Starting phenix.real_space_refine on Tue Jan 21 17:37:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sgl_40461/01_2025/8sgl_40461.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sgl_40461/01_2025/8sgl_40461.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sgl_40461/01_2025/8sgl_40461.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sgl_40461/01_2025/8sgl_40461.map" model { file = "/net/cci-nas-00/data/ceres_data/8sgl_40461/01_2025/8sgl_40461.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sgl_40461/01_2025/8sgl_40461.cif" } resolution = 2.9 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= 0.048 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 420 5.16 5 C 42118 2.51 5 N 11736 2.21 5 O 13046 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 53 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: 67432 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: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "N" Number of atoms: 2298 Number of conformers: 1 Conformer: "" Number of residues, atoms: 300, 2298 Classifications: {'peptide': 300} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 293} 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: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 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: 34.73, per 1000 atoms: 0.52 Number of scatterers: 67432 At special positions: 0 Unit cell: (179.86, 176.686, 180.918, 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 420 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13046 8.00 N 11736 7.00 C 42118 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 "HETATM67211 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67339 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67083 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: 13.52 Conformation dependent library (CDL) restraints added in 7.8 seconds 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16322 Finding SS restraints... Secondary structure from input PDB file: 353 helices and 104 sheets defined 55.2% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.50 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.689A 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 109 removed outlier: 3.603A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 140 through 144 Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.192A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.150A 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 258 through 281 removed outlier: 4.502A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.046A 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: 3.560A pdb=" N MET A 344 " --> pdb=" O GLU A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 428 removed outlier: 4.265A pdb=" N THR A 428 " --> pdb=" O GLU A 424 " (cutoff:3.500A) Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.724A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.032A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.591A 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 144 Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 169 through 174 removed outlier: 6.486A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.766A 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: 3.527A 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 removed outlier: 3.569A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 427 removed outlier: 3.739A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.004A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.700A 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: 4.418A 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: 4.233A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.795A 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 173 removed outlier: 3.526A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.542A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (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 292 removed outlier: 3.841A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (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 442 Processing helix chain 'D' and resid 445 through 459 removed outlier: 4.320A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 4.031A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.552A 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 105 through 125 removed outlier: 4.256A pdb=" N VAL E 110 " --> pdb=" O THR E 106 " (cutoff:3.500A) removed outlier: 3.642A 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: 6.556A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 4.149A 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 294 Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.750A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.799A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.878A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.751A 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 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.625A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.585A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.583A pdb=" N VAL G 122 " --> pdb=" O HIS G 118 " (cutoff:3.500A) Processing helix chain 'G' and resid 148 through 161 Processing helix chain 'G' and resid 163 through 167 removed outlier: 4.207A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.689A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.650A 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 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 removed outlier: 3.574A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.616A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.148A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix removed outlier: 3.878A pdb=" N GLU H 114 " --> pdb=" O PRO H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.570A pdb=" N ILE H 121 " --> pdb=" O HIS H 117 " (cutoff:3.500A) Processing helix chain 'H' and resid 147 through 164 Processing helix chain 'H' and resid 168 through 170 No H-bonds generated for 'chain 'H' and resid 168 through 170' Processing helix chain 'H' and resid 171 through 185 removed outlier: 3.646A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.522A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.598A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.386A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.465A 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 removed outlier: 3.516A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 144 through 147' Processing helix chain 'Q' and resid 156 through 171 removed outlier: 4.257A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.518A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N SER Q 170 " --> pdb=" O THR Q 166 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LYS Q 171 " --> pdb=" O SER Q 167 " (cutoff:3.500A) Processing helix chain 'Q' and resid 175 through 190 removed outlier: 4.318A pdb=" N LEU Q 179 " --> pdb=" O ASN Q 175 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE Q 190 " --> pdb=" O ALA Q 186 " (cutoff:3.500A) Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 4.854A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.896A 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 340 through 344 removed outlier: 3.596A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.893A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.277A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 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: 3.671A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.892A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 3.962A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.590A 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: 3.701A 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: 3.612A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.762A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.366A 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: 4.253A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.784A 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: 3.665A 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 91 through 110 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 144 through 157 removed outlier: 4.179A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.195A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 258 through 281 removed outlier: 4.563A pdb=" N GLN a 262 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 5.232A 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 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 Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.512A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.811A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.793A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 168 Processing helix chain 'b' and resid 169 through 174 removed outlier: 6.603A pdb=" N LEU b 172 " --> pdb=" O SER b 169 " (cutoff:3.500A) removed outlier: 3.648A 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 208 through 212 removed outlier: 3.599A pdb=" N SER b 212 " --> pdb=" O LEU b 209 " (cutoff:3.500A) Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.574A 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 428 Processing helix chain 'b' and resid 431 through 453 Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.545A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.714A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 4.106A 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 173 removed outlier: 3.791A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 4.481A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 178 removed outlier: 4.221A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 Proline residue: d 185 - end of helix removed outlier: 3.596A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N ILE d 195 " --> pdb=" O VAL d 191 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 3.729A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 