Starting phenix.real_space_refine on Mon Oct 14 01:12:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/10_2024/8shg_40487.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/10_2024/8shg_40487.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/10_2024/8shg_40487.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/10_2024/8shg_40487.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/10_2024/8shg_40487.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8shg_40487/10_2024/8shg_40487.cif" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.044 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 421 5.16 5 C 42266 2.51 5 N 11770 2.21 5 O 13094 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 38 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5477/modules/chem_data/mon_lib" Total number of atoms: 67663 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 985 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 985 Classifications: {'peptide': 130} Link IDs: {'PTRANS': 3, 'TRANS': 126} Chain breaks: 5 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1555 Number of conformers: 1 Conformer: "" Number of residues, atoms: 195, 1555 Classifications: {'peptide': 195} Link IDs: {'PTRANS': 5, 'TRANS': 189} Chain breaks: 5 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 34.01, per 1000 atoms: 0.50 Number of scatterers: 67663 At special positions: 0 Unit cell: (178.802, 177.744, 181.976, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 421 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13094 8.00 N 11770 7.00 C 42266 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 "HETATM67570 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67314 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67442 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.54 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: 16370 Finding SS restraints... Secondary structure from input PDB file: 369 helices and 100 sheets defined 56.3% alpha, 14.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.30 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.635A pdb=" N ARG A 18 " --> pdb=" O GLY A 14 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.592A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.049A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.347A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.555A pdb=" N MET A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.658A pdb=" N GLN A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 256 through 258 No H-bonds generated for 'chain 'A' and resid 256 through 258' Processing helix chain 'A' and resid 259 through 281 removed outlier: 3.823A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.792A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (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: 3.505A 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 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 433 through 445 removed outlier: 4.028A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 4.087A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.580A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.421A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.632A 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: 3.577A 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: 3.555A 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: 3.699A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.043A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.658A 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: 4.406A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.506A 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: 3.764A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.846A 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: 3.585A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.654A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 194 Proline residue: D 185 - end of helix removed outlier: 3.708A pdb=" N VAL D 194 " --> pdb=" O ALA D 190 " (cutoff:3.500A) Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 3.845A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 445 through 459 removed outlier: 4.382A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 469 removed outlier: 3.958A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.591A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.620A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (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: 6.462A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 4.022A 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: 3.871A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.929A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.945A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.642A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.673A pdb=" N MET E 460 " --> pdb=" O GLU E 456 " (cutoff:3.500A) Processing helix chain 'E' and resid 469 through 484 Processing helix chain 'E' and resid 500 through 505 removed outlier: 3.541A pdb=" N GLN E 504 " --> pdb=" O ASP E 500 " (cutoff:3.500A) Processing helix chain 'E' and resid 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.716A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.818A 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: 3.590A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.643A 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: 4.194A 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 306 Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.508A pdb=" N ARG G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.515A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.519A pdb=" N THR H 39 " --> pdb=" O VAL H 36 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.645A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.228A 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: 3.666A 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: 3.729A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 removed outlier: 3.547A pdb=" N MET H 227 " --> pdb=" O GLY H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.603A 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: 3.513A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.081A 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: 5.073A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.877A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.424A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 166 removed outlier: 3.674A pdb=" N VAL Q 160 " --> pdb=" O ASP Q 156 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 4.889A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.905A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 430 removed outlier: 3.801A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 444 removed outlier: 4.226A 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 501 through 520 Processing helix chain 'Q' and resid 535 through 539 Processing helix chain 'Z' and resid 3 through 7 Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.723A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.571A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.761A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.009A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.611A 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: 3.640A 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: 3.603A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 328 removed outlier: 3.776A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 removed outlier: 3.742A pdb=" N LEU Z 344 " --> pdb=" O PRO Z 341 " (cutoff:3.500A) Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.534A pdb=" N ASP Z 404 " --> pdb=" O ASN Z 400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.203A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.558A 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 '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 removed outlier: 3.563A pdb=" N LEU a 75 " --> pdb=" O ALA a 71 " (cutoff:3.500A) Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.705A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 3.770A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.332A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.847A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.764A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 428 removed outlier: 4.326A 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 removed outlier: 3.506A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 removed outlier: 3.642A pdb=" N LEU a 483 " --> pdb=" O ARG a 480 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 480 through 484' Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.436A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.646A 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: 3.583A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.163A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.788A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.912A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.639A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 