Starting phenix.real_space_refine on Mon Jan 20 22:06:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shd_40484/01_2025/8shd_40484.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shd_40484/01_2025/8shd_40484.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8shd_40484/01_2025/8shd_40484.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shd_40484/01_2025/8shd_40484.map" model { file = "/net/cci-nas-00/data/ceres_data/8shd_40484/01_2025/8shd_40484.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shd_40484/01_2025/8shd_40484.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.049 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 407 5.16 5 C 41267 2.51 5 N 11494 2.21 5 O 12789 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 49 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 66069 Number of models: 1 Model: "" Number of chains: 49 Chain: "N" Number of atoms: 946 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 946 Classifications: {'peptide': 126} Link IDs: {'PTRANS': 3, 'TRANS': 122} 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: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 32.61, per 1000 atoms: 0.49 Number of scatterers: 66069 At special positions: 0 Unit cell: (179.86, 177.744, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 407 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 12789 8.00 N 11494 7.00 C 41267 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 "HETATM65976 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65720 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM65848 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: 13.08 Conformation dependent library (CDL) restraints added in 6.9 seconds 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15998 Finding SS restraints... Secondary structure from input PDB file: 355 helices and 99 sheets defined 56.2% alpha, 14.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.26 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.631A 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: 3.669A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.658A 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 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: 4.083A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.019A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.860A 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: 3.511A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.602A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 4.221A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 433 through 445 removed outlier: 3.760A 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: 3.706A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.318A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.554A 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: 3.578A 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: 4.360A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.543A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 removed outlier: 3.530A 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 427 removed outlier: 3.772A pdb=" N ARG B 427 " --> pdb=" O GLN B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 430 through 454 removed outlier: 4.093A pdb=" N VAL B 434 " --> pdb=" O GLY B 430 " (cutoff:3.500A) Proline residue: B 447 - end of helix removed outlier: 3.613A 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: 4.452A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 3.725A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.822A 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: 3.549A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.565A 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: 3.691A 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: 3.776A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.980A 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: 4.297A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.993A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.657A pdb=" N ARG E 24 " --> pdb=" O ASP E 21 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 21 through 25' Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.611A 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 125 removed outlier: 3.606A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 151 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.541A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 4.007A 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: 3.794A 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 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.637A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N CYS E 440 " --> pdb=" O GLU E 436 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.541A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.565A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.523A 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: 3.654A 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 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.710A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.086A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.554A 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: 4.262A 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 339 through 343 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.559A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 removed outlier: 3.500A pdb=" N ARG G 449 " --> pdb=" O GLU G 445 " (cutoff:3.500A) Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.559A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 removed outlier: 3.552A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.723A 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: 3.699A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.238A 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: 3.663A 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: 3.599A 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: 3.506A pdb=" N MET H 227 " --> pdb=" O GLY H 224 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.569A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.517A 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: 3.589A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 453 Processing helix chain 'H' and resid 456 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.405A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.980A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.324A 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 166 removed outlier: 4.303A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.909A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.665A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 428 Processing helix chain 'Q' and resid 433 through 444 removed outlier: 4.104A 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 'Z' and resid 3 through 8 removed outlier: 3.726A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.816A 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: 3.607A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.838A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.193A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 removed outlier: 3.586A 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: 3.609A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 removed outlier: 3.825A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 318 through 329 removed outlier: 4.320A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.538A 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: 4.147A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.668A 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: 3.704A pdb=" N ARG a 18 " --> pdb=" O GLY a 14 " (cutoff:3.500A) removed outlier: 3.598A 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: 3.704A 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: 3.817A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.298A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 258 through 280 removed outlier: 4.617A pdb=" N GLN a 262 " --> pdb=" O GLU a 258 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.780A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 433 through 445 Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.908A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.439A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.499A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.625A 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: 3.539A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 431 through 453 Proline residue: b 447 - end of helix Processing helix chain 'b' and resid 457 through 472 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 107 through 126 removed outlier: 3.892A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 