removed outlier: 3.560A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.903A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.843A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 25 removed outlier: 3.560A pdb=" N LYS e 25 " --> pdb=" O GLN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.856A 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: 4.302A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 152 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.483A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.950A 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: 3.906A 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 removed outlier: 3.566A pdb=" N LEU e 353 " --> pdb=" O ALA e 350 " (cutoff:3.500A) Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 440 removed outlier: 3.961A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.901A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.569A 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 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.636A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.856A 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: 3.733A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 141 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: 3.842A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 Processing helix chain 'g' and resid 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 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 426 Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' 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 36 through 40 Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.668A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.239A 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: 3.723A 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: 3.760A 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 removed outlier: 3.532A pdb=" N SER h 284 " --> pdb=" O LYS h 280 " (cutoff:3.500A) 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: 3.635A pdb=" N LEU h 342 " --> pdb=" O ALA h 339 " (cutoff:3.500A) Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.512A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.088A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.817A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.755A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.509A 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 168 removed outlier: 4.304A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.368A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 176 through 190 Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 286 removed outlier: 4.789A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.722A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.697A 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 428 Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.161A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 Processing helix chain 'z' and resid 16 through 35 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: 3.669A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.744A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.236A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.619A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 189 No H-bonds generated for 'chain 'z' and resid 187 through 189' Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.762A 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: 3.543A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.689A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 317 through 329 removed outlier: 3.637A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.222A 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 removed outlier: 3.537A pdb=" N ASP z 404 " --> pdb=" O ASN z 400 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 430 through 432 No H-bonds generated for 'chain 'z' and resid 430 through 432' Processing helix chain 'z' and resid 433 through 445 Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.540A 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 498 through 517 Processing helix chain 'N' and resid 249 through 252 Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.562A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.764A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.553A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA3, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA4, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA5, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.313A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.523A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.516A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.516A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.656A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.069A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.240A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.623A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.282A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.390A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.820A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.611A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 61 through 64 removed outlier: 7.063A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.967A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.648A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB4, first strand: chain 'B' and resid 199 through 205 removed outlier: 6.652A pdb=" N HIS B 200 " --> pdb=" O ILE B 373 " (cutoff:3.500A) removed outlier: 7.550A pdb=" N LEU B 375 " --> pdb=" O HIS B 200 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ILE B 202 " --> pdb=" O LEU B 375 " (cutoff:3.500A) removed outlier: 7.942A pdb=" N GLY B 377 " --> pdb=" O ILE B 202 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N LYS B 204 " --> pdb=" O GLY B 377 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.402A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.773A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB7, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB8, first strand: chain 'D' and resid 208 through 214 removed outlier: 3.900A pdb=" N GLY D 392 " --> pdb=" O LYS D 213 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.833A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.081A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.009A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.323A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.554A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.329A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 491 through 494 Processing sheet with id=AC2, first strand: chain 'E' and resid 28 through 29 removed outlier: 7.212A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.111A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC4, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.804A 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: 6.614A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.614A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.980A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.862A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.739A 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: 6.397A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.549A 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: 6.667A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.405A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.993A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.370A 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 17 removed outlier: 6.336A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.534A 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: 6.880A pdb=" N MET Z 44 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 3.869A pdb=" N GLN Q 523 " --> pdb=" O MET Z 44 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.932A 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: 6.564A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.426A 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: 6.431A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.258A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.651A 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: 6.323A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.071A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.849A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.163A 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 Processing sheet with id=AF4, first strand: chain 'a' and resid 9 through 13 removed outlier: 4.483A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.327A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.509A 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: 7.281A pdb=" N ASP a 42 " --> pdb=" O ASP g 521 " (cutoff:3.500A) removed outlier: 8.565A pdb=" N VAL g 523 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N MET a 44 " --> pdb=" O VAL g 523 " (cutoff:3.500A) removed outlier: 8.244A pdb=" N GLY g 525 " --> pdb=" O MET a 44 " (cutoff:3.500A) removed outlier: 8.401A pdb=" N VAL a 46 " --> pdb=" O GLY g 525 " (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 199 removed outlier: 6.249A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.343A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.573A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.665A 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: 6.573A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.665A 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: 9.200A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.337A 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: 