195 Proline residue: d 185 - end of helix removed outlier: 3.608A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) removed outlier: 3.595A 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: 3.748A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.656A 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: 5.033A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 21 through 25 removed outlier: 3.616A pdb=" N LYS e 25 " --> pdb=" O GLN e 22 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.544A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 107 through 127 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: 6.513A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.961A 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: 3.874A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 440 removed outlier: 3.873A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.824A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.612A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 500 through 505 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 38 removed outlier: 3.678A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.901A 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: 3.623A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.586A 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: 3.888A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.602A pdb=" N ALA g 172 " --> pdb=" O TRP g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.677A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 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 removed outlier: 3.617A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.505A pdb=" N LEU h 40 " --> pdb=" O ARG h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.749A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.156A 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: 3.695A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 removed outlier: 3.574A pdb=" N GLN h 151 " --> pdb=" O ASP h 147 " (cutoff:3.500A) Processing helix chain 'h' and resid 171 through 185 removed outlier: 3.594A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 removed outlier: 3.537A 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: 3.570A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.279A 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 28 through 45 removed outlier: 4.476A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 157 through 168 removed outlier: 4.221A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.547A 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: 4.930A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.629A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.748A pdb=" N THR q 286 " --> pdb=" O ALA q 282 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.775A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.346A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 removed outlier: 3.522A pdb=" N VAL q 463 " --> pdb=" O LYS q 459 " (cutoff:3.500A) Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.631A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.548A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.705A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.508A pdb=" N LEU z 148 " --> pdb=" O ASP z 144 " (cutoff:3.500A) removed outlier: 4.049A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.604A 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: 3.716A 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: 3.634A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.817A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.299A 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: 4.109A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.648A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 57 through 62 Processing helix chain 'P' and resid 62 through 85 removed outlier: 3.918A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 removed outlier: 3.653A pdb=" N GLN P 139 " --> pdb=" O PHE P 136 " (cutoff:3.500A) Processing helix chain 'P' and resid 141 through 151 removed outlier: 4.589A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 168 through 176 removed outlier: 3.970A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) Processing helix chain 'P' and resid 194 through 209 removed outlier: 3.844A pdb=" N MET P 198 " --> pdb=" O GLY P 194 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 226 through 232 removed outlier: 3.795A pdb=" N ASN P 231 " --> pdb=" O GLN P 227 " (cutoff:3.500A) Processing helix chain 'P' and resid 250 through 256 removed outlier: 4.286A pdb=" N GLN P 254 " --> pdb=" O ARG P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 270 removed outlier: 3.513A pdb=" N LEU P 264 " --> pdb=" O PHE P 260 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 202 through 203 removed outlier: 3.585A pdb=" N GLN N 231 " --> pdb=" O LEU N 221 " (cutoff:3.500A) removed outlier: 6.466A pdb=" N ASP N 223 " --> pdb=" O LEU N 229 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU N 229 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 243 through 246 removed outlier: 4.622A pdb=" N THR N 253 " --> pdb=" O ALA N 246 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N GLN N 275 " --> pdb=" O VAL N 265 " (cutoff:3.500A) removed outlier: 6.708A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 286 through 289 removed outlier: 3.739A pdb=" N GLY N 299 " --> pdb=" O SER N 286 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.586A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.358A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.874A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.528A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 55 Processing sheet with id=AA6, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA7, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.377A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.582A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.571A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.571A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.066A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.233A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.193A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.528A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.294A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.366A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.627A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 61 through 64 removed outlier: 7.005A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.053A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.883A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB6, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.817A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.436A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB9, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC1, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.252A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.363A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.176A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.311A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.688A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.688A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.689A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.538A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 5.740A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.207A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.380A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.804A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 28 through 29 removed outlier: 7.266A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC7, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.711A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.739A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.739A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.146A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.717A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.636A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.351A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.727A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU Z 12 " --> pdb=" O ARG Z 523 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.855A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.357A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.376A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.969A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.251A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD8, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.313A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.066A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.703A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE2, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE3, first strand: chain 'H' and resid 