0.8602 (mmt) REVERT: E 96 LYS cc_start: 0.8651 (tptp) cc_final: 0.8330 (tptt) REVERT: E 121 GLU cc_start: 0.8636 (tm-30) cc_final: 0.8170 (tp30) REVERT: H 316 GLU cc_start: 0.8463 (tm-30) cc_final: 0.8059 (tp30) REVERT: Z 15 ARG cc_start: 0.8499 (ttm110) cc_final: 0.8268 (mtp-110) REVERT: d 374 LEU cc_start: 0.9291 (tp) cc_final: 0.9059 (tt) REVERT: d 458 MET cc_start: 0.8880 (tpp) cc_final: 0.8140 (mpp) REVERT: g 52 ASP cc_start: 0.8089 (t70) cc_final: 0.7202 (t70) REVERT: g 54 MET cc_start: 0.8410 (mpp) cc_final: 0.7994 (mpp) REVERT: q 296 LYS cc_start: 0.9101 (ptmt) cc_final: 0.8791 (pttm) REVERT: q 318 LYS cc_start: 0.8649 (pttp) cc_final: 0.8365 (pttp) REVERT: z 389 ASP cc_start: 0.8766 (m-30) cc_final: 0.8536 (m-30) REVERT: P 63 ILE cc_start: 0.8154 (pt) cc_final: 0.7836 (mm) REVERT: P 85 GLU cc_start: 0.8690 (tt0) cc_final: 0.8232 (tt0) REVERT: P 148 MET cc_start: 0.8651 (mpp) cc_final: 0.8268 (mpp) outliers start: 21 outliers final: 16 residues processed: 565 average time/residue: 0.6125 time to fit residues: 598.9562 Evaluate side-chains 523 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 507 time to evaluate : 5.909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 464 GLU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain h residue 144 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 341 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 802 optimal weight: 7.9990 chunk 133 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 829 optimal weight: 0.7980 chunk 76 optimal weight: 9.9990 chunk 331 optimal weight: 7.9990 chunk 581 optimal weight: 7.9990 chunk 557 optimal weight: 10.0000 chunk 320 optimal weight: 10.0000 chunk 138 optimal weight: 8.9990 chunk 45 optimal weight: 7.9990 overall best weight: 6.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN B 73 ASN B 302 GLN D 178 GLN H 21 GLN H 25 ASN H 448 GLN Q 303 HIS Q 316 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN q 461 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 346 HIS ** P 199 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 231 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2894 r_free = 0.2894 target = 0.072387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2625 r_free = 0.2625 target = 0.058783 restraints weight = 158098.349| |-----------------------------------------------------------------------------| r_work (start): 0.2620 rms_B_bonded: 2.66 r_work: 0.2480 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2347 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.2347 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2351 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2351 r_free = 0.2351 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 = 0.2351 r_free = 0.2351 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2351 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8883 moved from start: 0.1125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 67506 Z= 0.549 Angle : 0.694 10.708 91143 Z= 0.346 Chirality : 0.047 0.211 10855 Planarity : 0.004 0.068 11637 Dihedral : 7.651 178.499 9375 Min Nonbonded Distance : 1.785 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 0.86 % Allowed : 7.14 % Favored : 92.00 % 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: 1.38 (0.09), residues: 8630 helix: 2.14 (0.08), residues: 4494 sheet: 0.00 (0.16), residues: 1112 loop : -0.59 (0.11), residues: 3024 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP G 168 HIS 0.008 0.001 HIS G 111 PHE 0.024 0.002 PHE a 167 TYR 0.023 0.002 TYR Q 304 ARG 0.006 0.001 ARG g 216 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 494 time to evaluate : 5.878 Fit side-chains REVERT: A 246 MET cc_start: 0.9277 (mmm) cc_final: 0.8781 (mmt) REVERT: A 295 MET cc_start: 0.7998 (OUTLIER) cc_final: 0.7755 (ptt) REVERT: B 302 GLN cc_start: 0.9499 (OUTLIER) cc_final: 0.9272 (tt0) REVERT: D 399 GLU cc_start: 0.8926 (mp0) cc_final: 0.8725 (mp0) REVERT: E 96 LYS cc_start: 0.8832 (tptp) cc_final: 0.8468 (tptt) REVERT: E 121 GLU cc_start: 0.8897 (tm-30) cc_final: 0.8418 (tp30) REVERT: E 485 MET cc_start: 0.8967 (mpp) cc_final: 0.8719 (mpp) REVERT: G 274 TYR cc_start: 0.9571 (t80) cc_final: 0.9283 (t80) REVERT: H 2 MET cc_start: 0.7863 (mmm) cc_final: 0.7595 (mmt) REVERT: H 316 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8332 (tp30) REVERT: Z 190 MET cc_start: 0.9415 (mmp) cc_final: 