4.337A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.657A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.007A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.036A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.907A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG7, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.738A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.442A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 6.387A pdb=" N PHE b 290 " --> pdb=" O ILE b 312 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.442A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.668A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 9.032A pdb=" N ALA b 332 " --> pdb=" O ILE b 237 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N ILE b 239 " --> pdb=" O ALA b 332 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH2, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH3, first strand: chain 'd' and resid 208 through 212 removed outlier: 6.380A pdb=" N LYS d 209 " --> pdb=" O ILE d 388 " (cutoff:3.500A) removed outlier: 7.423A pdb=" N VAL d 390 " --> pdb=" O LYS d 209 " (cutoff:3.500A) removed outlier: 6.496A pdb=" N VAL d 211 " --> pdb=" O VAL d 390 " (cutoff:3.500A) No H-bonds generated for sheet with id=AH3 Processing sheet with id=AH4, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.613A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.293A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N VAL d 297 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.659A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.746A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.798A 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 29 removed outlier: 4.396A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.210A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.884A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.666A 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: 3.836A 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: 6.456A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 7.268A pdb=" N LEU e 299 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 5.804A pdb=" N LYS e 247 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N ILE e 301 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.706A 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: 7.294A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.592A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (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: 3.884A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (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 310 through 312 removed outlier: 6.468A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 8.965A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) 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: 6.445A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.762A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ2, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ3, first strand: chain 'h' and resid 405 through 407 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 23 removed outlier: 4.866A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.829A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.661A 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: 3.783A 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: 6.576A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.202A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 8.008A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.080A 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 191 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: 9.067A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 8.016A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.365A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.534A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.946A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.181A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.261A 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 'N' and resid 97 through 99 removed outlier: 6.910A pdb=" N VAL N 393 " --> pdb=" O ARG N 98 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'N' and resid 108 through 112 Processing sheet with id=AK9, first strand: chain 'N' and resid 128 through 130 Processing sheet with id=AL1, first strand: chain 'N' and resid 150 through 155 Processing sheet with id=AL2, first strand: chain 'N' and resid 198 through 203 removed outlier: 6.647A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.788A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AL3, first strand: chain 'N' and resid 240 through 245 removed outlier: 6.425A pdb=" N GLY N 257 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.419A pdb=" N LEU N 243 " --> pdb=" O VAL N 255 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N VAL N 255 " --> pdb=" O LEU N 243 " (cutoff:3.500A) Processing sheet with id=AL4, first strand: chain 'N' and resid 284 through 289 removed outlier: 6.645A pdb=" N GLY N 299 " --> pdb=" O ASN N 285 " (cutoff:3.500A) removed outlier: 4.504A pdb=" N VAL N 287 " --> pdb=" O ALA N 297 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N ALA N 297 " --> pdb=" O VAL N 287 " (cutoff:3.500A) removed outlier: 4.735A pdb=" N TYR N 289 " --> pdb=" O ALA N 295 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA N 295 " --> pdb=" O TYR N 289 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N CYS N 305 " --> pdb=" O ILE N 318 " (cutoff:3.500A) removed outlier: 4.748A pdb=" N ILE N 318 " --> pdb=" O CYS N 305 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N LEU N 307 " --> pdb=" O VAL N 316 " (cutoff:3.500A) Processing sheet with id=AL5, first strand: chain 'N' and resid 328 through 331 removed outlier: 3.937A pdb=" N SER N 361 " --> pdb=" O VAL N 351 " (cutoff:3.500A) 4099 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: 35.75 Time building geometry restraints manager: 15.94 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: 22692 1.34 - 1.46: 11924 1.46 - 1.58: 32816 1.58 - 1.70: 48 1.70 - 1.81: 738 Bond restraints: 68218 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.53e+01 bond pdb=" F2 AF3 A 603 " pdb="AL AF3 A 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 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 6.37e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 68213 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.93: 91581 2.93 - 5.87: 504 5.87 - 8.80: 48 8.80 - 11.73: 0 11.73 - 14.67: 1 Bond angle restraints: 92134 Sorted by residual: angle pdb=" CA LEU d 513 " pdb=" CB LEU d 513 " pdb=" CG LEU d 513 " ideal model delta sigma weight residual 116.30 130.97 -14.67 3.50e+00 8.16e-02 1.76e+01 angle pdb=" CA MET B 160 " pdb=" CB MET B 160 " pdb=" CG MET B 160 " ideal model delta sigma weight residual 114.10 120.95 -6.85 2.00e+00 2.50e-01 1.17e+01 angle pdb=" C GLN q 472 " pdb=" N GLU q 473 " pdb=" CA GLU q 473 " ideal model delta sigma weight residual 121.58 114.90 6.68 1.95e+00 2.63e-01 1.17e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 121.06 -7.88 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.02 -7.84 2.37e+00 1.78e-01 1.10e+01 ... (remaining 92129 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.93: 41460 35.93 - 71.85: 599 71.85 - 107.78: 58 107.78 - 143.71: 10 143.71 - 179.64: 5 Dihedral angle restraints: 42132 sinusoidal: 16920 harmonic: 25212 Sorted by residual: 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 -60.00 119.64 -179.64 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.18 -169.18 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual 300.00 131.76 168.24 1 2.00e+01 2.50e-03 4.75e+01 ... (remaining 42129 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 8021 0.040 - 0.081: 2057 0.081 - 0.121: 821 0.121 - 0.161: 59 0.161 - 0.202: 5 Chirality restraints: 10963 Sorted by residual: chirality pdb=" CB VAL h 36 " pdb=" CA VAL h 36 " pdb=" CG1 VAL h 36 " pdb=" CG2 VAL h 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 9.05e-01 chirality pdb=" CA ILE B 11 " pdb=" N ILE B 11 " pdb=" C ILE B 11 " pdb=" CB ILE B 11 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.17 2.00e-01 2.50e+01 7.01e-01 ... (remaining 10960 not shown) Planarity restraints: 11759 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS a 73 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.88e+00 pdb=" C LYS a 73 " -0.045 2.00e-02 2.50e+03 pdb=" O LYS a 73 " 0.017 2.00e-02 2.50e+03 pdb=" N VAL a 74 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.035 5.00e-02 4.00e+02 5.28e-02 4.47e+00 pdb=" N PRO e 441 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS A 73 " -0.009 2.00e-02 2.50e+03 1.85e-02 3.41e+00 pdb=" C LYS A 73 " 0.032 2.00e-02 2.50e+03 pdb=" O LYS A 73 " -0.012 2.00e-02 2.50e+03 pdb=" N VAL A 74 " -0.011 2.00e-02 2.50e+03 ... (remaining 11756 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 568 2.53 - 3.12: 50838 3.12 - 3.71: 105788 3.71 - 4.31: 149819 4.31 - 4.90: 257997 Nonbonded interactions: 565010 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.932 2.120 nonbonded pdb=" O3B ADP z 601 " pdb="MG MG z 602 " model vdw 1.946 2.170 nonbonded pdb=" O3A ADP B 601 " pdb="MG MG B 602 " model vdw 1.948 2.170 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.954 2.170 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.962 2.120 ... (remaining 565005 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 4 through 535 or resid 601 through 603)) selection = chain 'a' } ncs_group { reference = (chain 'B' and (resid 2 through 526 or resid 601 through 603)) selection = chain 'b' } ncs_group { reference = (chain 'D' and ((resid 19 and (name N or name CA or name C or name O or name CB \ )) or resid 20 through 538 or resid 601 through 603)) selection = chain 'd' } ncs_group { reference = (chain 'E' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) selection = (chain 'e' and (resid 2 through 8 or resid 10 through 536 or resid 601 through 6 \ 03)) } ncs_group { reference = (chain 'G' and (resid 5 through 528 or resid 601 through 603)) selection = (chain 'g' and (resid 5 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.940 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.080 Extract box with map and model: 2.250 Check model and map are aligned: 0.390 Set scattering table: 0.510 Process input model: 135.310 Find NCS groups from input model: 5.610 Set up NCS constraints: 0.430 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:11.