405 through 407 Processing sheet with id=AE4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE5, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.178A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.625A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 149 through 150 removed outlier: 4.000A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.569A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.439A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 220 through 223 removed outlier: 3.558A pdb=" N MET Q 221 " --> pdb=" O PHE Q 363 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 311 through 314 removed outlier: 7.158A pdb=" N VAL Q 241 " --> pdb=" O LEU Q 333 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF2, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF3, first strand: chain 'Z' and resid 191 through 196 removed outlier: 3.581A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF5, first strand: chain 'Z' and resid 311 through 313 removed outlier: 6.468A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.322A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'Z' and resid 477 through 479 removed outlier: 3.735A pdb=" N MET Z 487 " --> pdb=" O GLY Z 478 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 9 through 13 removed outlier: 6.404A pdb=" N ASP d 58 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 4.181A pdb=" N ASP a 529 " --> pdb=" O ASP d 58 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.262A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N VAL g 523 " --> pdb=" O MET a 44 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG1, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG2, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.407A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.426A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 8.044A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.561A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.561A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.702A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.258A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N LYS e 263 " --> pdb=" O ALA h 253 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG7, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.399A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.645A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 61 through 64 removed outlier: 7.003A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.020A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH1, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.784A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.346A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.346A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.398A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) removed outlier: 8.975A pdb=" N ALA b 332 " --> pdb=" O ILE b 237 " (cutoff:3.500A) removed outlier: 6.615A pdb=" N ILE b 239 " --> pdb=" O ALA b 332 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH5, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH6, first strand: chain 'd' and resid 208 through 212 Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.605A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.699A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 7.142A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N VAL d 297 " --> pdb=" O LYS d 245 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH9, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.501A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.432A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI2, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.214A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.305A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.679A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.176A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI3, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.524A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.425A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.279A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.663A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI6, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI7, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.853A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI9, first strand: chain 'g' and resid 310 through 312 removed outlier: 6.377A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 8.924A pdb=" N VAL g 332 " --> pdb=" O ILE g 238 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N LEU g 240 " --> pdb=" O VAL g 332 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ2, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.560A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.713A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ5, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ6, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ7, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ8, first strand: chain 'q' and resid 20 through 23 removed outlier: 5.038A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.149A 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: 7.777A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.701A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.663A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.379A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK3, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK4, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK5, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK6, first strand: chain 'z' and resid 192 through 196 removed outlier: 6.333A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.183A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK7, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK8, first strand: chain 'z' and resid 311 through 313 removed outlier: 6.021A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.260A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.410A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AL1, first strand: chain 'P' and resid 215 through 218 removed outlier: 7.898A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.290A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.828A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.877A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE P 248 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N LYS P 240 " --> pdb=" O LEU P 244 " (cutoff:3.500A) removed outlier: 5.254A pdb=" N LEU P 244 " --> pdb=" O LYS P 240 " (cutoff:3.500A) 4120 hydrogen bonds defined for protein. 11751 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: 34.25 Time building geometry restraints manager: 15.88 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: 22765 1.34 - 1.46: 10351 1.46 - 1.58: 34520 1.58 - 1.69: 49 1.69 - 1.81: 744 Bond restraints: 68429 Sorted by residual: bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.45e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.35e+01 ... (remaining 68424 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.91: 91287 1.91 - 3.83: 813 3.83 - 5.74: 228 5.74 - 7.66: 47 7.66 - 9.57: 3 Bond angle restraints: 92378 Sorted by residual: angle pdb=" C ALA q 530 " pdb=" CA ALA q 530 " pdb=" CB ALA q 530 " ideal model delta sigma weight residual 117.23 110.32 6.91 1.36e+00 5.41e-01 2.58e+01 angle pdb=" CA PRO a 478 " pdb=" N PRO a 478 " pdb=" CD PRO a 478 " ideal model delta sigma weight residual 112.00 106.26 5.74 1.40e+00 5.10e-01 1.68e+01 angle pdb=" CA ALA q 530 " pdb=" C ALA q 530 " pdb=" N GLY q 531 " ideal model delta sigma weight residual 119.98 116.89 3.09 8.50e-01 1.38e+00 1.32e+01 angle pdb=" N ASP E 231 " pdb=" CA ASP E 231 " pdb=" C ASP E 231 " ideal model delta sigma weight residual 112.25 107.54 4.71 1.36e+00 5.41e-01 1.20e+01 angle pdb=" C ILE B 11 " pdb=" N PHE B 12 " pdb=" CA PHE B 12 " ideal model delta sigma weight residual 122.19 130.07 -7.88 2.30e+00 1.89e-01 1.17e+01 ... (remaining 92373 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.05: 41643 35.05 - 70.11: 592 70.11 - 105.16: 56 105.16 - 140.22: 10 140.22 - 175.27: 5 Dihedral angle restraints: 42306 sinusoidal: 17035 harmonic: 25271 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 300.00 124.73 175.27 1 2.00e+01 2.50e-03 4.79e+01 dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 111.72 -171.72 1 2.00e+01 2.50e-03 4.77e+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 -60.00 111.66 -171.66 1 2.00e+01 2.50e-03 4.77e+01 ... (remaining 42303 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 9590 0.061 - 0.123: 1353 0.123 - 0.184: 49 0.184 - 0.245: 0 0.245 - 0.306: 1 Chirality restraints: 10993 Sorted by residual: chirality pdb=" CB VAL P 55 " pdb=" CA VAL P 55 " pdb=" CG1 VAL P 55 " pdb=" CG2 VAL P 55 " both_signs ideal model delta sigma weight residual False -2.63 -2.32 -0.31 2.00e-01 2.50e+01 2.35e+00 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 chirality pdb=" CA ILE E 533 " pdb=" N ILE E 533 " pdb=" C ILE E 533 " pdb=" CB ILE E 533 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.33e-01 ... (remaining 10990 not shown) Planarity restraints: 11793 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA B 7 " -0.043 5.00e-02 4.00e+02 6.48e-02 6.73e+00 pdb=" N PRO B 8 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.036 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP E 231 " 0.012 2.00e-02 2.50e+03 2.37e-02 5.60e+00 pdb=" C ASP E 231 " -0.041 2.00e-02 2.50e+03 pdb=" O ASP E 231 " 0.016 2.00e-02 2.50e+03 pdb=" N LYS E 232 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " -0.039 5.00e-02 4.00e+02 5.66e-02 5.13e+00 pdb=" N PRO a 478 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " -0.032 5.00e-02 4.00e+02 ... (remaining 11790 not shown) Histogram of nonbonded interaction distances: 1.96 - 2.55: 603 2.55 - 3.13: 52464 3.13 - 3.72: 107125 3.72 - 4.31: 148798 4.31 - 4.90: 254797 Nonbonded interactions: 563787 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.958 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.965 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.970 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.980 2.120 nonbonded pdb="MG MG G 602 " pdb=" F2 AF3 G 603 " model vdw 1.989 2.120 ... (remaining 563782 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: 1.