0.9214 (mmp) REVERT: Z 244 VAL cc_start: 0.9132 (OUTLIER) cc_final: 0.8891 (t) REVERT: Z 520 GLU cc_start: 0.9232 (tt0) cc_final: 0.9005 (tt0) REVERT: b 87 MET cc_start: 0.9418 (ttp) cc_final: 0.9182 (ttp) REVERT: e 122 GLN cc_start: 0.8995 (tm130) cc_final: 0.8634 (tm-30) REVERT: g 52 ASP cc_start: 0.8289 (t70) cc_final: 0.7398 (t70) REVERT: g 54 MET cc_start: 0.8464 (mpp) cc_final: 0.8013 (mpp) REVERT: h 283 HIS cc_start: 0.8618 (m170) cc_final: 0.8414 (m170) REVERT: q 393 ASP cc_start: 0.8998 (m-30) cc_final: 0.8788 (m-30) REVERT: z 244 VAL cc_start: 0.8999 (OUTLIER) cc_final: 0.8715 (t) REVERT: P 63 ILE cc_start: 0.8208 (pt) cc_final: 0.7856 (mm) REVERT: P 85 GLU cc_start: 0.8505 (tt0) cc_final: 0.8193 (mp0) REVERT: P 91 LEU cc_start: 0.5607 (tp) cc_final: 0.5142 (tt) outliers start: 62 outliers final: 40 residues processed: 537 average time/residue: 0.6185 time to fit residues: 576.8163 Evaluate side-chains 513 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 469 time to evaluate : 5.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 462 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 485 ILE Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 455 CYS Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 351 THR Chi-restraints excluded: chain Q residue 25 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 438 SER Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 228 VAL Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 440 CYS Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain g residue 182 MET Chi-restraints excluded: chain h residue 15 SER Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 233 LEU Chi-restraints excluded: chain P residue 273 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 244 optimal weight: 1.9990 chunk 853 optimal weight: 9.9990 chunk 520 optimal weight: 5.9990 chunk 441 optimal weight: 2.9990 chunk 763 optimal weight: 0.9990 chunk 655 optimal weight: 3.9990 chunk 238 optimal weight: 7.9990 chunk 851 optimal weight: 30.0000 chunk 854 optimal weight: 0.0000 chunk 376 optimal weight: 0.8980 chunk 675 optimal weight: 2.9990 overall best weight: 1.3790 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN B 302 GLN B 498 GLN G 474 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN Q 316 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 497 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN q 53 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2972 r_free = 0.2972 target = 0.076727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2706 r_free = 0.2706 target = 0.062777 restraints weight = 155460.572| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.74 r_work: 0.2570 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2567 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2567 r_free = 0.2567 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2567 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8744 moved from start: 0.1046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 67506 Z= 0.170 Angle : 0.536 8.624 91143 Z= 0.266 Chirality : 0.041 0.197 10855 Planarity : 0.003 0.064 11637 Dihedral : 7.349 173.422 9375 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.13 % Favored : 96.86 % Rotamer: Outliers : 0.72 % Allowed : 8.74 % Favored : 90.54 % 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: 8630 helix: 2.38 (0.08), residues: 4496 sheet: 0.03 (0.16), residues: 1106 loop : -0.51 (0.11), residues: 3028 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP G 168 HIS 0.007 0.001 HIS P 186 PHE 0.018 0.001 PHE P 170 TYR 0.015 0.001 TYR h 475 ARG 0.006 0.000 ARG d 496 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 569 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 517 time to evaluate : 5.969 Fit side-chains REVERT: A 246 MET cc_start: 0.9154 (mmm) cc_final: 0.8642 (mmt) REVERT: A 388 MET cc_start: 0.9428 (mtp) cc_final: 0.8880 (mtp) REVERT: B 415 MET cc_start: 0.9370 (mmm) cc_final: 0.9143 (mmp) REVERT: B 452 ASP cc_start: 0.8739 (m-30) cc_final: 0.8504 (m-30) REVERT: D 373 LEU cc_start: 0.9096 (mt) cc_final: 0.8830 (mt) REVERT: D 399 GLU cc_start: 0.8684 (OUTLIER) cc_final: 0.8421 (mp0) REVERT: E 96 LYS cc_start: 0.8666 (tptp) cc_final: 0.8428 (tptt) REVERT: E 121 GLU cc_start: 0.8660 (tm-30) cc_final: 0.8180 (tp30) REVERT: E 485 MET cc_start: 0.8674 (mpp) cc_final: 0.8446 (mpp) REVERT: G 