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 157.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 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 : 0.005 0.162 68218 Z= 0.318 Angle : 0.553 14.667 92134 Z= 0.270 Chirality : 0.042 0.202 10963 Planarity : 0.003 0.053 11759 Dihedral : 14.206 179.636 25810 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % 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: 1.62 (0.09), residues: 8734 helix: 2.36 (0.08), residues: 4379 sheet: 0.11 (0.15), residues: 1259 loop : -0.35 (0.11), residues: 3096 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP N 394 HIS 0.013 0.001 HIS z 161 PHE 0.024 0.001 PHE b 12 TYR 0.015 0.001 TYR N 155 ARG 0.006 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 607 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 607 time to evaluate : 6.221 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7420 (t0) cc_final: 0.7027 (t0) REVERT: A 388 MET cc_start: 0.9331 (mtp) cc_final: 0.9033 (mtm) REVERT: G 15 LYS cc_start: 0.8792 (mptt) cc_final: 0.8573 (mmmt) REVERT: G 229 MET cc_start: 0.9437 (mtt) cc_final: 0.9174 (mtt) REVERT: G 521 ASP cc_start: 0.7914 (t70) cc_final: 0.7578 (t70) REVERT: H 440 LYS cc_start: 0.9113 (ttmt) cc_final: 0.8886 (ttpp) REVERT: a 10 ASP cc_start: 0.8403 (m-30) cc_final: 0.8142 (m-30) REVERT: a 473 GLU cc_start: 0.8076 (tm-30) cc_final: 0.7782 (tm-30) REVERT: d 186 MET cc_start: 0.8929 (ttm) cc_final: 0.8705 (ttp) REVERT: e 146 GLU cc_start: 0.8004 (tp30) cc_final: 0.7656 (tp30) REVERT: g 52 ASP cc_start: 0.7363 (t0) cc_final: 0.6915 (t0) REVERT: g 54 MET cc_start: 0.8205 (mpp) cc_final: 0.7995 (mpt) REVERT: g 69 GLU cc_start: 0.8350 (mm-30) cc_final: 0.7892 (mp0) REVERT: g 395 MET cc_start: 0.9314 (mtm) cc_final: 0.9097 (mtm) REVERT: h 324 MET cc_start: 0.8964 (mmm) cc_final: 0.8704 (mmm) REVERT: z 353 TYR cc_start: 0.8619 (t80) cc_final: 0.8341 (t80) REVERT: N 209 GLN cc_start: 0.8547 (mp10) cc_final: 0.8077 (mp10) REVERT: N 326 PHE cc_start: 0.7730 (m-80) cc_final: 0.7346 (m-80) REVERT: N 394 TRP cc_start: 0.7556 (m-90) cc_final: 0.5769 (m-90) outliers start: 0 outliers final: 0 residues processed: 607 average time/residue: 1.5770 time to fit residues: 1236.0275 Evaluate side-chains 472 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 472 time to evaluate : 5.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 733 optimal weight: 0.1980 chunk 658 optimal weight: 0.9990 chunk 365 optimal weight: 0.9980 chunk 224 optimal weight: 9.9990 chunk 444 optimal weight: 10.0000 chunk 351 optimal weight: 6.9990 chunk 681 optimal weight: 0.0030 chunk 263 optimal weight: 5.9990 chunk 414 optimal weight: 10.0000 chunk 506 optimal weight: 6.9990 chunk 789 optimal weight: 10.0000 overall best weight: 1.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS ** H 470 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 17 GLN ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 205 GLN d 468 ASN g 12 GLN z 84 GLN z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.074977 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.060461 restraints weight = 217084.214| |-----------------------------------------------------------------------------| r_work (start): 0.2748 rms_B_bonded: 3.22 r_work: 0.2599 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2596 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2596 r_free = 0.2596 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2596 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.0763 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 68218 Z= 0.198 Angle : 0.563 12.822 92134 Z= 0.280 Chirality : 0.042 0.162 10963 Planarity : 0.003 0.060 11759 Dihedral : 7.307 179.503 9484 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 0.77 % Allowed : 5.89 % Favored : 93.34 % 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: 8734 helix: 2.39 (0.08), residues: 4419 sheet: 0.12 (0.15), residues: 1217 loop : -0.39 (0.11), residues: 3098 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 132 HIS 0.010 0.001 HIS z 161 PHE 0.017 0.001 PHE A 167 TYR 0.013 0.001 TYR N 344 ARG 0.012 0.000 ARG H 425 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 514 time to evaluate : 6.249 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7643 (t0) cc_final: 0.7332 (t0) REVERT: A 48 ASP cc_start: 0.8102 (OUTLIER) cc_final: 0.7715 (p0) REVERT: A 430 MET cc_start: 0.7819 (mmm) cc_final: 0.7479 (mmt) REVERT: B 197 GLU cc_start: 0.9064 (mm-30) cc_final: 0.8758 (mm-30) REVERT: D 458 MET cc_start: 0.8536 (tpp) cc_final: 0.7586 (mpp) REVERT: G 15 LYS cc_start: 0.8638 (mptt) cc_final: 0.8337 (mmmt) REVERT: G 521 ASP cc_start: 0.8182 (t70) cc_final: 0.7696 (t70) REVERT: H 81 ASP cc_start: 0.8841 (OUTLIER) cc_final: 0.8458 (m-30) REVERT: H 187 ASP cc_start: 0.8604 (p0) cc_final: 0.8236 (p0) REVERT: H 440 LYS cc_start: 0.9244 (ttmt) cc_final: 0.9017 (ttpp) REVERT: Z 44 MET cc_start: 0.8515 (mtm) cc_final: 0.8286 (mtp) REVERT: Z 357 GLU cc_start: 0.8533 (tt0) cc_final: 0.8291 (pp20) REVERT: a 10 ASP cc_start: 0.8751 (m-30) cc_final: 0.8434 (m-30) REVERT: a 23 MET cc_start: 0.8301 (OUTLIER) cc_final: 0.8091 (tmm) REVERT: a 473 GLU cc_start: 0.8326 (tm-30) cc_final: 0.7979 (tm-30) REVERT: e 4 MET cc_start: 0.6149 (tmt) cc_final: 0.5076 (mpm) REVERT: e 146 GLU cc_start: 0.8794 (tp30) cc_final: 0.8290 (tp30) REVERT: e 426 GLU cc_start: 0.9125 (mp0) cc_final: 0.8834 (mp0) REVERT: e 446 TYR cc_start: 0.8637 (m-80) cc_final: 0.8416 (m-80) REVERT: g 52 ASP cc_start: 0.7735 (t0) cc_final: 0.7154 (t0) REVERT: g 54 MET cc_start: 0.8578 (mpp) cc_final: 0.8175 (mpt) REVERT: g 151 MET cc_start: 0.9110 (tpt) cc_final: 0.8702 (tpt) REVERT: g 415 GLU cc_start: 0.9096 (mp0) cc_final: 0.8835 (mp0) REVERT: h 227 MET cc_start: 0.9436 (OUTLIER) cc_final: 0.9221 (mtp) REVERT: h 324 MET cc_start: 0.9311 (mmm) cc_final: 0.9045 (mmm) REVERT: h 524 ARG cc_start: 0.7804 (tmt170) cc_final: 0.7460 (tmm160) REVERT: q 26 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8525 (pm20) REVERT: q 116 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8835 (tt0) REVERT: z 353 TYR cc_start: 0.8806 (t80) cc_final: 0.8466 (t80) REVERT: z 487 MET cc_start: 0.8699 (ppp) cc_final: 0.8463 (ppp) REVERT: N 125 GLN cc_start: 0.8000 (tm-30) cc_final: 0.7727 (tm-30) REVERT: N 132 TRP cc_start: 0.7954 (OUTLIER) cc_final: 0.7415 (p90) REVERT: N 145 MET cc_start: 0.7092 (mmm) cc_final: 0.6799 (mmm) REVERT: N 193 MET cc_start: 0.6923 (OUTLIER) cc_final: 0.6484 (mpm) REVERT: N 319 TYR cc_start: 0.7031 (m-80) cc_final: 0.6714 (m-80) REVERT: N 326 PHE cc_start: 0.7462 (m-80) cc_final: 0.7117 (m-80) REVERT: N 394 TRP cc_start: 0.7915 (m-90) cc_final: 0.7246 (m-90) outliers start: 56 outliers final: 13 residues processed: 535 average time/residue: 1.5494 time to fit residues: 1081.5367 Evaluate side-chains 492 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 471 time to evaluate : 6.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain D residue 446 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 23 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 116 GLU Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain N residue 132 TRP Chi-restraints excluded: chain N residue 193 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 204 optimal weight: 8.9990 chunk 336 optimal weight: 10.0000 chunk 338 optimal weight: 2.9990 chunk 120 optimal weight: 5.9990 chunk 735 optimal weight: 5.9990 chunk 558 optimal weight: 9.9990 chunk 185 optimal weight: 7.9990 chunk 54 optimal weight: 5.9990 chunk 12 optimal weight: 10.0000 chunk 270 optimal weight: 7.9990 chunk 664 optimal weight: 0.8980 overall best weight: 4.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 450 ASN G 111 HIS Z 161 HIS Z 453 GLN g 12 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.072046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.058025 restraints weight = 183802.521| |-----------------------------------------------------------------------------| r_work (start): 0.2690 rms_B_bonded: 2.90 r_work: 0.2550 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2550 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2550 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2550 r_free = 0.2550 target_work(ls_wunit_k1) = 0.052 | | 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) = 0.052 | | 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: 0.8599 moved from start: 0.0941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.059 68218 Z= 0.395 Angle : 0.613 9.631 92134 Z= 0.304 Chirality : 0.044 0.180 10963 Planarity : 0.003 0.061 11759 Dihedral : 7.188 176.326 9484 Min Nonbonded Distance : 1.745 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.22 % Allowed : 7.81 % Favored : 90.98 % 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: 1.50 (0.09), residues: 8734 helix: 2.26 (0.08), residues: 4437 sheet: -0.02 (0.15), residues: 1203 loop : -0.45 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP N 132 HIS 0.014 0.001 HIS Z 161 PHE 0.018 0.002 PHE a 167 TYR 0.014 0.001 TYR Q 304 ARG 0.012 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 470 time to evaluate : 6.073 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7698 (t0) cc_final: 0.7271 (t0) REVERT: A 48 ASP cc_start: 0.8431 (OUTLIER) cc_final: 0.8002 (p0) REVERT: B 197 GLU cc_start: 0.9089 (mm-30) cc_final: 0.8854 (mm-30) REVERT: D 57 MET cc_start: 0.9322 (mmm) cc_final: 0.9048 (mmm) REVERT: D 458 MET cc_start: 0.8623 (tpp) cc_final: 0.8358 (tpp) REVERT: G 15 LYS cc_start: 0.8687 (mptt) cc_final: 0.8348 (mmmt) REVERT: G 521 ASP cc_start: 0.8197 (t70) cc_final: 0.7734 (t70) REVERT: H 11 GLU cc_start: 0.8308 (pm20) cc_final: 0.7768 (pp20) REVERT: H 81 ASP cc_start: 0.8868 (OUTLIER) cc_final: 0.8482 (m-30) REVERT: H 440 LYS cc_start: 