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.060 Extract box with map and model: 2.170 Check model and map are aligned: 0.410 Set scattering table: 0.500 Process input model: 133.450 Find NCS groups from input model: 5.990 Set up NCS constraints: 0.400 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:11.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8547 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 68429 Z= 0.267 Angle : 0.520 9.569 92378 Z= 0.256 Chirality : 0.041 0.306 10993 Planarity : 0.003 0.065 11793 Dihedral : 13.865 175.271 25936 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.24 % Favored : 96.74 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 8734 helix: 2.46 (0.08), residues: 4429 sheet: 0.26 (0.16), residues: 1178 loop : -0.42 (0.11), residues: 3127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.009 0.001 HIS z 161 PHE 0.029 0.001 PHE z 289 TYR 0.018 0.001 TYR b 213 ARG 0.008 0.000 ARG g 20 *********************** 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 585 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 585 time to evaluate : 6.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8623 (mpp) cc_final: 0.8395 (mpp) REVERT: A 248 LEU cc_start: 0.8949 (tp) cc_final: 0.8737 (tm) REVERT: B 197 GLU cc_start: 0.8477 (mp0) cc_final: 0.8241 (mp0) REVERT: B 221 ASP cc_start: 0.8739 (t70) cc_final: 0.8408 (t0) REVERT: D 25 GLN cc_start: 0.9081 (tp-100) cc_final: 0.8654 (tp-100) REVERT: E 4 MET cc_start: 0.5010 (tmm) cc_final: 0.4661 (tmm) REVERT: E 464 GLU cc_start: 0.8597 (tp30) cc_final: 0.8395 (tp30) REVERT: E 532 ASP cc_start: 0.7366 (m-30) cc_final: 0.6696 (m-30) REVERT: G 15 LYS cc_start: 0.8901 (mptt) cc_final: 0.8663 (mptp) REVERT: G 47 MET cc_start: 0.8801 (mtp) cc_final: 0.8465 (mtp) REVERT: H 10 LYS cc_start: 0.8706 (ttmt) cc_final: 0.8462 (ttpp) REVERT: H 394 MET cc_start: 0.9061 (mmm) cc_final: 0.8614 (mmm) REVERT: Z 10 LYS cc_start: 0.9151 (mtmm) cc_final: 0.8941 (mtmm) REVERT: Z 17 GLN cc_start: 0.8636 (mp10) cc_final: 0.8281 (mp10) REVERT: a 68 GLU cc_start: 0.8957 (mm-30) cc_final: 0.8709 (mm-30) REVERT: a 306 MET cc_start: 0.8150 (mmt) cc_final: 0.7918 (mpt) REVERT: g 12 GLN cc_start: 0.8759 (tp-100) cc_final: 0.8533 (tp-100) REVERT: g 47 MET cc_start: 0.9226 (mmp) cc_final: 0.9009 (mmp) REVERT: h 14 ASP cc_start: 0.8357 (t70) cc_final: 0.8131 (t0) REVERT: h 324 MET cc_start: 0.9209 (mmm) cc_final: 0.9008 (mmm) REVERT: q 249 MET cc_start: 0.8681 (pmm) cc_final: 0.8451 (pmm) REVERT: q 296 LYS cc_start: 0.8961 (ptmm) cc_final: 0.8713 (pttm) REVERT: z 381 LYS cc_start: 0.8498 (tptt) cc_final: 0.8028 (tppt) outliers start: 0 outliers final: 1 residues processed: 585 average time/residue: 1.5868 time to fit residues: 1195.5586 Evaluate side-chains 460 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 459 time to evaluate : 6.204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 519 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 735 optimal weight: 7.9990 chunk 660 optimal weight: 10.0000 chunk 366 optimal weight: 0.9990 chunk 225 optimal weight: 6.9990 chunk 445 optimal weight: 5.9990 chunk 352 optimal weight: 0.0170 chunk 682 optimal weight: 1.9990 chunk 264 optimal weight: 8.9990 chunk 415 optimal weight: 0.9990 chunk 508 optimal weight: 3.9990 chunk 790 optimal weight: 8.9990 overall best weight: 1.6026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN N 252 ASN A 164 ASN A 534 HIS ** H 30 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 316 ASN Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 217 ASN a 534 HIS ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 129 HIS ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN d 537 ASN ** e 55 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 122 GLN q 475 ASN z 23 ASN z 161 HIS z 382 HIS P 56 ASN P 153 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.0756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 68429 Z= 0.188 Angle : 0.547 10.255 92378 Z= 0.272 Chirality : 0.042 0.305 10993 Planarity : 0.003 0.064 11793 Dihedral : 7.239 179.844 9498 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.20 % Favored : 96.78 % Rotamer: Outliers : 0.67 % Allowed : 5.36 % Favored : 93.97 % 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: 2.45 (0.08), residues: 4487 sheet: 0.28 (0.16), residues: 1120 loop : -0.51 (0.11), residues: 3127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.009 0.001 HIS z 161 PHE 0.019 0.001 PHE P 267 TYR 0.017 0.001 TYR Z 353 ARG 0.008 0.000 ARG E 24 *********************** 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 553 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 504 time to evaluate : 6.271 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8654 (mpp) cc_final: 0.8299 (mpp) REVERT: A 248 LEU cc_start: 0.8893 (tp) cc_final: 0.8672 (tm) REVERT: A 306 MET cc_start: 0.8965 (mtp) cc_final: 0.8740 (mtm) REVERT: B 221 ASP cc_start: 0.8746 (t70) cc_final: 0.8371 (t0) REVERT: D 25 GLN cc_start: 0.9049 (tp-100) cc_final: 0.8663 (tp-100) REVERT: D 60 MET cc_start: 0.8658 (ttt) cc_final: 0.8435 (tpp) REVERT: E 4 MET cc_start: 0.4884 (tmm) cc_final: 0.4456 (tmm) REVERT: E 464 GLU cc_start: 0.8586 (tp30) cc_final: 0.8322 (tp30) REVERT: E 468 MET cc_start: 0.8451 (mtt) cc_final: 0.8109 (mtt) REVERT: G 15 LYS cc_start: 0.8726 (mptt) cc_final: 0.8472 (mptp) REVERT: G 47 MET cc_start: 0.8833 (mtp) cc_final: 0.8458 (mtp) REVERT: G 521 ASP cc_start: 0.7832 (t70) cc_final: 0.7559 (t70) REVERT: H 394 MET cc_start: 0.9108 (mmm) cc_final: 0.8746 (mmm) REVERT: Q 416 GLU cc_start: 0.8836 (mp0) cc_final: 0.8629 (mp0) REVERT: Z 17 GLN cc_start: 0.8634 (mp10) cc_final: 0.8299 (mp10) REVERT: a 68 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8757 (mm-30) REVERT: a 77 GLU cc_start: 0.7952 (mp0) cc_final: 0.7739 (mp0) REVERT: a 306 MET cc_start: 0.8269 (mmt) cc_final: 0.8048 (mpt) REVERT: a 344 MET cc_start: 0.9103 (mmp) cc_final: 0.8789 (mmm) REVERT: d 90 MET cc_start: 0.8770 (OUTLIER) cc_final: 0.7152 (mpt) REVERT: g 12 GLN cc_start: 0.8778 (tp-100) cc_final: 0.8544 (tp-100) REVERT: g 47 MET cc_start: 0.9173 (mmp) cc_final: 0.8955 (mmp) REVERT: h 14 ASP cc_start: 0.8287 (t70) cc_final: 0.8056 (t0) REVERT: q 249 MET cc_start: 0.8734 (pmm) cc_final: 0.8462 (pmm) REVERT: q 296 LYS cc_start: 0.8957 (ptmm) cc_final: 0.8709 (pttm) REVERT: z 381 LYS cc_start: 0.8280 (tptt) cc_final: 0.7856 (tppt) REVERT: z 388 LYS cc_start: 0.8955 (tppp) cc_final: 0.8710 (tttt) REVERT: z 526 MET cc_start: 0.8366 (pmm) cc_final: 0.8153 (pmm) outliers start: 49 outliers final: 9 residues processed: 520 average time/residue: 1.4960 time to fit residues: 1013.7784 Evaluate side-chains 472 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 462 time to evaluate : 6.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain q residue 266 MET Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain P residue 148 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 439 optimal weight: 7.9990 chunk 245 optimal weight: 0.4980 chunk 658 optimal weight: 10.0000 chunk 538 optimal weight: 4.9990 chunk 218 optimal weight: 0.0870 chunk 792 optimal weight: 4.9990 chunk 856 optimal weight: 50.0000 chunk 705 optimal weight: 0.9990 chunk 785 optimal weight: 0.7980 chunk 270 optimal weight: 0.0470 chunk 635 optimal weight: 1.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 ASN A 534 HIS G 390 ASN H 30 GLN Z 161 HIS ** Z 334 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS b 227 ASN ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN z 23 ASN z 161 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 68429 Z= 0.127 Angle : 0.511 8.856 92378 Z= 0.252 Chirality : 0.041 0.321 10993 Planarity : 0.003 0.060 11793 Dihedral : 6.981 179.053 9496 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.04 % Favored : 96.94 % Rotamer: Outliers : 0.76 % Allowed : 7.45 % Favored : 91.