28 ASN cc_start: 0.9044 (m-40) cc_final: 0.8563 (m-40) REVERT: G 365 ASP cc_start: 0.8912 (t0) cc_final: 0.8605 (t0) REVERT: H 316 GLU cc_start: 0.8547 (tm-30) cc_final: 0.8110 (tp30) REVERT: Z 244 VAL cc_start: 0.8874 (OUTLIER) cc_final: 0.8660 (t) REVERT: b 19 GLU cc_start: 0.7944 (mt-10) cc_final: 0.7679 (mt-10) REVERT: b 87 MET cc_start: 0.9290 (ttp) cc_final: 0.9051 (ttp) REVERT: b 215 ASP cc_start: 0.9029 (t0) cc_final: 0.8704 (t0) REVERT: e 288 MET cc_start: 0.9053 (OUTLIER) cc_final: 0.8703 (ptp) REVERT: g 52 ASP cc_start: 0.8099 (t70) cc_final: 0.7120 (t70) REVERT: g 54 MET cc_start: 0.8494 (mpp) cc_final: 0.8214 (mpp) REVERT: q 393 ASP cc_start: 0.8665 (m-30) cc_final: 0.8322 (m-30) REVERT: q 416 GLU cc_start: 0.8747 (mp0) cc_final: 0.8514 (mp0) REVERT: z 244 VAL cc_start: 0.8775 (OUTLIER) cc_final: 0.8480 (t) REVERT: P 85 GLU cc_start: 0.8403 (tt0) cc_final: 0.8096 (mp0) REVERT: P 91 LEU cc_start: 0.5480 (tp) cc_final: 0.5050 (tt) outliers start: 52 outliers final: 24 residues processed: 551 average time/residue: 0.6410 time to fit residues: 615.4460 Evaluate side-chains 517 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 489 time to evaluate : 5.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 ILE Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 144 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 230 optimal weight: 5.9990 chunk 482 optimal weight: 4.9990 chunk 456 optimal weight: 10.0000 chunk 737 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 144 optimal weight: 0.9980 chunk 504 optimal weight: 0.9990 chunk 101 optimal weight: 10.0000 chunk 582 optimal weight: 0.7980 chunk 232 optimal weight: 3.9990 chunk 113 optimal weight: 9.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 502 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2967 r_free = 0.2967 target = 0.076237 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.062153 restraints weight = 168663.581| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.84 r_work: 0.2547 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2547 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 67506 Z= 0.231 Angle : 0.541 8.796 91143 Z= 0.266 Chirality : 0.042 0.229 10855 Planarity : 0.003 0.063 11637 Dihedral : 7.263 173.775 9375 Min Nonbonded Distance : 1.885 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.52 % Rotamer: Outliers : 0.77 % Allowed : 9.64 % Favored : 89.58 % 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: 8630 helix: 2.41 (0.08), residues: 4496 sheet: 0.01 (0.16), residues: 1105 loop : -0.50 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.012 0.001 HIS P 186 PHE 0.017 0.001 PHE A 167 TYR 0.015 0.001 TYR D 24 ARG 0.004 0.000 ARG d 496 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 503 time to evaluate : 6.027 Fit side-chains REVERT: A 246 MET cc_start: 0.9162 (mmm) cc_final: 0.8696 (mmt) REVERT: A 388 MET cc_start: 0.9414 (mtp) cc_final: 0.9165 (mtp) REVERT: B 415 MET cc_start: 0.9435 (mmm) cc_final: 0.9212 (mmp) REVERT: D 373 LEU cc_start: 0.9127 (mt) cc_final: 0.8861 (mt) REVERT: D 399 GLU cc_start: 0.8759 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: E 96 LYS cc_start: 0.8671 (tptp) cc_final: 0.8403 (tptt) REVERT: E 121 GLU cc_start: 0.8664 (tm-30) cc_final: 0.8148 (tp30) REVERT: E 485 MET cc_start: 0.8713 (mpp) cc_final: 0.8480 (mpp) REVERT: G 365 ASP cc_start: 0.8952 (t0) cc_final: 0.8648 (t0) REVERT: H 316 GLU cc_start: 0.8577 (tm-30) cc_final: 0.8132 (tp30) REVERT: Z 244 VAL cc_start: 0.8946 (OUTLIER) cc_final: 0.8737 (t) REVERT: b 87 MET cc_start: 0.9320 (ttp) cc_final: 0.9089 (ttp) REVERT: b 215 ASP cc_start: 0.9009 (t0) cc_final: 0.8685 (t0) REVERT: d 458 MET cc_start: 0.8777 (mmm) cc_final: 0.8443 (mmm) REVERT: e 288 MET cc_start: 0.9075 (OUTLIER) cc_final: 0.8744 (ptp) REVERT: g 52 ASP cc_start: 0.8120 (t70) cc_final: 0.7117 (t70) REVERT: g 54 MET cc_start: 0.8507 (mpp) cc_final: 0.8214 (mpp) REVERT: g 183 VAL cc_start: 0.9241 (OUTLIER) cc_final: 0.8957 (p) REVERT: z 244 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8447 (t) REVERT: P 91 LEU cc_start: 0.5598 (tp) cc_final: 0.5168 (tt) outliers start: 56 outliers final: 38 residues processed: 543 average time/residue: 0.6003 time to fit residues: 568.5905 Evaluate side-chains 525 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 482 time to evaluate : 5.890 ------------------------------------------------------------------------------- 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 58 ASP Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 237 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 611 optimal weight: 0.9990 chunk 158 optimal weight: 3.9990 chunk 168 optimal weight: 1.9990 chunk 642 optimal weight: 6.9990 chunk 555 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 266 optimal weight: 4.9990 chunk 199 optimal weight: 10.0000 chunk 443 optimal weight: 9.