0.9247 (ttmt) cc_final: 0.9015 (ttpp) REVERT: Z 44 MET cc_start: 0.8552 (mtm) cc_final: 0.8313 (mtp) REVERT: Z 357 GLU cc_start: 0.8554 (tt0) cc_final: 0.8239 (pp20) REVERT: Z 358 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8627 (pt0) REVERT: Z 522 MET cc_start: 0.8881 (OUTLIER) cc_final: 0.8626 (mtt) REVERT: a 10 ASP cc_start: 0.8721 (m-30) cc_final: 0.8439 (m-30) REVERT: a 473 GLU cc_start: 0.8418 (tm-30) cc_final: 0.8081 (tm-30) REVERT: d 48 ILE cc_start: 0.8961 (OUTLIER) cc_final: 0.8648 (pp) REVERT: e 146 GLU cc_start: 0.8780 (tp30) cc_final: 0.8279 (tp30) REVERT: e 426 GLU cc_start: 0.9138 (mp0) cc_final: 0.8804 (mp0) REVERT: g 52 ASP cc_start: 0.7822 (t0) cc_final: 0.7233 (t0) REVERT: g 54 MET cc_start: 0.8642 (mpp) cc_final: 0.8165 (mpt) REVERT: g 415 GLU cc_start: 0.9059 (mp0) cc_final: 0.8802 (mp0) REVERT: h 227 MET cc_start: 0.9442 (mtp) cc_final: 0.9157 (mtp) REVERT: q 26 GLU cc_start: 0.8794 (OUTLIER) cc_final: 0.8513 (pm20) REVERT: z 244 VAL cc_start: 0.8423 (OUTLIER) cc_final: 0.8201 (t) REVERT: z 353 TYR cc_start: 0.8794 (t80) cc_final: 0.8498 (t80) REVERT: z 487 MET cc_start: 0.8756 (ppp) cc_final: 0.8481 (ppp) REVERT: N 125 GLN cc_start: 0.7850 (tm-30) cc_final: 0.7618 (tm-30) REVERT: N 132 TRP cc_start: 0.7983 (OUTLIER) cc_final: 0.7571 (p90) REVERT: N 145 MET cc_start: 0.7208 (mmm) cc_final: 0.6860 (mmm) REVERT: N 305 CYS cc_start: 0.8911 (m) cc_final: 0.8643 (m) REVERT: N 326 PHE cc_start: 0.7309 (m-80) cc_final: 0.6977 (m-80) REVERT: N 394 TRP cc_start: 0.7714 (m-90) cc_final: 0.7084 (m-90) outliers start: 89 outliers final: 28 residues processed: 517 average time/residue: 1.5340 time to fit residues: 1035.3488 Evaluate side-chains 492 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 456 time to evaluate : 6.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 247 LYS Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 471 GLU Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 146 ILE Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 63 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 445 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 132 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 121 optimal weight: 3.9990 chunk 390 optimal weight: 7.9990 chunk 403 optimal weight: 6.9990 chunk 165 optimal weight: 6.9990 chunk 686 optimal weight: 5.9990 chunk 680 optimal weight: 0.9990 chunk 269 optimal weight: 1.9990 chunk 159 optimal weight: 9.9990 chunk 266 optimal weight: 2.9990 chunk 626 optimal weight: 6.9990 chunk 363 optimal weight: 3.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN D 502 ASN G 111 HIS Q 32 ASN Z 161 HIS g 12 GLN ** h 151 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.073292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2726 r_free = 0.2726 target = 0.059323 restraints weight = 176716.420| |-----------------------------------------------------------------------------| r_work (start): 0.2735 rms_B_bonded: 2.90 r_work: 0.2596 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2592 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2592 r_free = 0.2592 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2592 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8653 moved from start: 0.1022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 68218 Z= 0.269 Angle : 0.567 8.634 92134 Z= 0.280 Chirality : 0.042 0.160 10963 Planarity : 0.003 0.061 11759 Dihedral : 7.073 177.839 9484 Min Nonbonded Distance : 1.793 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 1.04 % Allowed : 9.26 % Favored : 89.70 % 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: 1.52 (0.09), residues: 8734 helix: 2.31 (0.08), residues: 4433 sheet: -0.03 (0.15), residues: 1202 loop : -0.46 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP N 132 HIS 0.014 0.001 HIS Z 161 PHE 0.018 0.001 PHE A 167 TYR 0.014 0.001 TYR b 456 ARG 0.011 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 478 time to evaluate : 6.207 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7532 (t0) cc_final: 0.7155 (t0) REVERT: A 48 ASP cc_start: 0.8599 (OUTLIER) cc_final: 0.8238 (p0) REVERT: A 430 MET cc_start: 0.7625 (mmm) cc_final: 0.7362 (mmt) REVERT: B 197 GLU cc_start: 0.9084 (mm-30) cc_final: 0.8875 (mm-30) REVERT: D 57 MET cc_start: 0.9409 (mmm) cc_final: 0.9171 (mmm) REVERT: D 458 MET cc_start: 0.8703 (tpp) cc_final: 0.8391 (tpp) REVERT: G 15 LYS cc_start: 0.8739 (mptt) cc_final: 0.8418 (mmmt) REVERT: G 521 ASP cc_start: 0.8158 (t70) cc_final: 0.7649 (t70) REVERT: H 11 GLU cc_start: 0.8316 (pm20) cc_final: 0.7767 (pp20) REVERT: H 81 ASP cc_start: 0.8861 (OUTLIER) cc_final: 0.8474 (m-30) REVERT: H 440 LYS cc_start: 0.9281 (ttmt) cc_final: 0.9041 (ttpp) REVERT: Z 44 MET cc_start: 0.8578 (mtm) cc_final: 0.8354 (mtp) REVERT: Z 357 GLU cc_start: 0.8522 (tt0) cc_final: 0.8316 (pp20) REVERT: Z 358 GLU cc_start: 0.8866 (OUTLIER) cc_final: 0.8623 (pt0) REVERT: Z 522 MET cc_start: 0.8840 (OUTLIER) cc_final: 0.8593 (mtt) REVERT: a 10 ASP cc_start: 0.8690 (m-30) cc_final: 0.8440 (m-30) REVERT: a 68 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.8632 (mm-30) REVERT: a 473 GLU cc_start: 0.8470 (tm-30) cc_final: 0.8120 (tm-30) REVERT: b 353 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8257 (tmm) REVERT: b 415 MET cc_start: 0.9407 (mmm) cc_final: 0.9042 (mmp) REVERT: d 48 ILE cc_start: 0.8798 (OUTLIER) cc_final: 0.8547 (pp) REVERT: e 146 GLU cc_start: 0.8812 (tp30) cc_final: 0.8312 (tp30) REVERT: e 426 GLU cc_start: 0.9161 (mp0) cc_final: 0.8864 (mp0) REVERT: e 446 TYR cc_start: 0.8688 (m-80) cc_final: 0.8482 (m-80) REVERT: g 52 ASP cc_start: 0.7849 (t0) cc_final: 0.7171 (t0) REVERT: g 54 MET cc_start: 0.8659 (mpp) cc_final: 0.8144 (mpt) REVERT: g 151 MET cc_start: 0.9149 (tpp) cc_final: 0.8829 (tpt) REVERT: h 227 MET cc_start: 0.9487 (mtp) cc_final: 0.9177 (mtp) REVERT: h 524 ARG cc_start: 0.7679 (tmt170) cc_final: 0.7390 (tmm160) REVERT: q 26 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8519 (pm20) REVERT: z 353 TYR cc_start: 0.8837 (t80) cc_final: 0.8534 (t80) REVERT: N 125 GLN cc_start: 0.7788 (tm-30) cc_final: 0.7502 (tm-30) REVERT: N 145 MET cc_start: 0.7299 (mmm) cc_final: 0.7025 (mmm) REVERT: N 305 CYS cc_start: 0.8930 (m) cc_final: 0.8716 (m) REVERT: N 326 PHE cc_start: 0.7446 (m-80) cc_final: 0.7115 (m-80) REVERT: N 394 TRP cc_start: 0.7764 (m-90) cc_final: 0.6312 (m-90) outliers start: 76 outliers final: 29 residues processed: 526 average time/residue: 1.5812 time to fit residues: 1090.8463 Evaluate side-chains 498 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 461 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain Z residue 522 MET Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain g residue 46 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 428 optimal weight: 3.9990 chunk 707 optimal weight: 10.0000 chunk 615 optimal weight: 0.5980 chunk 16 optimal weight: 7.9990 chunk 128 optimal weight: 4.9990 chunk 602 optimal weight: 0.9980 chunk 852 optimal weight: 0.0370 chunk 378 optimal weight: 3.9990 chunk 669 optimal weight: 3.9990 chunk 71 optimal weight: 5.9990 chunk 382 optimal weight: 9.9990 overall best weight: 1.9262 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS Z 161 HIS e 504 GLN g 12 GLN h 151 GLN ** q 471 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 = 0.3005 r_free = 0.3005 target = 0.074084 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2742 r_free = 0.2742 target = 0.060085 restraints weight = 180834.360| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.92 r_work: 0.2616 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2616 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2603 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2603 r_free = 0.2603 target_work(ls_wunit_k1) = 0.054 | | 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) = 0.054 | | 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: 0.8652 moved from start: 0.1072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 68218 Z= 0.210 Angle : 0.550 8.852 92134 Z= 0.270 Chirality : 0.042 0.159 10963 Planarity : 0.003 0.060 11759 Dihedral : 6.978 179.652 9484 Min Nonbonded Distance : 1.777 Molprobity Statistics. All-atom Clashscore : 5.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.94 % Allowed : 10.28 % Favored : 88.77 % 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: 1.60 (0.09), residues: 8734 helix: 2.38 (0.08), residues: 4429 sheet: -0.03 (0.15), residues: 1200 loop : -0.42 (0.11), residues: 3105 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.015 0.001 HIS Z 161 PHE 0.019 0.001 PHE A 167 TYR 0.014 0.001 TYR b 456 ARG 0.013 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 560 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 491 time to evaluate : 6.230 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7520 (t0) cc_final: 0.7164 (t0) REVERT: A 48 ASP cc_start: 0.8692 (OUTLIER) cc_final: 0.8315 (p0) REVERT: A 430 MET cc_start: 0.7688 (mmm) cc_final: 0.7420 (mmt) REVERT: D 57 MET cc_start: 0.9388 (mmm) cc_final: 0.9131 (mmm) REVERT: D 458 MET cc_start: 0.8711 (tpp) cc_final: 0.8396 (tpp) REVERT: G 15 LYS cc_start: 0.8747 (mptt) cc_final: 0.8423 (mmmt) REVERT: G 521 ASP cc_start: 0.8136 (t70) cc_final: 0.7623 (t70) REVERT: H 11 GLU cc_start: 0.8323 (pm20) cc_final: 0.7765 (pp20) REVERT: H 81 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8461 (m-30) REVERT: H 440 LYS cc_start: 0.9310 (ttmt) cc_final: 0.9063 (ttpp) REVERT: Z 44 MET cc_start: 0.8561 (mtm) cc_final: 0.8346 (mtp) REVERT: Z 357 GLU cc_start: 0.8517 (tt0) cc_final: 0.8282 (pp20) REVERT: a 10 ASP cc_start: 0.8687 (m-30) cc_final: 0.8435 (m-30) REVERT: a 68 GLU cc_start: 0.8886 (OUTLIER) cc_final: 0.8632 (mm-30) REVERT: a 480 ARG cc_start: 0.8431 (mtp180) cc_final: 0.8219 (mtp85) REVERT: b 353 MET cc_start: 0.9208 (OUTLIER) cc_final: 0.8207 (tmm) REVERT: b 415 MET cc_start: 0.9442 (mmm) cc_final: 0.8975 (mmp) REVERT: d 48 ILE cc_start: 0.8847 (OUTLIER) cc_final: 0.8608 (pp) REVERT: e 146 GLU cc_start: 0.8803 (tp30) cc_final: 0.8301 (tp30) REVERT: e 426 GLU cc_start: 0.9142 (mp0) cc_final: 0.8856 (mp0) REVERT: e 446 TYR cc_start: 0.8750 (m-80) cc_final: 0.8530 (m-80) REVERT: g 52 ASP cc_start: 0.7868 (t0) cc_final: 0.7184 (t0) REVERT: g 54 MET cc_start: 0.8691 (mpp) cc_final: 0.8134 (mpt) REVERT: g 151 MET cc_start: 0.9139 (tpp) cc_final: 0.8809 (tpt) REVERT: h 227 MET cc_start: 0.9499 (mtp) cc_final: 0.9169 (mtp) REVERT: h 524 ARG cc_start: 0.7666 (tmt170) cc_final: 0.7375 (tmm160) REVERT: q 26 GLU cc_start: 0.8774 (pm20) cc_final: 0.8516 (pm20) REVERT: z 353 TYR cc_start: 0.8820 (t80) cc_final: 0.8563 (t80) REVERT: N 125 GLN cc_start: 0.7765 (tm-30) cc_final: 0.7467 (tm-30) REVERT: N 145 MET cc_start: 0.7311 (mmm) cc_final: 0.6948 (mmm) REVERT: N 305 CYS cc_start: 0.8937 (m) cc_final: 0.8721 (m) REVERT: N 319 TYR cc_start: 0.7032 (m-80) cc_final: 0.6765 (m-80) REVERT: N 326 PHE cc_start: 0.7506 (m-80) cc_final: 0.7107 (m-80) REVERT: N 391 LEU cc_start: 0.9514 (OUTLIER) cc_final: 0.9250 (tm) REVERT: N 394 TRP cc_start: 0.7821 (m-90) cc_final: 0.6356 (m-90) outliers start: 69 outliers final: 29 residues processed: 535 average time/residue: 1.5660 time to fit residues: 1090.2724 Evaluate side-chains 499 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 464 time to evaluate : 6.