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8734 helix: 2.53 (0.08), residues: 4491 sheet: 0.22 (0.16), residues: 1102 loop : -0.49 (0.11), residues: 3141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.010 0.001 HIS z 161 PHE 0.029 0.001 PHE H 455 TYR 0.012 0.001 TYR q 505 ARG 0.004 0.000 ARG E 24 *********************** 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 588 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 532 time to evaluate : 6.243 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8582 (mpp) cc_final: 0.8303 (mpp) REVERT: A 5 LEU cc_start: 0.8710 (OUTLIER) cc_final: 0.8116 (tt) REVERT: A 248 LEU cc_start: 0.8863 (tp) cc_final: 0.8642 (tm) REVERT: B 221 ASP cc_start: 0.8756 (t70) cc_final: 0.8392 (t0) REVERT: B 480 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8854 (mmp) REVERT: D 25 GLN cc_start: 0.8995 (tp-100) cc_final: 0.8571 (tp-100) REVERT: E 4 MET cc_start: 0.4956 (tmm) cc_final: 0.4460 (tmm) REVERT: E 464 GLU cc_start: 0.8568 (tp30) cc_final: 0.8326 (tp30) REVERT: E 468 MET cc_start: 0.8532 (mtt) cc_final: 0.8231 (mtt) REVERT: G 15 LYS cc_start: 0.8699 (mptt) cc_final: 0.8423 (mptp) REVERT: G 47 MET cc_start: 0.8802 (mtp) cc_final: 0.8330 (mtp) REVERT: H 394 MET cc_start: 0.9084 (mmm) cc_final: 0.8672 (mmm) REVERT: Q 311 MET cc_start: 0.8951 (ttt) cc_final: 0.8526 (ttm) REVERT: Q 416 GLU cc_start: 0.8863 (mp0) cc_final: 0.8662 (mp0) REVERT: Q 526 MET cc_start: 0.9115 (mtm) cc_final: 0.8895 (mtm) REVERT: Z 17 GLN cc_start: 0.8647 (mp10) cc_final: 0.8279 (mp10) REVERT: a 306 MET cc_start: 0.8259 (mmt) cc_final: 0.8002 (mmt) REVERT: b 445 MET cc_start: 0.8434 (tpp) cc_final: 0.8225 (mmm) REVERT: d 90 MET cc_start: 0.8728 (OUTLIER) cc_final: 0.7091 (mpt) REVERT: e 160 LYS cc_start: 0.9176 (mtmm) cc_final: 0.8903 (mttp) REVERT: e 288 MET cc_start: 0.9081 (ptp) cc_final: 0.8816 (ptp) REVERT: e 468 MET cc_start: 0.8732 (mtp) cc_final: 0.8413 (mtp) REVERT: g 12 GLN cc_start: 0.8755 (tp-100) cc_final: 0.8507 (tp-100) REVERT: g 20 ARG cc_start: 0.8295 (tpp80) cc_final: 0.8014 (tpp80) REVERT: g 47 MET cc_start: 0.9145 (mmp) cc_final: 0.8934 (mmp) REVERT: g 358 GLU cc_start: 0.7911 (tt0) cc_final: 0.7509 (tt0) REVERT: g 527 LYS cc_start: 0.9030 (mmmt) cc_final: 0.8626 (tppt) REVERT: h 14 ASP cc_start: 0.8301 (t70) cc_final: 0.8050 (t0) REVERT: q 249 MET cc_start: 0.8745 (pmm) cc_final: 0.8457 (pmm) REVERT: q 296 LYS cc_start: 0.8942 (ptmm) cc_final: 0.8698 (pttm) REVERT: z 244 VAL cc_start: 0.8480 (OUTLIER) cc_final: 0.8141 (t) REVERT: z 381 LYS cc_start: 0.8204 (tptt) cc_final: 0.7776 (tppt) REVERT: z 388 LYS cc_start: 0.8932 (tppp) cc_final: 0.8713 (tttt) REVERT: P 198 MET cc_start: 0.8198 (OUTLIER) cc_final: 0.7989 (pp-130) outliers start: 56 outliers final: 13 residues processed: 557 average time/residue: 1.4911 time to fit residues: 1085.0122 Evaluate side-chains 499 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 481 time to evaluate : 6.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 519 ILE Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain P residue 198 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 782 optimal weight: 2.9990 chunk 595 optimal weight: 1.9990 chunk 411 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 378 optimal weight: 8.9990 chunk 532 optimal weight: 4.9990 chunk 795 optimal weight: 0.3980 chunk 841 optimal weight: 10.0000 chunk 415 optimal weight: 7.9990 chunk 753 optimal weight: 8.9990 chunk 226 optimal weight: 10.0000 overall best weight: 3.4788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 209 GLN A 69 HIS A 265 GLN A 534 HIS Z 161 HIS ** a 164 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 46 ASN g 390 ASN z 161 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8588 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 68429 Z= 0.308 Angle : 0.568 11.215 92378 Z= 0.281 Chirality : 0.043 0.203 10993 Planarity : 0.003 0.063 11793 Dihedral : 6.971 179.591 9496 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.71 % Favored : 96.27 % Rotamer: Outliers : 1.06 % Allowed : 8.42 % Favored : 90.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.09), residues: 8734 helix: 2.46 (0.08), residues: 4507 sheet: 0.13 (0.16), residues: 1111 loop : -0.48 (0.11), residues: 3116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP N 222 HIS 0.011 0.001 HIS z 161 PHE 0.019 0.001 PHE e 386 TYR 0.014 0.001 TYR Z 353 ARG 0.007 0.000 ARG E 24 *********************** 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 562 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 484 time to evaluate : 6.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8685 (mpp) cc_final: 0.8284 (mpm) REVERT: N 209 GLN cc_start: 0.8974 (mt0) cc_final: 0.8620 (pt0) REVERT: A 5 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8342 (tt) REVERT: A 44 MET cc_start: 0.8796 (mtt) cc_final: 0.8539 (mtt) REVERT: A 106 GLU cc_start: 0.8577 (tp30) cc_final: 0.8237 (tp30) REVERT: A 248 LEU cc_start: 0.8952 (tp) cc_final: 0.8721 (tm) REVERT: A 508 ILE cc_start: 0.8662 (tp) cc_final: 0.8443 (tp) REVERT: B 221 ASP cc_start: 0.8789 (t70) cc_final: 0.8420 (t0) REVERT: D 25 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8631 (tp-100) REVERT: D 67 ASP cc_start: 0.8722 (m-30) cc_final: 0.8396 (m-30) REVERT: D 399 GLU cc_start: 0.8472 (OUTLIER) cc_final: 0.7612 (mp0) REVERT: E 4 MET cc_start: 0.5123 (tmm) cc_final: 0.4629 (tmt) REVERT: E 231 ASP cc_start: 0.8460 (t0) cc_final: 0.8215 (t0) REVERT: E 464 GLU cc_start: 0.8610 (tp30) cc_final: 0.8364 (tp30) REVERT: E 468 MET cc_start: 0.8576 (mtt) cc_final: 0.8243 (mtt) REVERT: E 522 GLN cc_start: 0.8811 (OUTLIER) cc_final: 0.7486 (mp10) REVERT: G 15 LYS cc_start: 0.8708 (mptt) cc_final: 0.8473 (mptp) REVERT: G 47 MET cc_start: 0.8858 (mtp) cc_final: 0.8493 (mtp) REVERT: H 17 GLN cc_start: 0.8684 (OUTLIER) cc_final: 0.8159 (tm-30) REVERT: H 394 MET cc_start: 0.9107 (mmm) cc_final: 0.8656 (mmm) REVERT: Q 416 GLU cc_start: 0.8865 (mp0) cc_final: 0.8604 (mp0) REVERT: Z 17 GLN cc_start: 0.8643 (mp10) cc_final: 0.8321 (mp10) REVERT: b 415 MET cc_start: 0.9408 (OUTLIER) cc_final: 0.9152 (mmp) REVERT: d 60 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.8540 (ttp) REVERT: d 90 MET cc_start: 0.8760 (OUTLIER) cc_final: 0.7252 (mpt) REVERT: e 48 MET cc_start: 0.9031 (mmm) cc_final: 0.8692 (mmm) REVERT: e 288 MET cc_start: 0.9221 (OUTLIER) cc_final: 0.8923 (ptp) REVERT: g 12 GLN cc_start: 0.8772 (tp-100) cc_final: 0.8519 (tp-100) REVERT: g 358 GLU cc_start: 0.8000 (tt0) cc_final: 0.7514 (tt0) REVERT: g 527 LYS cc_start: 0.9018 (mmmt) cc_final: 0.8501 (mmmt) REVERT: h 14 ASP cc_start: 0.8285 (t70) cc_final: 0.8055 (t0) REVERT: h 221 SER cc_start: 0.9201 (m) cc_final: 0.8984 (p) REVERT: q 249 MET cc_start: 0.8767 (pmm) cc_final: 0.8470 (pmm) REVERT: q 296 LYS cc_start: 0.8955 (ptmm) cc_final: 0.8679 (pttm) REVERT: z 244 VAL cc_start: 0.8552 (OUTLIER) cc_final: 0.8216 (t) REVERT: z 381 LYS cc_start: 0.8347 (tptt) cc_final: 0.7909 (tppt) REVERT: P 293 SER cc_start: 0.7388 (p) cc_final: 0.7149 (p) outliers start: 78 outliers final: 26 residues processed: 528 average time/residue: 1.4793 time to fit residues: 1023.9147 Evaluate side-chains 506 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 471 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 415 MET Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 300 MET Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 701 optimal weight: 0.5980 chunk 477 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 626 optimal weight: 10.0000 chunk 347 optimal weight: 9.9990 chunk 718 optimal weight: 2.9990 chunk 581 optimal weight: 0.6980 chunk 0 optimal weight: 30.0000 chunk 429 optimal weight: 9.9990 chunk 755 optimal weight: 0.9990 chunk 212 optimal weight: 10.0000 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS H 233 HIS Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** b 122 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1135 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 68429 Z= 0.275 Angle : 0.554 11.221 92378 Z= 0.273 Chirality : 0.042 0.156 10993 Planarity : 0.003 0.064 11793 Dihedral : 6.949 179.061 9496 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 1.06 % Allowed : 9.22 % Favored : 89.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.67 (0.09), residues: 8734 helix: 2.42 (0.08), residues: 4513 sheet: 0.08 (0.16), residues: 1102 loop : -0.48 (0.11), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP N 222 HIS 0.011 0.001 HIS z 161 PHE 0.018 0.001 PHE B 252 TYR 0.012 0.001 TYR Z 239 ARG 0.005 0.000 ARG E 24 *********************** 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 569 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 78 poor density : 491 time to evaluate : 6.