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN E 139 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 276 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2976 r_free = 0.2976 target = 0.076899 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.062995 restraints weight = 157946.327| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.76 r_work: 0.2560 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2560 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2565 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2565 r_free = 0.2565 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2565 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 67506 Z= 0.203 Angle : 0.530 8.985 91143 Z= 0.261 Chirality : 0.041 0.211 10855 Planarity : 0.003 0.062 11637 Dihedral : 7.161 172.396 9375 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.33 % Favored : 96.66 % Rotamer: Outliers : 0.91 % Allowed : 10.15 % Favored : 88.93 % 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: 1.70 (0.09), residues: 8630 helix: 2.45 (0.08), residues: 4498 sheet: 0.03 (0.16), residues: 1109 loop : -0.50 (0.11), residues: 3023 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.006 0.001 HIS G 111 PHE 0.017 0.001 PHE A 167 TYR 0.017 0.001 TYR D 24 ARG 0.004 0.000 ARG d 496 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 505 time to evaluate : 6.043 Fit side-chains REVERT: A 246 MET cc_start: 0.9191 (mmm) cc_final: 0.8696 (mmt) REVERT: D 373 LEU cc_start: 0.9105 (mt) cc_final: 0.8832 (mt) REVERT: D 399 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8509 (mp0) REVERT: E 96 LYS cc_start: 0.8654 (tptp) cc_final: 0.8417 (tptt) REVERT: E 121 GLU cc_start: 0.8658 (tm-30) cc_final: 0.8122 (tp30) REVERT: E 485 MET cc_start: 0.8681 (mpp) cc_final: 0.8432 (mpp) REVERT: G 365 ASP cc_start: 0.8919 (t0) cc_final: 0.8596 (t0) REVERT: H 316 GLU cc_start: 0.8517 (tm-30) cc_final: 0.8108 (tp30) REVERT: Z 15 ARG cc_start: 0.8517 (ttm110) cc_final: 0.8304 (mtp-110) REVERT: a 384 MET cc_start: 0.9009 (ttt) cc_final: 0.8759 (ttt) REVERT: b 87 MET cc_start: 0.9327 (ttp) cc_final: 0.9099 (ttp) REVERT: b 215 ASP cc_start: 0.8978 (t0) cc_final: 0.8677 (t0) REVERT: e 288 MET cc_start: 0.9050 (OUTLIER) cc_final: 0.8732 (ptp) REVERT: g 52 ASP cc_start: 0.8103 (t70) cc_final: 0.7081 (t70) REVERT: g 54 MET cc_start: 0.8477 (mpp) cc_final: 0.8184 (mpp) REVERT: g 183 VAL cc_start: 0.9211 (OUTLIER) cc_final: 0.8935 (p) REVERT: q 393 ASP cc_start: 0.8672 (m-30) cc_final: 0.8458 (m-30) REVERT: q 522 ASP cc_start: 0.8987 (t0) cc_final: 0.8738 (t0) REVERT: z 244 VAL cc_start: 0.8740 (OUTLIER) cc_final: 0.8449 (t) REVERT: P 91 LEU cc_start: 0.5555 (tp) cc_final: 0.5141 (tt) REVERT: P 273 LEU cc_start: 0.4839 (OUTLIER) cc_final: 0.4591 (mm) outliers start: 66 outliers final: 46 residues processed: 552 average time/residue: 0.6190 time to fit residues: 602.3115 Evaluate side-chains 540 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 489 time to evaluate : 5.846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 183 VAL Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 144 LYS Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 273 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 717 optimal weight: 0.6980 chunk 22 optimal weight: 10.0000 chunk 673 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 666 optimal weight: 5.9990 chunk 296 optimal weight: 8.9990 chunk 851 optimal weight: 7.9990 chunk 340 optimal weight: 10.0000 chunk 367 optimal weight: 9.9990 chunk 19 optimal weight: 0.6980 chunk 481 optimal weight: 10.0000 overall best weight: 3.