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 21 LYS Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 864 optimal weight: 1.9990 chunk 679 optimal weight: 10.0000 chunk 176 optimal weight: 0.9980 chunk 737 optimal weight: 6.9990 chunk 668 optimal weight: 2.9990 chunk 725 optimal weight: 1.9990 chunk 356 optimal weight: 7.9990 chunk 279 optimal weight: 6.9990 chunk 453 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 82 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN G 111 HIS G 390 ASN Z 161 HIS g 12 GLN g 526 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.074612 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2750 r_free = 0.2750 target = 0.060502 restraints weight = 189379.947| |-----------------------------------------------------------------------------| r_work (start): 0.2761 rms_B_bonded: 3.00 r_work: 0.2622 rms_B_bonded: 3.32 restraints_weight: 0.5000 r_work (final): 0.2622 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2607 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2607 r_free = 0.2607 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2607 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 68218 Z= 0.199 Angle : 0.543 9.131 92134 Z= 0.266 Chirality : 0.041 0.164 10963 Planarity : 0.003 0.062 11759 Dihedral : 6.874 178.594 9484 Min Nonbonded Distance : 1.672 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.19 % Allowed : 10.56 % Favored : 88.25 % 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: 8734 helix: 2.43 (0.08), residues: 4429 sheet: -0.02 (0.15), residues: 1204 loop : -0.40 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 132 HIS 0.015 0.001 HIS Z 161 PHE 0.018 0.001 PHE A 167 TYR 0.014 0.001 TYR b 456 ARG 0.016 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 489 time to evaluate : 6.191 Fit side-chains revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7509 (t0) cc_final: 0.7197 (t0) REVERT: A 48 ASP cc_start: 0.8762 (OUTLIER) cc_final: 0.8364 (p0) REVERT: A 430 MET cc_start: 0.7796 (mmm) cc_final: 0.7549 (mmt) REVERT: D 57 MET cc_start: 0.9394 (mmm) cc_final: 0.9183 (mmm) REVERT: D 261 ASP cc_start: 0.8862 (m-30) cc_final: 0.8152 (t0) REVERT: D 458 MET cc_start: 0.8721 (tpp) cc_final: 0.8394 (tpp) REVERT: E 4 MET cc_start: 0.3810 (pmm) cc_final: 0.3516 (pmm) REVERT: G 15 LYS cc_start: 0.8745 (mptt) cc_final: 0.8419 (mmmt) REVERT: G 521 ASP cc_start: 0.8119 (t70) cc_final: 0.7575 (t70) REVERT: H 11 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7772 (pp20) REVERT: H 81 ASP cc_start: 0.8846 (OUTLIER) cc_final: 0.8485 (m-30) REVERT: H 227 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8060 (mpp) REVERT: H 440 LYS cc_start: 0.9308 (ttmt) cc_final: 0.9062 (ttpp) REVERT: Z 44 MET cc_start: 0.8577 (mtm) cc_final: 0.8347 (mtp) REVERT: Z 357 GLU cc_start: 0.8531 (tt0) cc_final: 0.8304 (pp20) REVERT: a 10 ASP cc_start: 0.8679 (m-30) cc_final: 0.8418 (m-30) REVERT: a 68 GLU cc_start: 0.8897 (OUTLIER) cc_final: 0.8644 (mm-30) REVERT: b 353 MET cc_start: 0.9195 (OUTLIER) cc_final: 0.8218 (tmm) REVERT: b 415 MET cc_start: 0.9458 (mmm) cc_final: 0.9057 (mmp) REVERT: d 48 ILE cc_start: 0.8686 (OUTLIER) cc_final: 0.8468 (pp) REVERT: e 146 GLU cc_start: 0.8813 (tp30) cc_final: 0.8311 (tp30) REVERT: e 426 GLU cc_start: 0.9142 (mp0) cc_final: 0.8861 (mp0) REVERT: e 446 TYR cc_start: 0.8794 (m-80) cc_final: 0.8496 (m-80) REVERT: g 52 ASP cc_start: 0.7922 (t0) cc_final: 0.7276 (t0) REVERT: g 54 MET cc_start: 0.8677 (mpp) cc_final: 0.8173 (mpt) REVERT: g 151 MET cc_start: 0.9168 (tpp) cc_final: 0.8818 (tpt) REVERT: h 1 MET cc_start: 0.5501 (tmt) cc_final: 0.5020 (ttp) REVERT: h 227 MET cc_start: 0.9514 (mtp) cc_final: 0.9180 (mtp) REVERT: h 455 PHE cc_start: 0.8236 (m-10) cc_final: 0.8035 (m-10) REVERT: h 524 ARG cc_start: 0.7661 (tmt170) cc_final: 0.7363 (tmm160) REVERT: q 26 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8533 (pm20) REVERT: z 353 TYR cc_start: 0.8861 (t80) cc_final: 0.8618 (t80) REVERT: N 125 GLN cc_start: 0.7721 (tm-30) cc_final: 0.7383 (tm-30) REVERT: N 132 TRP cc_start: 0.8074 (OUTLIER) cc_final: 0.7687 (p90) REVERT: N 145 MET cc_start: 0.7287 (mmm) cc_final: 0.6904 (mmm) REVERT: N 170 LYS cc_start: 0.8020 (tppt) cc_final: 0.7633 (tptt) REVERT: N 305 CYS cc_start: 0.8926 (m) cc_final: 0.8719 (m) REVERT: N 319 TYR cc_start: 0.7125 (m-80) cc_final: 0.6914 (m-80) REVERT: N 326 PHE cc_start: 0.7564 (m-80) cc_final: 0.7152 (m-80) REVERT: N 391 LEU cc_start: 0.9537 (OUTLIER) cc_final: 0.9235 (tm) REVERT: N 394 TRP cc_start: 0.7809 (m-90) cc_final: 0.6353 (m-90) outliers start: 87 outliers final: 36 residues processed: 547 average time/residue: 1.4917 time to fit residues: 1070.0317 Evaluate side-chains 514 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 468 time to evaluate : 6.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 330 THR Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 58 ASP Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain g residue 46 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 132 TRP Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 419 optimal weight: 9.9990 chunk 101 optimal weight: 8.9990 chunk 97 optimal weight: 3.9990 chunk 563 optimal weight: 0.9980 chunk 779 optimal weight: 7.9990 chunk 722 optimal weight: 0.6980 chunk 170 optimal weight: 6.9990 chunk 742 optimal weight: 0.9980 chunk 741 optimal weight: 0.9990 chunk 456 optimal weight: 10.0000 chunk 464 optimal weight: 10.0000 overall best weight: 1.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS Z 161 HIS g 12 GLN h 501 ASN q 41 GLN q 53 ASN ** q 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.075200 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2765 r_free = 0.2765 target = 0.061228 restraints weight = 178736.723| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 2.92 r_work: 0.2639 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.2639 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2629 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2629 r_free = 0.2629 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 = 0.2629 r_free = 0.2629 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2629 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8639 moved from start: 0.1210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68218 Z= 0.180 Angle : 0.538 9.658 92134 Z= 0.263 Chirality : 0.041 0.171 10963 Planarity : 0.003 0.061 11759 Dihedral : 6.783 176.304 9484 Min Nonbonded Distance : 1.653 Molprobity Statistics. All-atom Clashscore : 5.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.18 % Allowed : 11.08 % Favored : 87.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 8734 helix: 2.47 (0.08), residues: 4428 sheet: -0.02 (0.15), residues: 1205 loop : -0.40 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 132 HIS 0.017 0.001 HIS Z 161 PHE 0.018 0.001 PHE A 167 TYR 0.014 0.001 TYR b 456 ARG 0.008 0.000 ARG G 167 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 497 time to evaluate : 6.230 Fit side-chains REVERT: A 430 MET cc_start: 0.7852 (mmm) cc_final: 0.7536 (mmt) REVERT: D 57 MET cc_start: 0.9391 (mmm) cc_final: 0.9159 (mmm) REVERT: D 261 ASP cc_start: 0.8832 (m-30) cc_final: 0.8160 (t0) REVERT: D 458 MET cc_start: 0.8715 (tpp) cc_final: 0.8443 (tpp) REVERT: D 493 ILE cc_start: 0.9362 (OUTLIER) cc_final: 0.9128 (mm) REVERT: D 505 GLU cc_start: 0.8700 (OUTLIER) cc_final: 0.8432 (pm20) REVERT: E 4 MET cc_start: 0.4095 (pmm) cc_final: 0.3739 (pmm) REVERT: G 15 LYS cc_start: 0.8743 (mptt) cc_final: 0.8413 (mmmt) REVERT: G 521 ASP cc_start: 0.8032 (t70) cc_final: 0.7504 (t70) REVERT: H 11 GLU cc_start: 0.8317 (OUTLIER) cc_final: 0.7760 (pp20) REVERT: H 81 ASP cc_start: 0.8831 (OUTLIER) cc_final: 0.8462 (m-30) REVERT: H 187 ASP cc_start: 0.8544 (p0) cc_final: 0.8327 (p0) REVERT: H 440 LYS cc_start: 0.9298 (ttmt) cc_final: 0.9047 (ttpp) REVERT: Z 358 GLU cc_start: 0.8776 (OUTLIER) cc_final: 0.8541 (pt0) REVERT: a 10 ASP cc_start: 0.8669 (m-30) cc_final: 0.8415 (m-30) REVERT: a 68 GLU cc_start: 0.8899 (OUTLIER) cc_final: 0.8646 (mm-30) REVERT: b 415 MET cc_start: 0.9458 (mmm) cc_final: 0.9040 (mmp) REVERT: d 48 ILE cc_start: 0.8735 (OUTLIER) cc_final: 0.8520 (pp) REVERT: e 146 GLU cc_start: 0.8800 (tp30) cc_final: 0.8303 (tp30) REVERT: e 426 GLU cc_start: 0.9131 (mp0) cc_final: 0.8853 (mp0) REVERT: e 443 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8258 (tm) REVERT: e 446 TYR cc_start: 0.8802 (m-80) cc_final: 0.8508 (m-80) REVERT: g 52 ASP cc_start: 0.7926 (t0) cc_final: 0.7271 (t0) REVERT: g 54 MET cc_start: 0.8671 (mpp) cc_final: 0.8128 (mpt) REVERT: g 151 MET cc_start: 0.9181 (tpp) cc_final: 0.8801 (tpt) REVERT: h 1 MET cc_start: 0.5499 (tmt) cc_final: 0.5175 (tmm) REVERT: h 227 MET cc_start: 0.9516 (mtp) cc_final: 0.9173 (mtp) REVERT: h 518 GLU cc_start: 0.9126 (tt0) cc_final: 0.8848 (tt0) REVERT: h 524 ARG cc_start: 0.7645 (tmt170) cc_final: 0.7346 (tmm160) REVERT: q 26 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8502 (pm20) REVERT: z 358 GLU cc_start: 0.7877 (mm-30) cc_final: 0.7602 (mm-30) REVERT: N 125 GLN cc_start: 0.7694 (tm-30) cc_final: 0.7342 (tm-30) REVERT: N 132 TRP cc_start: 0.8117 (OUTLIER) cc_final: 0.7685 (p90) REVERT: N 141 HIS cc_start: 0.7616 (OUTLIER) cc_final: 0.7247 (p90) REVERT: N 145 MET cc_start: 0.7365 (mmm) cc_final: 0.6984 (mmm) REVERT: N 170 LYS cc_start: 0.8059 (tppt) cc_final: 0.7706 (tptt) REVERT: N 326 PHE cc_start: 0.7498 (m-80) cc_final: 0.7091 (m-80) REVERT: N 391 LEU cc_start: 0.9542 (OUTLIER) cc_final: 0.9245 (tm) REVERT: N 394 TRP cc_start: 0.7781 (m-90) cc_final: 0.6390 (m-90) outliers start: 86 outliers final: 40 residues processed: 546 average time/residue: 1.5115 time to fit residues: 1079.4439 Evaluate side-chains 523 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 471 time to evaluate : 6.