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8698 (mpp) cc_final: 0.8244 (mpm) REVERT: A 5 LEU cc_start: 0.8836 (OUTLIER) cc_final: 0.8443 (tt) REVERT: A 44 MET cc_start: 0.8786 (mtt) cc_final: 0.8529 (mtt) REVERT: A 106 GLU cc_start: 0.8541 (tp30) cc_final: 0.8158 (tp30) REVERT: A 248 LEU cc_start: 0.8950 (tp) cc_final: 0.8729 (tm) REVERT: A 508 ILE cc_start: 0.8653 (tp) cc_final: 0.8428 (tp) REVERT: B 221 ASP cc_start: 0.8778 (t70) cc_final: 0.8409 (t0) REVERT: D 25 GLN cc_start: 0.9069 (tp-100) cc_final: 0.8650 (tp-100) REVERT: D 399 GLU cc_start: 0.8458 (OUTLIER) cc_final: 0.7621 (mp0) REVERT: E 4 MET cc_start: 0.5152 (tmm) cc_final: 0.4630 (tmm) REVERT: E 229 ILE cc_start: 0.9104 (OUTLIER) cc_final: 0.8883 (tp) REVERT: E 231 ASP cc_start: 0.8433 (t0) cc_final: 0.8194 (t0) REVERT: E 464 GLU cc_start: 0.8614 (tp30) cc_final: 0.8365 (tp30) REVERT: E 468 MET cc_start: 0.8561 (mtt) cc_final: 0.8218 (mtt) REVERT: E 522 GLN cc_start: 0.8756 (OUTLIER) cc_final: 0.7448 (mp10) REVERT: G 47 MET cc_start: 0.8857 (mtp) cc_final: 0.8473 (mtp) REVERT: G 521 ASP cc_start: 0.7712 (t70) cc_final: 0.7364 (t70) REVERT: H 394 MET cc_start: 0.9101 (mmm) cc_final: 0.8647 (mmm) REVERT: Q 416 GLU cc_start: 0.8878 (mp0) cc_final: 0.8609 (mp0) REVERT: Q 526 MET cc_start: 0.9102 (mtm) cc_final: 0.8876 (mtm) REVERT: Z 17 GLN cc_start: 0.8635 (mp10) cc_final: 0.8317 (mp10) REVERT: a 77 GLU cc_start: 0.8024 (mp0) cc_final: 0.7777 (mp0) REVERT: b 415 MET cc_start: 0.9410 (mmm) cc_final: 0.9176 (mmm) REVERT: d 60 MET cc_start: 0.8853 (OUTLIER) cc_final: 0.8138 (tpp) REVERT: d 90 MET cc_start: 0.8768 (OUTLIER) cc_final: 0.7286 (mpt) REVERT: e 48 MET cc_start: 0.9075 (mmm) cc_final: 0.8752 (mmm) REVERT: e 61 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.7723 (mmm) REVERT: e 199 MET cc_start: 0.7222 (mmp) cc_final: 0.6995 (mpp) REVERT: g 12 GLN cc_start: 0.8762 (tp-100) cc_final: 0.8511 (tp-100) REVERT: g 358 GLU cc_start: 0.7982 (tt0) cc_final: 0.7487 (tt0) REVERT: g 527 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8605 (tppt) REVERT: h 14 ASP cc_start: 0.8278 (t70) cc_final: 0.8025 (t0) REVERT: h 221 SER cc_start: 0.9243 (m) cc_final: 0.9010 (p) REVERT: q 249 MET cc_start: 0.8706 (pmm) cc_final: 0.8408 (pmm) REVERT: q 296 LYS cc_start: 0.8940 (ptmm) cc_final: 0.8607 (pttp) REVERT: z 17 GLN cc_start: 0.8354 (mp10) cc_final: 0.8049 (pm20) REVERT: z 244 VAL cc_start: 0.8507 (OUTLIER) cc_final: 0.8161 (t) REVERT: z 381 LYS cc_start: 0.8303 (tptt) cc_final: 0.7865 (tppt) REVERT: z 388 LYS cc_start: 0.8996 (ttpt) cc_final: 0.8773 (ttpt) REVERT: P 293 SER cc_start: 0.7362 (p) cc_final: 0.7124 (p) outliers start: 78 outliers final: 35 residues processed: 539 average time/residue: 1.4745 time to fit residues: 1046.2132 Evaluate side-chains 514 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 471 time to evaluate : 6.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 157 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 232 LYS Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 372 LEU Chi-restraints excluded: chain h residue 31 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 300 MET Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 44 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 283 optimal weight: 10.0000 chunk 758 optimal weight: 0.8980 chunk 166 optimal weight: 9.9990 chunk 494 optimal weight: 0.8980 chunk 207 optimal weight: 9.9990 chunk 842 optimal weight: 1.9990 chunk 699 optimal weight: 7.9990 chunk 390 optimal weight: 0.8980 chunk 70 optimal weight: 9.9990 chunk 278 optimal weight: 0.9980 chunk 442 optimal weight: 1.9990 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS b 122 HIS ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 526 HIS z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 68429 Z= 0.152 Angle : 0.519 10.989 92378 Z= 0.255 Chirality : 0.041 0.165 10993 Planarity : 0.003 0.063 11793 Dihedral : 6.818 177.358 9496 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.25 % Favored : 96.72 % Rotamer: Outliers : 0.94 % Allowed : 9.96 % Favored : 89.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.75 (0.09), residues: 8734 helix: 2.53 (0.08), residues: 4502 sheet: 0.07 (0.16), residues: 1106 loop : -0.46 (0.11), residues: 3126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.020 0.001 PHE h 455 TYR 0.013 0.001 TYR Z 239 ARG 0.006 0.000 ARG E 24 *********************** 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 564 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 69 poor density : 495 time to evaluate : 6.488 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8623 (mpp) cc_final: 0.8217 (mpm) REVERT: A 44 MET cc_start: 0.8747 (mtt) cc_final: 0.8476 (mtt) REVERT: A 106 GLU cc_start: 0.8485 (tp30) cc_final: 0.8118 (tp30) REVERT: A 248 LEU cc_start: 0.8905 (tp) cc_final: 0.8680 (tm) REVERT: B 221 ASP cc_start: 0.8758 (t70) cc_final: 0.8393 (t0) REVERT: D 25 GLN cc_start: 0.9028 (tp-100) cc_final: 0.8634 (tp-100) REVERT: D 399 GLU cc_start: 0.8412 (OUTLIER) cc_final: 0.7560 (mp0) REVERT: D 486 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8790 (mm-40) REVERT: E 4 MET cc_start: 0.5178 (tmm) cc_final: 0.4682 (tmt) REVERT: E 231 ASP cc_start: 0.8354 (t0) cc_final: 0.8129 (t0) REVERT: E 464 GLU cc_start: 0.8587 (tp30) cc_final: 0.8331 (tp30) REVERT: E 468 MET cc_start: 0.8533 (mtt) cc_final: 0.8242 (mtt) REVERT: E 522 GLN cc_start: 0.8742 (OUTLIER) cc_final: 0.7455 (mp10) REVERT: G 47 MET cc_start: 0.8802 (mtp) cc_final: 0.8403 (mtp) REVERT: H 394 MET cc_start: 0.9070 (mmm) cc_final: 0.8616 (mmm) REVERT: Q 311 MET cc_start: 0.8821 (ttt) cc_final: 0.8378 (ttm) REVERT: Q 416 GLU cc_start: 0.8875 (mp0) cc_final: 0.8633 (mp0) REVERT: Q 526 MET cc_start: 0.9099 (mtm) cc_final: 0.8865 (mtm) REVERT: Z 17 GLN cc_start: 0.8622 (mp10) cc_final: 0.8300 (mp10) REVERT: a 77 GLU cc_start: 0.8049 (mp0) cc_final: 0.7798 (mp0) REVERT: a 306 MET cc_start: 0.8308 (OUTLIER) cc_final: 0.7858 (mmm) REVERT: b 415 MET cc_start: 0.9412 (mmm) cc_final: 0.9160 (mmm) REVERT: d 60 MET cc_start: 0.8873 (OUTLIER) cc_final: 0.8191 (tpp) REVERT: d 90 MET cc_start: 0.8727 (OUTLIER) cc_final: 0.7212 (mpt) REVERT: e 61 MET cc_start: 0.9185 (OUTLIER) cc_final: 0.7627 (mmm) REVERT: e 288 MET cc_start: 0.9124 (OUTLIER) cc_final: 0.8828 (ptp) REVERT: g 12 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8486 (tp-100) REVERT: g 20 ARG cc_start: 0.8297 (tpp80) cc_final: 0.8041 (tpp80) REVERT: g 395 MET cc_start: 0.9255 (mtt) cc_final: 0.8980 (mtt) REVERT: g 527 LYS cc_start: 0.8979 (mmmt) cc_final: 0.8586 (tppt) REVERT: h 14 ASP cc_start: 0.8270 (t70) cc_final: 0.8022 (t0) REVERT: q 249 MET cc_start: 0.8690 (pmm) cc_final: 0.8438 (pmm) REVERT: q 296 LYS cc_start: 0.8923 (ptmm) cc_final: 0.8652 (pttm) REVERT: z 17 GLN cc_start: 0.8355 (mp10) cc_final: 0.8063 (pm20) REVERT: z 207 ILE cc_start: 0.9085 (OUTLIER) cc_final: 0.8873 (mt) REVERT: z 244 VAL cc_start: 0.8455 (OUTLIER) cc_final: 0.8098 (t) REVERT: z 381 LYS cc_start: 0.8230 (tptt) cc_final: 0.7781 (tppt) REVERT: P 293 SER cc_start: 0.7345 (p) cc_final: 0.7102 (p) outliers start: 69 outliers final: 25 residues processed: 543 average time/residue: 1.5000 time to fit residues: 1072.4124 Evaluate side-chains 513 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 479 time to evaluate : 6.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 245 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 401 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 812 optimal weight: 9.9990 chunk 94 optimal weight: 4.9990 chunk 480 optimal weight: 9.9990 chunk 615 optimal weight: 10.0000 chunk 476 optimal weight: 0.9990 chunk 709 optimal weight: 0.8980 chunk 470 optimal weight: 6.9990 chunk 839 optimal weight: 3.9990 chunk 525 optimal weight: 5.9990 chunk 511 optimal weight: 1.9990 chunk 387 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 534 HIS ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8564 moved from start: 0.1235 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 68429 Z= 0.187 Angle : 0.531 14.181 92378 Z= 0.259 Chirality : 0.041 0.174 10993 Planarity : 0.003 0.061 11793 Dihedral : 6.743 179.166 9496 Min Nonbonded Distance : 1.922 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 0.89 % Allowed : 10.60 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8734 helix: 2.55 (0.08), residues: 4502 sheet: 0.07 (0.16), residues: 1097 loop : -0.46 (0.11), residues: 3135 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.015 0.001 PHE H 455 TYR 0.029 0.001 TYR N 174 ARG 0.008 0.000 ARG E 24 *********************** 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 557 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 492 time to evaluate : 6.