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.075656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2688 r_free = 0.2688 target = 0.061994 restraints weight = 143999.683| |-----------------------------------------------------------------------------| r_work (start): 0.2684 rms_B_bonded: 2.61 r_work: 0.2550 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2418 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2418 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2424 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2424 r_free = 0.2424 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 = 0.2424 r_free = 0.2424 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2424 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 67506 Z= 0.295 Angle : 0.561 9.363 91143 Z= 0.276 Chirality : 0.042 0.217 10855 Planarity : 0.003 0.063 11637 Dihedral : 7.189 174.161 9375 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 5.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.72 % Favored : 96.27 % Rotamer: Outliers : 1.00 % Allowed : 10.58 % Favored : 88.42 % 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: 1.64 (0.09), residues: 8630 helix: 2.42 (0.08), residues: 4490 sheet: -0.01 (0.16), residues: 1101 loop : -0.54 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.006 0.001 HIS G 111 PHE 0.019 0.001 PHE A 167 TYR 0.019 0.001 TYR h 475 ARG 0.004 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 564 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 72 poor density : 492 time to evaluate : 5.923 Fit side-chains REVERT: A 246 MET cc_start: 0.9243 (mmm) cc_final: 0.8764 (mmt) REVERT: B 247 ASP cc_start: 0.8534 (t0) cc_final: 0.8250 (t0) REVERT: B 323 LEU cc_start: 0.9501 (OUTLIER) cc_final: 0.9294 (mm) REVERT: D 373 LEU cc_start: 0.9153 (mt) cc_final: 0.8872 (mt) REVERT: D 399 GLU cc_start: 0.8966 (OUTLIER) cc_final: 0.8713 (mp0) REVERT: E 96 LYS cc_start: 0.8736 (tptp) cc_final: 0.8427 (tptt) REVERT: E 121 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8289 (tp30) REVERT: E 485 MET cc_start: 0.8875 (mpp) cc_final: 0.8633 (mpp) REVERT: G 365 ASP cc_start: 0.9021 (t0) cc_final: 0.8683 (t0) REVERT: H 316 GLU cc_start: 0.8752 (tm-30) cc_final: 0.8323 (tp30) REVERT: Z 15 ARG cc_start: 0.8622 (ttm110) cc_final: 0.8408 (mtp-110) REVERT: b 87 MET cc_start: 0.9433 (ttp) cc_final: 0.9217 (ttp) REVERT: b 215 ASP cc_start: 0.9144 (t0) cc_final: 0.8820 (t0) REVERT: d 227 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9173 (pt) REVERT: e 288 MET cc_start: 0.9148 (OUTLIER) cc_final: 0.8859 (ptp) REVERT: g 52 ASP cc_start: 0.8276 (t70) cc_final: 0.7286 (t70) REVERT: g 54 MET cc_start: 0.8494 (mpp) cc_final: 0.8192 (mpp) REVERT: z 244 VAL cc_start: 0.8827 (OUTLIER) cc_final: 0.8523 (t) REVERT: P 91 LEU cc_start: 0.5635 (tp) cc_final: 0.5206 (tt) REVERT: P 148 MET cc_start: 0.8325 (mmt) cc_final: 0.8039 (mpp) REVERT: P 162 PHE cc_start: 0.7054 (t80) cc_final: 0.6843 (t80) REVERT: P 273 LEU cc_start: 0.5211 (OUTLIER) cc_final: 0.4978 (mm) outliers start: 72 outliers final: 51 residues processed: 547 average time/residue: 0.6025 time to fit residues: 572.0972 Evaluate side-chains 533 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 476 time to evaluate : 5.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 521 ASP Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 147 ASP Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 250 ILE Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 477 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 273 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 177 optimal weight: 0.8980 chunk 522 optimal weight: 4.9990 chunk 569 optimal weight: 3.9990 chunk 66 optimal weight: 8.9990 chunk 746 optimal weight: 1.9990 chunk 117 optimal weight: 0.9990 chunk 148 optimal weight: 5.9990 chunk 329 optimal weight: 5.9990 chunk 162 optimal weight: 0.5980 chunk 90 optimal weight: 9.9990 chunk 317 optimal weight: 5.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2982 r_free = 0.2982 target = 0.077195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2716 r_free = 0.2716 target = 0.063273 restraints weight = 158575.875| |-----------------------------------------------------------------------------| r_work (start): 0.2706 rms_B_bonded: 2.77 r_work: 0.2567 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2567 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 67506 Z= 0.183 Angle : 0.532 10.141 91143 Z= 0.261 Chirality : 0.041 0.207 10855 Planarity : 0.003 0.062 11637 Dihedral : 7.065 170.262 9375 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.27 % Favored : 96.72 % Rotamer: Outliers : 0.83 % Allowed : 11.08 % Favored : 88.09 % 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: 8630 helix: 2.49 (0.08), residues: 4499 sheet: 0.05 (0.16), residues: 1094 loop : -0.50 (0.11), residues: 3037 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.006 0.001 HIS z 161 PHE 0.023 0.001 PHE P 170 TYR 0.020 0.001 TYR D 24 ARG 0.004 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 500 time to evaluate : 5.943 Fit side-chains REVERT: B 247 ASP cc_start: 0.8371 (t0) cc_final: 0.8117 (t0) REVERT: B 323 LEU cc_start: 0.9455 (OUTLIER) cc_final: 0.9250 (mm) REVERT: D 25 GLN cc_start: 0.8988 (tp40) cc_final: 0.8758 (tp40) REVERT: D 373 LEU cc_start: 0.9119 (mt) cc_final: 0.8828 (mt) REVERT: D 399 GLU cc_start: 0.8763 (OUTLIER) cc_final: 0.8489 (mp0) REVERT: E 96 LYS cc_start: 0.8644 (tptp) cc_final: 0.8427 (tptt) REVERT: E 121 GLU cc_start: 0.8646 (tm-30) cc_final: 0.8084 (tp30) REVERT: E 485 MET cc_start: 0.8670 (mpp) cc_final: 0.8439 (mpp) REVERT: G 365 ASP cc_start: 0.8877 (t0) cc_final: 0.8514 (t0) REVERT: H 316 GLU cc_start: 0.8558 (tm-30) cc_final: 0.8124 (tp30) REVERT: b 87 MET cc_start: 0.9330 (ttp) cc_final: 0.9105 (ttp) REVERT: b 215 ASP cc_start: 0.8967 (t0) cc_final: 0.8660 (t0) REVERT: d 429 GLU cc_start: 0.8492 (mp0) cc_final: 0.7989 (mp0) REVERT: e 288 MET cc_start: 0.9041 (OUTLIER) cc_final: 0.8719 (ptp) REVERT: g 52 ASP cc_start: 0.8112 (t70) cc_final: 0.7045 (t70) REVERT: g 54 MET cc_start: 0.8413 (mpp) cc_final: 0.8125 (mpp) REVERT: h 219 THR cc_start: 0.9105 (p) cc_final: 0.8802 (p) REVERT: z 244 VAL cc_start: 0.8689 (OUTLIER) cc_final: 0.8385 (t) REVERT: P 91 LEU cc_start: 0.5596 (tp) cc_final: 0.5178 (tt) REVERT: P 162 PHE cc_start: 0.7002 (t80) cc_final: 0.6785 (t80) REVERT: P 273 LEU cc_start: 0.5164 (OUTLIER) cc_final: 0.4951 (mm) outliers start: 60 outliers final: 45 residues processed: 544 average time/residue: 0.6160 time to fit residues: 584.7408 Evaluate side-chains 538 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 488 time to evaluate : 6.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 168 ILE Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 477 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 194 VAL Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 273 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 772 optimal weight: 5.9990 chunk 817 optimal weight: 1.9990 chunk 484 optimal weight: 4.9990 chunk 159 optimal weight: 4.9990 chunk 429 optimal weight: 7.9990 chunk 810 optimal weight: 2.9990 chunk 427 optimal weight: 7.9990 chunk 697 optimal weight: 0.9980 chunk 460 optimal weight: 2.9990 chunk 124 optimal weight: 10.0000 chunk 575 optimal weight: 4.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN Q 316 ASN ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2959 r_free = 0.2959 target = 0.075836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2691 r_free = 0.2691 target = 0.061926 restraints weight = 159753.224| |-----------------------------------------------------------------------------| r_work (start): 0.2688 rms_B_bonded: 2.75 r_work: 0.2549 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2549 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2550 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8760 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 67506 Z= 0.261 Angle : 0.553 9.408 91143 Z= 0.271 Chirality : 0.042 0.214 10855 Planarity : 0.003 0.062 11637 Dihedral : 7.051 170.090 9375 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.69 % Favored : 96.30 % Rotamer: Outliers : 0.84 % Allowed : 11.22 % Favored : 87.94 % 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: 8630 helix: 2.46 (0.08), residues: 4492 sheet: 0.01 (0.16), residues: 1096 loop : -0.53 (0.11), residues: 3042 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 319 HIS 0.006 0.001 HIS G 111 PHE 0.020 0.001 PHE P 170 TYR 0.022 0.001 TYR D 24 ARG 0.008 0.000 ARG Z 15 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 490 time to evaluate : 6.022 Fit side-chains REVERT: A 246 MET cc_start: 0.9199 (mmm) cc_final: 0.8749 (mmt) REVERT: B 247 ASP cc_start: 0.8437 (t0) cc_final: 0.8180 (t0) REVERT: B 323 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9263 (mm) REVERT: D 25 GLN cc_start: 0.9015 (tp40) cc_final: 0.8810 (tp40) REVERT: D 373 LEU cc_start: 0.9117 (mt) cc_final: 0.8845 (mt) REVERT: D 399 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8501 (mp0) REVERT: E 96 LYS cc_start: 0.8674 (tptp) cc_final: 0.8353 (tptt) REVERT: E 121 GLU cc_start: 0.8659 (tm-30) cc_final: 0.8114 (tp30) REVERT: E 485 MET cc_start: 0.8732 (mpp) cc_final: 0.8516 (mpp) REVERT: G 365 ASP cc_start: 0.8897 (t0) cc_final: 0.8549 (t0) REVERT: H 316 GLU cc_start: 0.8586 (tm-30) cc_final: 0.8165 (tp30) REVERT: b 87 MET cc_start: 0.9358 (ttp) cc_final: 0.9138 (ttp) REVERT: b 215 ASP cc_start: 0.9004 (t0) cc_final: 0.8690 (t0) REVERT: d 227 LEU cc_start: 0.9299 (OUTLIER) cc_final: 0.9083 (pt) REVERT: e 288 MET cc_start: 0.9059 (OUTLIER) cc_final: 0.8777 (ptp) REVERT: g 52 ASP cc_start: 0.8131 (t70) cc_final: 0.7052 (t70) REVERT: g 54 MET cc_start: 0.8431 (mpp) cc_final: 0.8120 (mpp) REVERT: h 219 THR cc_start: 0.9130 (p) cc_final: 0.8825 (p) REVERT: z 244 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8403 (t) REVERT: P 84 MET cc_start: 0.6017 (mmt) cc_final: 0.5447 (mpp) REVERT: P 91 LEU cc_start: 0.5607 (tp) cc_final: 0.5159 (tt) REVERT: P 162 PHE cc_start: 0.7009 (t80) cc_final: 0.6792 (t80) outliers start: 61 outliers final: 51 residues processed: 537 average time/residue: 0.6591 time to fit residues: 621.4044 Evaluate side-chains 538 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 482 time to evaluate : 5.942 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 ASP Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain E residue 494 LEU Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain G residue 151 MET Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 477 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 469 optimal weight: 0.9990 chunk 2 optimal weight: 8.9990 chunk 22 optimal weight: 8.9990 chunk 597 optimal weight: 0.7980 chunk 240 optimal weight: 5.9990 chunk 180 optimal weight: 0.6980 chunk 601 optimal weight: 4.9990 chunk 578 optimal weight: 0.9990 chunk 446 optimal weight: 4.9990 chunk 542 optimal weight: 10.0000 chunk 183 optimal weight: 9.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN E 472 GLN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN Z 294 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2983 r_free = 0.2983 target = 0.077075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2722 r_free = 0.2722 target = 0.063415 restraints weight = 147563.713| |-----------------------------------------------------------------------------| r_work (start): 0.2717 rms_B_bonded: 2.63 r_work: 0.2582 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8736 moved from start: 0.1263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 67506 Z= 0.184 Angle : 0.533 10.502 91143 Z= 0.261 Chirality : 0.041 0.209 10855 Planarity : 0.003 0.062 11637 Dihedral : 6.901 165.111 9375 Min Nonbonded Distance : 1.894 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.35 % Favored : 96.64 % Rotamer: Outliers : 0.79 % Allowed : 11.40 % Favored : 87.81 % 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: 1.74 (0.09), residues: 8630 helix: 2.51 (0.08), residues: 4497 sheet: 0.03 (0.16), residues: 1097 loop : -0.49 (0.11), residues: 3036 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 319 HIS 0.006 0.001 HIS z 161 PHE 0.021 0.001 PHE P 170 TYR 0.024 0.001 TYR D 24 ARG 0.006 0.000 ARG Z 15 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17260 Ramachandran restraints generated. 8630 Oldfield, 0 Emsley, 8630 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 499 time to evaluate : 6.062 Fit side-chains REVERT: A 246 MET cc_start: 0.9177 (mmm) cc_final: 0.8703 (mmt) REVERT: B 247 ASP cc_start: 0.8393 (t0) cc_final: 0.8138 (t0) REVERT: B 323 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9240 (mm) REVERT: D 373 LEU cc_start: 0.9116 (mt) cc_final: 0.8834 (mt) REVERT: D 399 GLU cc_start: 0.8756 (OUTLIER) cc_final: 0.8480 (mp0) REVERT: E 96 LYS cc_start: 0.8643 (tptp) cc_final: 0.8425 (tptt) REVERT: E 121 GLU cc_start: 0.8638 (tm-30) cc_final: 0.8073 (tp30) REVERT: E 485 MET cc_start: 0.8671 (mpp) cc_final: 0.8448 (mpp) REVERT: G 365 ASP cc_start: 0.8846 (t0) cc_final: 0.8523 (t0) REVERT: H 316 GLU cc_start: 0.8561 (tm-30) cc_final: 0.8104 (tp30) REVERT: a 384 MET cc_start: 0.8938 (ttt) cc_final: 0.8692 (ttt) REVERT: b 87 MET cc_start: 0.9339 (ttp) cc_final: 0.9117 (ttp) REVERT: b 215 ASP cc_start: 0.8958 (t0) cc_final: 0.8654 (t0) REVERT: d 227 LEU cc_start: 0.9280 (OUTLIER) cc_final: 0.9069 (pt) REVERT: d 429 GLU cc_start: 