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 358 GLU Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 371 MET Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain g residue 46 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 430 CYS Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain N residue 132 TRP Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 375 optimal weight: 9.9990 chunk 613 optimal weight: 6.9990 chunk 422 optimal weight: 10.0000 chunk 523 optimal weight: 6.9990 chunk 198 optimal weight: 0.9990 chunk 275 optimal weight: 7.9990 chunk 545 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 733 optimal weight: 10.0000 chunk 554 optimal weight: 0.9980 chunk 538 optimal weight: 0.8980 overall best weight: 3.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 350 GLN G 111 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.073254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2725 r_free = 0.2725 target = 0.059432 restraints weight = 169572.082| |-----------------------------------------------------------------------------| r_work (start): 0.2734 rms_B_bonded: 2.82 r_work: 0.2599 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2599 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2594 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2594 r_free = 0.2594 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2594 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 68218 Z= 0.314 Angle : 0.588 10.142 92134 Z= 0.289 Chirality : 0.043 0.192 10963 Planarity : 0.003 0.061 11759 Dihedral : 6.851 179.240 9484 Min Nonbonded Distance : 1.510 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 1.15 % Allowed : 11.54 % Favored : 87.30 % 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: 1.57 (0.09), residues: 8734 helix: 2.37 (0.08), residues: 4440 sheet: -0.09 (0.15), residues: 1217 loop : -0.46 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 132 HIS 0.015 0.001 HIS Z 161 PHE 0.018 0.001 PHE N 233 TYR 0.018 0.001 TYR z 353 ARG 0.011 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 553 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 469 time to evaluate : 6.060 Fit side-chains REVERT: A 47 ASP cc_start: 0.7926 (t0) cc_final: 0.7556 (t0) REVERT: A 48 ASP cc_start: 0.8978 (OUTLIER) cc_final: 0.8638 (p0) REVERT: D 57 MET cc_start: 0.9409 (mmm) cc_final: 0.9136 (mmm) REVERT: D 261 ASP cc_start: 0.8809 (m-30) cc_final: 0.8124 (t0) REVERT: D 355 MET cc_start: 0.9244 (mmm) cc_final: 0.9015 (mtp) REVERT: D 399 GLU cc_start: 0.8894 (OUTLIER) cc_final: 0.7885 (mp0) REVERT: D 458 MET cc_start: 0.8776 (tpp) cc_final: 0.8425 (tpp) REVERT: D 505 GLU cc_start: 0.8718 (OUTLIER) cc_final: 0.8482 (pm20) REVERT: E 4 MET cc_start: 0.3976 (OUTLIER) cc_final: 0.3643 (pmm) REVERT: E 288 MET cc_start: 0.8797 (OUTLIER) cc_final: 0.8564 (ptm) REVERT: G 15 LYS cc_start: 0.8754 (mptt) cc_final: 0.8418 (mmmt) REVERT: G 521 ASP cc_start: 0.8162 (t70) cc_final: 0.7659 (t70) REVERT: H 11 GLU cc_start: 0.8348 (OUTLIER) cc_final: 0.7834 (pp20) REVERT: H 81 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8484 (m-30) REVERT: H 440 LYS cc_start: 0.9273 (ttmt) cc_final: 0.9025 (ttpp) REVERT: Z 44 MET cc_start: 0.8599 (mtm) cc_final: 0.8360 (mtp) REVERT: a 10 ASP cc_start: 0.8655 (m-30) cc_final: 0.8392 (m-30) REVERT: a 68 GLU cc_start: 0.8896 (OUTLIER) cc_final: 0.8630 (mm-30) REVERT: a 473 GLU cc_start: 0.8547 (OUTLIER) cc_final: 0.7956 (tm-30) REVERT: d 48 ILE cc_start: 0.8727 (OUTLIER) cc_final: 0.8471 (pp) REVERT: d 60 MET cc_start: 0.9060 (OUTLIER) cc_final: 0.8542 (tpp) REVERT: e 146 GLU cc_start: 0.8805 (tp30) cc_final: 0.8311 (tp30) REVERT: e 426 GLU cc_start: 0.9155 (mp0) cc_final: 0.8823 (mp0) REVERT: e 443 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8256 (tm) REVERT: e 446 TYR cc_start: 0.8879 (m-80) cc_final: 0.8439 (m-80) REVERT: g 52 ASP cc_start: 0.7981 (t0) cc_final: 0.7278 (t0) REVERT: g 54 MET cc_start: 0.8723 (mpp) cc_final: 0.8193 (mpt) REVERT: g 151 MET cc_start: 0.9189 (tpp) cc_final: 0.8797 (tpt) REVERT: h 1 MET cc_start: 0.5486 (tmt) cc_final: 0.4998 (ttp) REVERT: h 227 MET cc_start: 0.9499 (mtp) cc_final: 0.9169 (mtp) REVERT: h 518 GLU cc_start: 0.9140 (tt0) cc_final: 0.8824 (tt0) REVERT: h 524 ARG cc_start: 0.7731 (tmt170) cc_final: 0.7404 (tmm160) REVERT: q 26 GLU cc_start: 0.8772 (OUTLIER) cc_final: 0.8506 (pm20) REVERT: N 125 GLN cc_start: 0.7552 (tm-30) cc_final: 0.7157 (tm-30) REVERT: N 132 TRP cc_start: 0.8136 (OUTLIER) cc_final: 0.7709 (p90) REVERT: N 141 HIS cc_start: 0.7680 (OUTLIER) cc_final: 0.7315 (p90) REVERT: N 145 MET cc_start: 0.7423 (mmm) cc_final: 0.7015 (mmm) REVERT: N 170 LYS cc_start: 0.8064 (tppt) cc_final: 0.7660 (tptt) REVERT: N 319 TYR cc_start: 0.6925 (m-80) cc_final: 0.6619 (m-80) REVERT: N 326 PHE cc_start: 0.7476 (m-80) cc_final: 0.7093 (m-80) REVERT: N 391 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9231 (tm) REVERT: N 394 TRP cc_start: 0.7779 (m-90) cc_final: 0.6385 (m-90) outliers start: 84 outliers final: 40 residues processed: 524 average time/residue: 1.5271 time to fit residues: 1051.4979 Evaluate side-chains 513 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 457 time to evaluate : 6.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 ASP Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 214 VAL Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain h residue 482 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 132 TRP Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 831 optimal weight: 3.9990 chunk 826 optimal weight: 0.8980 chunk 739 optimal weight: 5.9990 chunk 716 optimal weight: 6.9990 chunk 316 optimal weight: 8.9990 chunk 717 optimal weight: 0.6980 chunk 409 optimal weight: 1.9990 chunk 801 optimal weight: 7.9990 chunk 590 optimal weight: 7.9990 chunk 257 optimal weight: 5.9990 chunk 549 optimal weight: 4.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN h 501 ASN q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3000 r_free = 0.3000 target = 0.073912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2731 r_free = 0.2731 target = 0.059702 restraints weight = 196638.116| |-----------------------------------------------------------------------------| r_work (start): 0.2739 rms_B_bonded: 3.06 r_work: 0.2596 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.2596 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2591 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2591 r_free = 0.2591 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2591 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68218 Z= 0.247 Angle : 0.569 12.079 92134 Z= 0.279 Chirality : 0.042 0.196 10963 Planarity : 0.003 0.060 11759 Dihedral : 6.820 178.281 9484 Min Nonbonded Distance : 1.556 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 1.01 % Allowed : 11.86 % Favored : 87.13 % 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: 1.59 (0.09), residues: 8734 helix: 2.40 (0.08), residues: 4435 sheet: -0.12 (0.15), residues: 1204 loop : -0.43 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 132 HIS 0.016 0.001 HIS Z 161 PHE 0.018 0.001 PHE A 167 TYR 0.017 0.001 TYR b 456 ARG 0.013 0.000 ARG h 425 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 541 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 74 poor density : 467 time to evaluate : 6.219 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7429 (mmm) cc_final: 0.7199 (mmt) REVERT: D 57 MET cc_start: 0.9415 (mmm) cc_final: 0.9151 (mmm) REVERT: D 261 ASP cc_start: 0.8817 (m-30) cc_final: 0.8133 (t0) REVERT: D 355 MET cc_start: 0.9216 (mmm) cc_final: 0.8992 (mtp) REVERT: D 399 GLU cc_start: 0.8876 (OUTLIER) cc_final: 0.7888 (mp0) REVERT: D 458 MET cc_start: 0.8773 (tpp) cc_final: 0.8463 (tpp) REVERT: D 486 GLN cc_start: 0.9095 (mm110) cc_final: 0.8835 (mp10) REVERT: D 505 GLU cc_start: 0.8727 (OUTLIER) cc_final: 0.8495 (pm20) REVERT: E 4 MET cc_start: 0.3979 (OUTLIER) cc_final: 0.3604 (pmm) REVERT: G 15 LYS cc_start: 0.8755 (mptt) cc_final: 0.8418 (mmmt) REVERT: G 521 ASP cc_start: 0.8160 (t70) cc_final: 0.7662 (t70) REVERT: H 11 GLU cc_start: 0.8363 (OUTLIER) cc_final: 0.7829 (pp20) REVERT: H 81 ASP cc_start: 0.8840 (OUTLIER) cc_final: 0.8469 (m-30) REVERT: H 440 LYS cc_start: 0.9302 (ttmt) cc_final: 0.9066 (ttpp) REVERT: Z 357 GLU cc_start: 0.8461 (tt0) cc_final: 0.8162 (pp20) REVERT: a 10 ASP cc_start: 0.8683 (m-30) cc_final: 0.8421 (m-30) REVERT: a 68 GLU cc_start: 0.8926 (OUTLIER) cc_final: 0.8652 (mm-30) REVERT: a 473 GLU cc_start: 0.8486 (OUTLIER) cc_final: 0.8119 (tm-30) REVERT: b 353 MET cc_start: 0.9245 (OUTLIER) cc_final: 0.9005 (tpt) REVERT: d 48 ILE cc_start: 0.8857 (OUTLIER) cc_final: 0.8620 (pp) REVERT: d 60 MET cc_start: 0.9080 (OUTLIER) cc_final: 0.8539 (tpp) REVERT: e 146 GLU cc_start: 0.8823 (tp30) cc_final: 0.8326 (tp30) REVERT: e 426 GLU cc_start: 0.9164 (mp0) cc_final: 0.8855 (mp0) REVERT: e 443 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8178 (tm) REVERT: e 446 TYR cc_start: 0.8878 (m-80) cc_final: 0.8460 (m-80) REVERT: g 52 ASP cc_start: 0.7995 (t0) cc_final: 0.7288 (t0) REVERT: g 54 MET cc_start: 0.8769 (mpp) cc_final: 0.8238 (mpt) REVERT: g 151 MET cc_start: 0.9207 (tpp) cc_final: 0.8806 (tpt) REVERT: h 1 MET cc_start: 0.5477 (tmt) cc_final: 0.4991 (ttp) REVERT: h 11 GLU cc_start: 0.8411 (tp30) cc_final: 0.8205 (tp30) REVERT: h 227 MET cc_start: 0.9514 (mtp) cc_final: 0.9174 (mtp) REVERT: h 518 GLU cc_start: 0.9159 (tt0) cc_final: 0.8848 (tt0) REVERT: h 524 ARG cc_start: 0.7730 (tmt170) cc_final: 0.7403 (tmm160) REVERT: q 26 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8522 (pm20) REVERT: z 358 GLU cc_start: 0.7754 (mm-30) cc_final: 0.7499 (mm-30) REVERT: N 125 GLN cc_start: 0.7527 (tm-30) cc_final: 0.7124 (tm-30) REVERT: N 141 HIS cc_start: 0.7573 (OUTLIER) cc_final: 0.7257 (p90) REVERT: N 145 MET cc_start: 0.7446 (mmm) cc_final: 0.7021 (mmm) REVERT: N 170 LYS cc_start: 0.8026 (tppt) cc_final: 0.7644 (tptt) REVERT: N 319 TYR cc_start: 0.6891 (m-80) cc_final: 0.6598 (m-80) REVERT: N 326 PHE cc_start: 0.7466 (m-80) cc_final: 0.7050 (m-80) REVERT: N 391 LEU cc_start: 0.9534 (OUTLIER) cc_final: 0.9212 (tm) REVERT: N 394 TRP cc_start: 0.7761 (m-90) cc_final: 0.6349 (m-90) outliers start: 74 outliers final: 40 residues processed: 512 average time/residue: 1.5736 time to fit residues: 1056.8056 Evaluate side-chains 516 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 54 poor density : 462 time to evaluate : 6.