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8646 (mpp) cc_final: 0.8358 (mpp) REVERT: A 106 GLU cc_start: 0.8501 (tp30) cc_final: 0.8140 (tp30) REVERT: A 248 LEU cc_start: 0.8915 (tp) cc_final: 0.8689 (tm) REVERT: B 221 ASP cc_start: 0.8760 (t70) cc_final: 0.8373 (t0) REVERT: B 415 MET cc_start: 0.9364 (mmm) cc_final: 0.9144 (tpp) REVERT: D 25 GLN cc_start: 0.9030 (tp-100) cc_final: 0.8644 (tp-100) REVERT: D 486 GLN cc_start: 0.9022 (mm-40) cc_final: 0.8805 (mm-40) REVERT: E 4 MET cc_start: 0.5310 (tmm) cc_final: 0.4799 (tmm) REVERT: E 426 GLU cc_start: 0.8835 (mp0) cc_final: 0.8601 (mp0) REVERT: E 464 GLU cc_start: 0.8594 (tp30) cc_final: 0.8342 (tp30) REVERT: E 468 MET cc_start: 0.8545 (mtt) cc_final: 0.8257 (mtt) REVERT: E 522 GLN cc_start: 0.8746 (OUTLIER) cc_final: 0.7453 (mp10) REVERT: G 47 MET cc_start: 0.8810 (mtp) cc_final: 0.8407 (mtp) REVERT: G 521 ASP cc_start: 0.7654 (t70) cc_final: 0.7255 (t70) REVERT: H 394 MET cc_start: 0.9076 (mmm) cc_final: 0.8620 (mmm) REVERT: Q 311 MET cc_start: 0.8826 (ttt) cc_final: 0.8342 (ttm) REVERT: Q 416 GLU cc_start: 0.8880 (mp0) cc_final: 0.8631 (mp0) REVERT: Q 526 MET cc_start: 0.9104 (mtm) cc_final: 0.8871 (mtm) REVERT: Z 17 GLN cc_start: 0.8636 (mp10) cc_final: 0.8301 (mp10) REVERT: a 77 GLU cc_start: 0.8058 (mp0) cc_final: 0.7804 (mp0) REVERT: a 306 MET cc_start: 0.8406 (OUTLIER) cc_final: 0.7980 (mmm) REVERT: b 415 MET cc_start: 0.9415 (mmm) cc_final: 0.9146 (mmp) REVERT: d 60 MET cc_start: 0.8868 (OUTLIER) cc_final: 0.8197 (tpp) REVERT: d 90 MET cc_start: 0.8746 (OUTLIER) cc_final: 0.7221 (mpt) REVERT: e 48 MET cc_start: 0.9000 (mmm) cc_final: 0.8685 (mmm) REVERT: e 61 MET cc_start: 0.9180 (OUTLIER) cc_final: 0.7579 (mmm) REVERT: e 288 MET cc_start: 0.9153 (OUTLIER) cc_final: 0.8863 (ptp) REVERT: g 12 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8489 (tp-100) REVERT: g 20 ARG cc_start: 0.8304 (tpp80) cc_final: 0.8048 (tpp80) REVERT: g 527 LYS cc_start: 0.8981 (mmmt) cc_final: 0.8595 (tppt) REVERT: h 14 ASP cc_start: 0.8275 (t70) cc_final: 0.8030 (t0) REVERT: h 221 SER cc_start: 0.9257 (m) cc_final: 0.8962 (p) REVERT: q 249 MET cc_start: 0.8671 (pmm) cc_final: 0.8368 (pmm) REVERT: q 296 LYS cc_start: 0.8918 (ptmm) cc_final: 0.8645 (pttm) REVERT: z 17 GLN cc_start: 0.8376 (mp10) cc_final: 0.8092 (pm20) REVERT: z 207 ILE cc_start: 0.9071 (OUTLIER) cc_final: 0.8853 (mt) REVERT: z 244 VAL cc_start: 0.8467 (OUTLIER) cc_final: 0.8151 (t) REVERT: z 381 LYS cc_start: 0.8220 (tptt) cc_final: 0.7843 (tppt) REVERT: z 388 LYS cc_start: 0.8971 (ttpt) cc_final: 0.8759 (ttpt) REVERT: P 293 SER cc_start: 0.7259 (p) cc_final: 0.7006 (p) outliers start: 65 outliers final: 30 residues processed: 535 average time/residue: 1.5099 time to fit residues: 1064.2107 Evaluate side-chains 513 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 475 time to evaluate : 6.238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 401 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 519 optimal weight: 2.9990 chunk 335 optimal weight: 0.9980 chunk 501 optimal weight: 10.0000 chunk 252 optimal weight: 7.9990 chunk 164 optimal weight: 8.9990 chunk 162 optimal weight: 0.6980 chunk 533 optimal weight: 0.9980 chunk 571 optimal weight: 6.9990 chunk 415 optimal weight: 8.9990 chunk 78 optimal weight: 6.9990 chunk 659 optimal weight: 0.9980 overall best weight: 1.3382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS D 82 GLN Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 390 ASN z 161 HIS ** P 186 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 68429 Z= 0.161 Angle : 0.526 14.137 92378 Z= 0.257 Chirality : 0.041 0.186 10993 Planarity : 0.003 0.062 11793 Dihedral : 6.665 178.248 9496 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.68 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.23 % Favored : 96.75 % Rotamer: Outliers : 0.76 % Allowed : 11.05 % Favored : 88.18 % 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: 1.80 (0.09), residues: 8734 helix: 2.57 (0.08), residues: 4505 sheet: 0.10 (0.16), residues: 1107 loop : -0.46 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.015 0.001 HIS z 161 PHE 0.016 0.001 PHE B 252 TYR 0.019 0.001 TYR D 24 ARG 0.007 0.000 ARG E 24 *********************** 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 554 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 498 time to evaluate : 6.427 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8632 (mpp) cc_final: 0.8341 (mpp) REVERT: A 106 GLU cc_start: 0.8491 (tp30) cc_final: 0.8138 (tp30) REVERT: A 248 LEU cc_start: 0.8911 (tp) cc_final: 0.8681 (tm) REVERT: B 221 ASP cc_start: 0.8772 (t70) cc_final: 0.8416 (t0) REVERT: D 25 GLN cc_start: 0.9010 (tp-100) cc_final: 0.8682 (tp-100) REVERT: D 67 ASP cc_start: 0.8751 (m-30) cc_final: 0.8437 (m-30) REVERT: D 486 GLN cc_start: 0.9010 (mm-40) cc_final: 0.8799 (mm-40) REVERT: E 4 MET cc_start: 0.5318 (tmm) cc_final: 0.4867 (tmm) REVERT: E 426 GLU cc_start: 0.8837 (mp0) cc_final: 0.8606 (mp0) REVERT: E 464 GLU cc_start: 0.8592 (tp30) cc_final: 0.8338 (tp30) REVERT: E 468 MET cc_start: 0.8545 (mtt) cc_final: 0.8264 (mtt) REVERT: E 522 GLN cc_start: 0.8749 (OUTLIER) cc_final: 0.7410 (mp10) REVERT: G 47 MET cc_start: 0.8795 (mtp) cc_final: 0.8453 (mtp) REVERT: G 521 ASP cc_start: 0.7646 (t70) cc_final: 0.7204 (t70) REVERT: H 394 MET cc_start: 0.9073 (mmm) cc_final: 0.8617 (mmm) REVERT: Q 311 MET cc_start: 0.8826 (ttt) cc_final: 0.8337 (ttm) REVERT: Q 416 GLU cc_start: 0.8876 (mp0) cc_final: 0.8626 (mp0) REVERT: Q 526 MET cc_start: 0.9096 (mtm) cc_final: 0.8863 (mtm) REVERT: Z 17 GLN cc_start: 0.8634 (mp10) cc_final: 0.8292 (mp10) REVERT: a 77 GLU cc_start: 0.8079 (mp0) cc_final: 0.7825 (mp0) REVERT: a 306 MET cc_start: 0.8371 (OUTLIER) cc_final: 0.7936 (mmm) REVERT: b 244 MET cc_start: 0.8488 (mtm) cc_final: 0.8271 (mtp) REVERT: b 445 MET cc_start: 0.8540 (tpp) cc_final: 0.8293 (mmm) REVERT: d 60 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8185 (tpp) REVERT: d 90 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7143 (mpt) REVERT: e 48 MET cc_start: 0.9016 (mmm) cc_final: 0.8682 (mmm) REVERT: e 61 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.7497 (mmm) REVERT: e 288 MET cc_start: 0.9114 (OUTLIER) cc_final: 0.8829 (ptp) REVERT: g 12 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8484 (tp-100) REVERT: g 527 LYS cc_start: 0.8972 (mmmt) cc_final: 0.8579 (tppt) REVERT: h 14 ASP cc_start: 0.8276 (t70) cc_final: 0.8034 (t0) REVERT: h 221 SER cc_start: 0.9235 (m) cc_final: 0.8917 (p) REVERT: q 249 MET cc_start: 0.8680 (pmm) cc_final: 0.8435 (pmm) REVERT: q 296 LYS cc_start: 0.8909 (ptmm) cc_final: 0.8560 (ptmm) REVERT: z 17 GLN cc_start: 0.8363 (mp10) cc_final: 0.8083 (pm20) REVERT: z 207 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8775 (mt) REVERT: z 244 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8160 (t) REVERT: z 381 LYS cc_start: 0.8198 (tptt) cc_final: 0.7862 (tppt) REVERT: P 293 SER cc_start: 0.7220 (p) cc_final: 0.6957 (p) outliers start: 56 outliers final: 31 residues processed: 537 average time/residue: 1.4763 time to fit residues: 1047.9055 Evaluate side-chains 521 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 482 time to evaluate : 6.193 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 26 ASP Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 61 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 401 LYS Chi-restraints excluded: chain h residue 444 ILE Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 763 optimal weight: 5.9990 chunk 804 optimal weight: 5.9990 chunk 733 optimal weight: 7.9990 chunk 782 optimal weight: 10.0000 chunk 470 optimal weight: 8.9990 chunk 340 optimal weight: 7.9990 chunk 614 optimal weight: 0.0060 chunk 240 optimal weight: 0.7980 chunk 706 optimal weight: 0.8980 chunk 739 optimal weight: 0.9990 chunk 779 optimal weight: 1.9990 overall best weight: 0.9400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** b 285 HIS ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 474 ASN z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8544 moved from start: 0.1369 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 68429 Z= 0.143 Angle : 0.529 12.446 92378 Z= 0.257 Chirality : 0.041 0.256 10993 Planarity : 0.003 0.061 11793 Dihedral : 6.564 176.819 9496 Min Nonbonded Distance : 1.942 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.18 % Favored : 96.79 % Rotamer: Outliers : 0.68 % Allowed : 11.44 % Favored : 87.88 % 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: 1.83 (0.09), residues: 8734 helix: 2.60 (0.08), residues: 4509 sheet: 0.12 (0.16), residues: 1106 loop : -0.47 (0.11), residues: 3119 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.016 0.001 PHE B 252 TYR 0.029 0.001 TYR N 174 ARG 0.008 0.000 ARG E 24 *********************** 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 551 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 501 time to evaluate : 6.270 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8609 (mpp) cc_final: 0.8327 (mpp) REVERT: A 248 LEU cc_start: 0.8898 (tp) cc_final: 0.8666 (tm) REVERT: B 221 ASP cc_start: 0.8769 (t70) cc_final: 0.8428 (t0) REVERT: D 25 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8598 (tp-100) REVERT: D 67 ASP cc_start: 0.8760 (m-30) cc_final: 0.8460 (m-30) REVERT: E 4 MET cc_start: 0.5333 (tmm) cc_final: 0.4879 (tmm) REVERT: E 158 ASP cc_start: 0.8663 (t0) cc_final: 0.8348 (t0) REVERT: E 426 GLU cc_start: 0.8860 (mp0) cc_final: 0.8619 (mp0) REVERT: E 464 GLU cc_start: 0.8598 (tp30) cc_final: 0.8345 (tp30) REVERT: E 468 MET cc_start: 0.8550 (mtt) cc_final: 0.8309 (mtt) REVERT: E 522 GLN cc_start: 0.8744 (OUTLIER) cc_final: 0.7400 (mp10) REVERT: G 47 MET cc_start: 0.8786 (mtp) cc_final: 0.8444 (mtp) REVERT: G 521 ASP cc_start: 0.7602 (t70) cc_final: 