0.8480 (mp0) cc_final: 0.8206 (mp0) REVERT: e 288 MET cc_start: 0.9030 (OUTLIER) cc_final: 0.8710 (ptp) REVERT: g 52 ASP cc_start: 0.8106 (t70) cc_final: 0.7025 (t70) REVERT: g 54 MET cc_start: 0.8440 (mpp) cc_final: 0.8147 (mpp) REVERT: h 219 THR cc_start: 0.9099 (p) cc_final: 0.8795 (p) REVERT: z 244 VAL cc_start: 0.8725 (OUTLIER) cc_final: 0.8423 (t) REVERT: P 84 MET cc_start: 0.6057 (mmt) cc_final: 0.5443 (mpp) REVERT: P 91 LEU cc_start: 0.5590 (tp) cc_final: 0.5031 (tt) REVERT: P 162 PHE cc_start: 0.7090 (t80) cc_final: 0.6851 (t80) outliers start: 57 outliers final: 48 residues processed: 543 average time/residue: 0.6264 time to fit residues: 595.2526 Evaluate side-chains 542 residues out of total 7228 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 489 time to evaluate : 5.873 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 251 GLN Chi-restraints excluded: chain A residue 288 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 323 LEU Chi-restraints excluded: chain D residue 68 VAL Chi-restraints excluded: chain D residue 118 ASP Chi-restraints excluded: chain D residue 217 THR Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 430 ILE Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 47 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 9 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 113 LEU Chi-restraints excluded: chain H residue 6 VAL Chi-restraints excluded: chain H residue 145 LYS Chi-restraints excluded: chain H residue 178 MET Chi-restraints excluded: chain H residue 427 ILE Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 236 ASP Chi-restraints excluded: chain Q residue 312 LEU Chi-restraints excluded: chain Q residue 331 THR Chi-restraints excluded: chain Q residue 398 THR Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain Z residue 477 VAL Chi-restraints excluded: chain b residue 30 ILE Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 69 THR Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 304 ILE Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 6 VAL Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 341 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 168 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 341 LEU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 152 LEU Chi-restraints excluded: chain P residue 237 LEU Chi-restraints excluded: chain P residue 273 LEU Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 859 random chunks: chunk 819 optimal weight: 4.9990 chunk 563 optimal weight: 0.5980 chunk 521 optimal weight: 3.9990 chunk 276 optimal weight: 6.9990 chunk 484 optimal weight: 5.9990 chunk 180 optimal weight: 2.9990 chunk 55 optimal weight: 8.9990 chunk 587 optimal weight: 5.9990 chunk 755 optimal weight: 5.9990 chunk 580 optimal weight: 6.9990 chunk 523 optimal weight: 2.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 73 ASN E 472 GLN Q 316 ASN ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN ** z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.075573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2685 r_free = 0.2685 target = 0.061618 restraints weight = 162556.058| |-----------------------------------------------------------------------------| r_work (start): 0.2683 rms_B_bonded: 2.76 r_work: 0.2542 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2542 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2547 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2547 r_free = 0.2547 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2547 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8767 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 67506 Z= 0.284 Angle : 0.565 10.912 91143 Z= 0.276 Chirality : 0.042 0.193 10855 Planarity : 0.003 0.063 11637 Dihedral : 6.876 162.719 9375 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.71 % Favored : 96.28 % Rotamer: Outliers : 0.80 % Allowed : 11.39 % Favored : 87.81 % 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: 1.67 (0.09), residues: 8630 helix: 2.46 (0.08), residues: 4494 sheet: -0.04 (0.16), residues: 1107 loop : -0.53 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP Q 319 HIS 0.006 0.001 HIS G 111 PHE 0.020 0.001 PHE P 170 TYR 0.017 0.001 TYR h 475 ARG 0.009 0.000 ARG Z 15 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 25190.52 seconds wall clock time: 436 minutes 5.16 seconds (26165.16 seconds total)