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 233 HIS Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 477 optimal weight: 0.0070 chunk 543 optimal weight: 7.9990 chunk 412 optimal weight: 0.3980 chunk 618 optimal weight: 6.9990 chunk 174 optimal weight: 0.8980 chunk 664 optimal weight: 1.9990 chunk 361 optimal weight: 8.9990 chunk 66 optimal weight: 5.9990 chunk 547 optimal weight: 4.9990 chunk 589 optimal weight: 6.9990 chunk 745 optimal weight: 4.9990 overall best weight: 1.6602 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 111 HIS ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** g 12 GLN h 501 ASN q 41 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.074813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2749 r_free = 0.2749 target = 0.060547 restraints weight = 201225.802| |-----------------------------------------------------------------------------| r_work (start): 0.2760 rms_B_bonded: 3.10 r_work: 0.2617 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2617 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2606 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2606 r_free = 0.2606 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2606 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8652 moved from start: 0.1269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 68218 Z= 0.191 Angle : 0.554 11.736 92134 Z= 0.272 Chirality : 0.041 0.186 10963 Planarity : 0.003 0.058 11759 Dihedral : 6.752 175.628 9484 Min Nonbonded Distance : 1.587 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.36 % Favored : 96.64 % Rotamer: Outliers : 0.92 % Allowed : 12.13 % Favored : 86.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.09), residues: 8734 helix: 2.46 (0.08), residues: 4426 sheet: -0.12 (0.15), residues: 1214 loop : -0.39 (0.11), residues: 3094 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 132 HIS 0.017 0.001 HIS Z 161 PHE 0.020 0.001 PHE h 455 TYR 0.017 0.001 TYR b 456 ARG 0.012 0.000 ARG h 425 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17468 Ramachandran restraints generated. 8734 Oldfield, 0 Emsley, 8734 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 479 time to evaluate : 6.264 Fit side-chains revert: symmetry clash REVERT: A 430 MET cc_start: 0.7458 (mmm) cc_final: 0.7231 (mmt) REVERT: D 57 MET cc_start: 0.9395 (mmm) cc_final: 0.9127 (mmm) REVERT: D 261 ASP cc_start: 0.8809 (m-30) cc_final: 0.8074 (t0) REVERT: D 355 MET cc_start: 0.9222 (mmm) cc_final: 0.9003 (mtp) REVERT: D 458 MET cc_start: 0.8781 (tpp) cc_final: 0.8502 (tpp) REVERT: D 486 GLN cc_start: 0.9103 (mm110) cc_final: 0.8841 (mp10) REVERT: D 505 GLU cc_start: 0.8725 (OUTLIER) cc_final: 0.8496 (pm20) REVERT: E 4 MET cc_start: 0.4023 (OUTLIER) cc_final: 0.3643 (pmm) REVERT: G 15 LYS cc_start: 0.8776 (mptt) cc_final: 0.8426 (mmmt) REVERT: G 521 ASP cc_start: 0.8136 (t70) cc_final: 0.7645 (t70) REVERT: H 11 GLU cc_start: 0.8357 (OUTLIER) cc_final: 0.7821 (pp20) REVERT: H 81 ASP cc_start: 0.8856 (OUTLIER) cc_final: 0.8495 (m-30) REVERT: H 440 LYS cc_start: 0.9295 (ttmt) cc_final: 0.9054 (ttpp) REVERT: Z 357 GLU cc_start: 0.8460 (tt0) cc_final: 0.8256 (pp20) REVERT: a 10 ASP cc_start: 0.8702 (m-30) cc_final: 0.8447 (m-30) REVERT: a 68 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8660 (mm-30) REVERT: a 473 GLU cc_start: 0.8492 (OUTLIER) cc_final: 0.8152 (tm-30) REVERT: d 48 ILE cc_start: 0.8631 (OUTLIER) cc_final: 0.8424 (pp) REVERT: d 60 MET cc_start: 0.9105 (OUTLIER) cc_final: 0.8580 (tpp) REVERT: e 146 GLU cc_start: 0.8828 (tp30) cc_final: 0.8329 (tp30) REVERT: e 426 GLU cc_start: 0.9160 (mp0) cc_final: 0.8865 (mp0) REVERT: e 443 LEU cc_start: 0.8398 (OUTLIER) cc_final: 0.8115 (tm) REVERT: e 446 TYR cc_start: 0.8880 (m-80) cc_final: 0.8439 (m-80) REVERT: g 52 ASP cc_start: 0.7961 (t0) cc_final: 0.7248 (t0) REVERT: g 54 MET cc_start: 0.8766 (mpp) cc_final: 0.8231 (mpt) REVERT: g 151 MET cc_start: 0.9216 (tpp) cc_final: 0.8817 (tpt) REVERT: h 1 MET cc_start: 0.5454 (tmt) cc_final: 0.4980 (ttp) REVERT: h 227 MET cc_start: 0.9518 (mtp) cc_final: 0.9177 (mtp) REVERT: h 518 GLU cc_start: 0.9151 (tt0) cc_final: 0.8861 (tt0) REVERT: h 524 ARG cc_start: 0.7721 (tmt170) cc_final: 0.7291 (tmt170) REVERT: q 26 GLU cc_start: 0.8784 (OUTLIER) cc_final: 0.8523 (pm20) REVERT: z 358 GLU cc_start: 0.7710 (mm-30) cc_final: 0.7444 (mm-30) REVERT: N 125 GLN cc_start: 0.7512 (tm-30) cc_final: 0.7113 (tm-30) REVERT: N 141 HIS cc_start: 0.7603 (OUTLIER) cc_final: 0.7310 (p90) REVERT: N 145 MET cc_start: 0.7449 (mmm) cc_final: 0.7002 (mmm) REVERT: N 170 LYS cc_start: 0.8131 (tppt) cc_final: 0.7779 (tptt) REVERT: N 319 TYR cc_start: 0.6895 (m-80) cc_final: 0.6620 (m-80) REVERT: N 326 PHE cc_start: 0.7504 (m-80) cc_final: 0.7084 (m-80) REVERT: N 391 LEU cc_start: 0.9529 (OUTLIER) cc_final: 0.9221 (tm) REVERT: N 394 TRP cc_start: 0.7731 (m-90) cc_final: 0.6542 (m-90) outliers start: 67 outliers final: 40 residues processed: 523 average time/residue: 1.5316 time to fit residues: 1058.6871 Evaluate side-chains 514 residues out of total 7300 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 462 time to evaluate : 6.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 147 CYS Chi-restraints excluded: chain A residue 281 THR Chi-restraints excluded: chain A residue 329 SER Chi-restraints excluded: chain A residue 359 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 187 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain D residue 505 GLU Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain G residue 463 LEU Chi-restraints excluded: chain H residue 7 ILE Chi-restraints excluded: chain H residue 11 GLU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 114 GLU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 519 THR Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 117 GLU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 463 LEU Chi-restraints excluded: chain a residue 68 GLU Chi-restraints excluded: chain a residue 225 MET Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain a residue 473 GLU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain b residue 488 MET Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 323 MET Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 96 LYS Chi-restraints excluded: chain e residue 443 LEU Chi-restraints excluded: chain g residue 82 GLU Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 379 GLU Chi-restraints excluded: chain q residue 26 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain N residue 141 HIS Chi-restraints excluded: chain N residue 203 PHE Chi-restraints excluded: chain N residue 340 LEU Chi-restraints excluded: chain N residue 391 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 869 random chunks: chunk 782 optimal weight: 3.9990 chunk 339 optimal weight: 0.0470 chunk 583 optimal weight: 6.9990 chunk 153 optimal weight: 4.9990 chunk 158 optimal weight: 2.9990 chunk 185 optimal weight: 9.9990 chunk 531 optimal weight: 1.9990 chunk 694 optimal weight: 0.8980 chunk 678 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 459 optimal weight: 0.0020 overall best weight: 1.1890 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 22 GLN G 111 HIS Z 161 HIS g 12 GLN h 501 ASN q 41 GLN ** q 471 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3027 r_free = 0.3027 target = 0.075349 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2769 r_free = 0.2769 target = 0.061515 restraints weight = 171102.689| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 2.84 r_work: 0.2648 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2638 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2638 r_free = 0.2638 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 = 0.2638 r_free = 0.2638 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2638 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.1303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 68218 Z= 0.166 Angle : 0.548 11.527 92134 Z= 0.268 Chirality : 0.041 0.203 10963 Planarity : 0.003 0.060 11759 Dihedral : 6.704 173.201 9484 Min Nonbonded Distance : 1.616 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.77 % Allowed : 12.33 % Favored : 86.91 % 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: 8734 helix: 2.50 (0.08), residues: 4425 sheet: -0.10 (0.15), residues: 1210 loop : -0.38 (0.11), residues: 3099 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 132 HIS 0.017 0.001 HIS Z 161 PHE 0.019 0.001 PHE h 455 TYR 0.018 0.001 TYR b 456 ARG 0.012 0.000 ARG h 425 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31911.46 seconds wall clock time: 550 minutes 13.95 seconds (33013.95 seconds total)