0.7106 (t70) REVERT: H 394 MET cc_start: 0.9078 (mmm) cc_final: 0.8632 (mmm) REVERT: Q 311 MET cc_start: 0.8823 (ttt) cc_final: 0.8335 (ttm) REVERT: Q 416 GLU cc_start: 0.8868 (mp0) cc_final: 0.8623 (mp0) REVERT: Q 526 MET cc_start: 0.9102 (mtm) cc_final: 0.8868 (mtm) REVERT: Z 17 GLN cc_start: 0.8631 (mp10) cc_final: 0.8288 (mp10) REVERT: a 306 MET cc_start: 0.8329 (OUTLIER) cc_final: 0.7881 (mmm) REVERT: b 244 MET cc_start: 0.8430 (mtm) cc_final: 0.8223 (mtp) REVERT: b 445 MET cc_start: 0.8493 (tpp) cc_final: 0.8248 (mmm) REVERT: d 60 MET cc_start: 0.8878 (OUTLIER) cc_final: 0.8214 (tpp) REVERT: d 90 MET cc_start: 0.8708 (OUTLIER) cc_final: 0.7150 (mpt) REVERT: e 48 MET cc_start: 0.9000 (mmm) cc_final: 0.8651 (mmm) REVERT: e 288 MET cc_start: 0.9099 (OUTLIER) cc_final: 0.8823 (ptp) REVERT: g 12 GLN cc_start: 0.8740 (tp-100) cc_final: 0.8486 (tp-100) REVERT: g 114 GLU cc_start: 0.8328 (tp30) cc_final: 0.8007 (mm-30) REVERT: g 527 LYS cc_start: 0.8945 (mmmt) cc_final: 0.8569 (tppt) REVERT: h 14 ASP cc_start: 0.8291 (t70) cc_final: 0.8033 (t0) REVERT: h 221 SER cc_start: 0.9215 (m) cc_final: 0.8888 (p) REVERT: q 249 MET cc_start: 0.8656 (pmm) cc_final: 0.8330 (pmm) REVERT: q 296 LYS cc_start: 0.8900 (ptmm) cc_final: 0.8626 (pttm) REVERT: z 17 GLN cc_start: 0.8334 (mp10) cc_final: 0.8064 (pm20) REVERT: z 207 ILE cc_start: 0.8978 (OUTLIER) cc_final: 0.8774 (mt) REVERT: z 244 VAL cc_start: 0.8452 (OUTLIER) cc_final: 0.8147 (t) REVERT: z 381 LYS cc_start: 0.8154 (tptt) cc_final: 0.7817 (tppt) REVERT: P 186 HIS cc_start: 0.5175 (OUTLIER) cc_final: 0.4705 (t-90) outliers start: 50 outliers final: 28 residues processed: 533 average time/residue: 1.4790 time to fit residues: 1040.0782 Evaluate side-chains 516 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 480 time to evaluate : 6.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 275 MET Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 324 MET Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 401 LYS Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 148 MET Chi-restraints excluded: chain P residue 186 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 513 optimal weight: 9.9990 chunk 827 optimal weight: 1.9990 chunk 504 optimal weight: 10.0000 chunk 392 optimal weight: 10.0000 chunk 575 optimal weight: 8.9990 chunk 867 optimal weight: 0.6980 chunk 798 optimal weight: 4.9990 chunk 690 optimal weight: 5.9990 chunk 71 optimal weight: 0.0770 chunk 533 optimal weight: 10.0000 chunk 423 optimal weight: 2.9990 overall best weight: 2.1544 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS H 501 ASN Z 161 HIS ** a 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8566 moved from start: 0.1362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 68429 Z= 0.213 Angle : 0.548 13.378 92378 Z= 0.267 Chirality : 0.042 0.520 10993 Planarity : 0.003 0.061 11793 Dihedral : 6.534 172.008 9496 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.30 % Favored : 96.68 % Rotamer: Outliers : 0.57 % Allowed : 11.71 % Favored : 87.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.09), residues: 8734 helix: 2.59 (0.08), residues: 4505 sheet: 0.10 (0.16), residues: 1114 loop : -0.45 (0.11), residues: 3115 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 266 HIS 0.015 0.001 HIS z 161 PHE 0.013 0.001 PHE P 267 TYR 0.029 0.001 TYR Z 498 ARG 0.007 0.000 ARG E 24 ********************** 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 523 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 481 time to evaluate : 6.493 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8469 (tp30) cc_final: 0.7980 (tp30) REVERT: A 248 LEU cc_start: 0.8916 (tp) cc_final: 0.8685 (tm) REVERT: B 221 ASP cc_start: 0.8755 (t70) cc_final: 0.8405 (t0) REVERT: D 25 GLN cc_start: 0.9007 (tp-100) cc_final: 0.8692 (tp-100) REVERT: D 67 ASP cc_start: 0.8778 (m-30) cc_final: 0.8466 (m-30) REVERT: E 4 MET cc_start: 0.5350 (tmm) cc_final: 0.4891 (tmm) REVERT: E 158 ASP cc_start: 0.8680 (t0) cc_final: 0.8363 (t0) REVERT: E 231 ASP cc_start: 0.8290 (t0) cc_final: 0.7967 (t0) REVERT: E 426 GLU cc_start: 0.8883 (mp0) cc_final: 0.8617 (mp0) REVERT: E 464 GLU cc_start: 0.8609 (tp30) cc_final: 0.8358 (tp30) REVERT: E 468 MET cc_start: 0.8557 (mtt) cc_final: 0.8275 (mtt) REVERT: E 522 GLN cc_start: 0.8761 (OUTLIER) cc_final: 0.7426 (mp10) REVERT: G 47 MET cc_start: 0.8810 (mtp) cc_final: 0.8470 (mtp) REVERT: H 394 MET cc_start: 0.9077 (mmm) cc_final: 0.8621 (mmm) REVERT: Q 311 MET cc_start: 0.8849 (ttt) cc_final: 0.8375 (ttt) REVERT: Q 416 GLU cc_start: 0.8883 (mp0) cc_final: 0.8616 (mp0) REVERT: Q 526 MET cc_start: 0.9104 (mtm) cc_final: 0.8879 (mtm) REVERT: Z 17 GLN cc_start: 0.8643 (mp10) cc_final: 0.8298 (mp10) REVERT: a 306 MET cc_start: 0.8499 (OUTLIER) cc_final: 0.8087 (mmm) REVERT: d 60 MET cc_start: 0.8867 (OUTLIER) cc_final: 0.8168 (tpp) REVERT: d 90 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.7226 (mpt) REVERT: e 48 MET cc_start: 0.9004 (mmm) cc_final: 0.8660 (mmm) REVERT: e 288 MET cc_start: 0.9157 (OUTLIER) cc_final: 0.8872 (ptp) REVERT: g 12 GLN cc_start: 0.8750 (tp-100) cc_final: 0.8495 (tp-100) REVERT: g 114 GLU cc_start: 0.8398 (tp30) cc_final: 0.8057 (mm-30) REVERT: g 527 LYS cc_start: 0.8968 (mmmt) cc_final: 0.8581 (tppt) REVERT: h 14 ASP cc_start: 0.8273 (t70) cc_final: 0.8033 (t0) REVERT: h 221 SER cc_start: 0.9234 (m) cc_final: 0.8942 (p) REVERT: q 249 MET cc_start: 0.8666 (pmm) cc_final: 0.8363 (pmm) REVERT: q 266 MET cc_start: 0.9040 (mtp) cc_final: 0.8678 (mmm) REVERT: q 296 LYS cc_start: 0.8904 (ptmm) cc_final: 0.8576 (pttp) REVERT: z 17 GLN cc_start: 0.8333 (mp10) cc_final: 0.8053 (pm20) REVERT: z 207 ILE cc_start: 0.9038 (OUTLIER) cc_final: 0.8815 (mt) REVERT: z 244 VAL cc_start: 0.8494 (OUTLIER) cc_final: 0.8183 (t) REVERT: z 381 LYS cc_start: 0.8264 (tptt) cc_final: 0.7912 (tppt) REVERT: z 388 LYS cc_start: 0.9004 (ttpt) cc_final: 0.8793 (mtpt) REVERT: P 145 MET cc_start: 0.6669 (pmm) cc_final: 0.5351 (ptt) outliers start: 42 outliers final: 28 residues processed: 512 average time/residue: 1.5144 time to fit residues: 1022.4326 Evaluate side-chains 512 residues out of total 7328 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 477 time to evaluate : 6.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 355 MET Chi-restraints excluded: chain D residue 399 GLU Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 368 LYS Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain E residue 522 GLN Chi-restraints excluded: chain G residue 7 VAL Chi-restraints excluded: chain G residue 111 HIS Chi-restraints excluded: chain G residue 244 SER Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain Z residue 244 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 306 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain d residue 60 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 305 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 288 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain h residue 70 ASP Chi-restraints excluded: chain h residue 444 ILE Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 207 ILE Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain P residue 148 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 548 optimal weight: 0.6980 chunk 736 optimal weight: 6.9990 chunk 211 optimal weight: 2.9990 chunk 637 optimal weight: 0.3980 chunk 102 optimal weight: 9.9990 chunk 192 optimal weight: 3.9990 chunk 692 optimal weight: 2.9990 chunk 289 optimal weight: 10.0000 chunk 710 optimal weight: 3.9990 chunk 87 optimal weight: 1.9990 chunk 127 optimal weight: 6.9990 overall best weight: 1.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 534 HIS Z 161 HIS a 205 GLN ** d 235 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 318 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.071079 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2759 r_free = 0.2759 target = 0.056865 restraints weight = 179201.702| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 3.08 r_work: 0.2618 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2612 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2612 r_free = 0.2612 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2612 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.1371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 68429 Z= 0.192 Angle : 0.545 12.036 92378 Z= 0.265 Chirality : 0.042 0.543 10993 Planarity : 0.003 0.061 11793 Dihedral : 6.515 171.808 9496 Min Nonbonded Distance : 1.916 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.15 % Favored : 96.83 % Rotamer: Outliers : 0.57 % Allowed : 11.76 % Favored : 87.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.81 (0.09), residues: 8734 helix: 2.59 (0.08), residues: 4503 sheet: 0.10 (0.16), residues: 1110 loop : -0.45 (0.11), residues: 3121 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 266 HIS 0.016 0.001 HIS z 161 PHE 0.011 0.001 PHE B 252 TYR 0.032 0.001 TYR N 174 ARG 0.007 0.000 ARG E 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17003.89 seconds wall clock time: 298 minutes 21.36 seconds (17901.36 seconds total)