173 removed outlier: 3.538A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 4.509A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 178 removed outlier: 4.297A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 194 Proline residue: d 185 - end of helix removed outlier: 3.692A 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: 3.618A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.893A 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 removed outlier: 3.538A pdb=" N MET d 355 " --> pdb=" O THR d 352 " (cutoff:3.500A) Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 443 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.720A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.815A 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 removed outlier: 5.017A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.519A pdb=" N LEU e 34 " --> pdb=" O GLY e 30 " (cutoff:3.500A) Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 80 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 105 through 126 removed outlier: 3.520A pdb=" N VAL e 109 " --> pdb=" O GLY e 105 " (cutoff:3.500A) removed outlier: 4.303A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.544A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.848A 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: 3.866A 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: 3.793A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 444 through 456 Processing helix chain 'e' and resid 456 through 466 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: 3.768A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 39 through 41 No H-bonds generated for 'chain 'g' and resid 39 through 41' Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.756A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.539A 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: 4.030A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.536A 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: 3.656A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 427 removed outlier: 3.611A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.638A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.709A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 95 through 114 Proline residue: h 110 - end of helix Processing helix chain 'h' and resid 117 through 140 removed outlier: 3.748A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.512A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 removed outlier: 3.517A pdb=" N VAL h 341 " --> pdb=" O SER h 338 " (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: 3.698A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.174A 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: 4.559A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 removed outlier: 3.531A pdb=" N VAL q 147 " --> pdb=" O PRO q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 144 through 147' Processing helix chain 'q' and resid 157 through 168 removed outlier: 4.303A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.565A 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: 4.858A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.884A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) removed outlier: 3.754A 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: 3.699A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 444 removed outlier: 4.391A 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: 3.619A 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: 3.677A 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 66 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.603A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.809A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.169A 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 191 Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.706A 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: 3.675A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 308 removed outlier: 3.669A pdb=" N GLU z 308 " --> pdb=" O ALA z 304 " (cutoff:3.500A) Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.744A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.203A 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: 4.119A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.575A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing sheet with id=AA1, first strand: chain 'N' and resid 202 through 203 removed outlier: 3.620A pdb=" N LEU N 211 " --> pdb=" O SER N 202 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 242 through 244 Processing sheet with id=AA3, first strand: chain 'N' and resid 287 through 289 removed outlier: 3.621A pdb=" N ARG N 314 " --> pdb=" O ASP N 309 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.624A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.312A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.373A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.889A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.561A 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 removed outlier: 5.881A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) 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: 6.456A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.623A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.723A 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: 6.599A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.743A 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: 6.599A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.743A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'G' and resid 254 through 256 removed outlier: 8.908A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.272A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.274A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.502A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.569A 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 Processing sheet with id=AB3, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.334A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.667A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.481A 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: 7.013A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.107A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.953A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.759A 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: 3.780A 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: 6.424A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.319A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N SER B 345 " --> pdb=" O LYS B 236 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N LYS B 236 " --> pdb=" O SER B 345 " (cutoff:3.500A) removed outlier: 6.814A pdb=" N LYS B 347 " --> pdb=" O ASN B 234 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (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: 6.397A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.419A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.255A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.114A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.288A 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: 3.554A pdb=" N LEU D 361 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 3.554A pdb=" N LEU D 361 " --> pdb=" O THR D 377 " (cutoff:3.500A) removed outlier: 6.505A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N VAL D 297 " --> pdb=" O LYS D 245 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.670A 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: 7.185A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.229A 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: 6.534A pdb=" N LYS E 210 " --> pdb=" O ILE E 385 " (cutoff:3.500A) removed outlier: 7.486A pdb=" N ILE E 387 " --> pdb=" O LYS E 210 " (cutoff:3.500A) removed outlier: 6.695A pdb=" N GLU E 212 " --> pdb=" O ILE E 387 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLY E 389 " --> pdb=" O GLU E 212 " (cutoff:3.500A) removed outlier: 7.234A pdb=" N LYS E 214 " --> pdb=" O GLY E 389 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.395A pdb=" N LEU E 358 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU E 244 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN E 360 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS E 242 " --> pdb=" O GLN E 360 " (cutoff:3.500A) removed outlier: 7.538A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.921A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.572A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.618A 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: 6.395A pdb=" N LEU E 358 " --> pdb=" O GLU E 244 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU E 244 " --> pdb=" O LEU E 358 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N GLN E 360 " --> pdb=" O LYS E 242 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N LYS E 242 " --> pdb=" O GLN E 360 " (cutoff:3.500A) removed outlier: 8.709A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.551A 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: 6.360A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 3.571A 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: 6.745A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.317A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.096A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.259A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (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 240 removed outlier: 6.547A pdb=" N VAL G 239 " --> pdb=" O ILE G 291 " (cutoff:3.500A) 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: 6.247A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.646A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE3, first strand: chain 'H' and resid 309 through 311 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: 5.255A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.203A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.758A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N LYS Z 45 " --> pdb=" O THR Z 57 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.908A 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: 6.475A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.583A 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: 3.570A pdb=" N THR Q 358 " --> pdb=" O VAL Q 355 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 240 through 242 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: 6.409A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.119A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.638A 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 310 through 313 removed outlier: 6.293A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.182A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.003A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.276A 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: 3.621A 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: 4.345A pdb=" N ILE a 527 " --> pdb=" O ASP d 58 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N MET d 60 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 6.307A pdb=" N ASP a 529 " --> pdb=" O MET d 60 " (cutoff:3.500A) removed outlier: 7.804A pdb=" N GLN d 62 " --> pdb=" O ASP a 529 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE a 531 " --> pdb=" O GLN d 62 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.501A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (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: 6.395A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.779A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.082A 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: 6.535A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.626A 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: 6.535A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.626A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE a 286 " --> pdb=" O VAL a 308 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.166A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.304A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 6.750A pdb=" N LYS e 263 " --> pdb=" O ILE h 255 " (cutoff:3.500A) removed outlier: 8.027A pdb=" N VAL h 257 " --> pdb=" O LYS e 263 " (cutoff:3.500A) removed outlier: 6.005A pdb=" N LYS e 265 " --> pdb=" O VAL h 257 " (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: 4.416A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.468A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.685A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.514A 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: 7.139A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.220A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 5.977A 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: 3.729A 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: 6.424A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 7.040A 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: 6.424A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.539A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) removed outlier: 9.012A pdb=" N ALA b 332 " --> pdb=" O ILE b 237 " (cutoff:3.500A) removed outlier: 6.594A 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 214 removed outlier: 4.103A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.593A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N CYS d 379 " --> pdb=" O ALA d 359 " (cutoff:3.500A) removed outlier: 6.863A pdb=" N ALA d 359 " --> pdb=" O CYS d 379 " (cutoff:3.500A) removed outlier: 6.569A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 7.091A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 7.535A pdb=" N VAL d 297 " --> pdb=" O LYS d 243 " (cutoff:3.500A) removed outlier: 5.996A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.769A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.831A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (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 28 through 29 removed outlier: 4.479A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.398A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.655A 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: 6.269A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.411A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.681A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.485A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.113A 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: 6.598A pdb=" N LEU e 358 " --> pdb=" O GLU e 244 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLU e 244 " --> pdb=" O LEU e 358 " (cutoff:3.500A) removed outlier: 6.875A pdb=" N GLN e 360 " --> pdb=" O LYS e 242 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LYS e 242 " --> pdb=" O GLN e 360 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU e 299 " --> pdb=" O LYS e 247 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.218A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.602A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (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: 4.031A 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 238 through 241 removed outlier: 6.410A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.700A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 14 through 17 removed outlier: 4.304A pdb=" N VAL h 516 " --> pdb=" O ASN q 53 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N MET q 55 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N GLU h 518 " --> pdb=" O MET q 55 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N ILE q 57 " --> pdb=" O GLU h 518 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ILE h 520 " --> pdb=" O ILE q 57 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.618A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.624A 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 removed outlier: 3.521A pdb=" N ASP h 483 " --> pdb=" O ASP h 478 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 20 through 23 removed outlier: 5.262A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.577A 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: 3.877A 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 208 removed outlier: 6.498A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 7.951A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 7.044A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (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 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 310 through 313 removed outlier: 6.229A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.906A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) Processing sheet with id=AK9, first strand: chain 'z' and resid 477 through 479 4048 hydrogen bonds defined for protein. 11544 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 29.91 Time building geometry restraints manager: 15.24 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: 22222 1.34 - 1.46: 9077 1.46 - 1.58: 34747 1.58 - 1.69: 48 1.69 - 1.81: 722 Bond restraints: 66816 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.52e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.41e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.37e+01 bond pdb=" F2 AF3 H 603 " pdb="AL AF3 H 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.34e+01 ... (remaining 66811 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.58: 88545 1.58 - 3.16: 1238 3.16 - 4.75: 258 4.75 - 6.33: 173 6.33 - 7.91: 11 Bond angle restraints: 90225 Sorted by residual: angle pdb=" N ALA Z 162 " pdb=" CA ALA Z 162 " pdb=" C ALA Z 162 " ideal model delta sigma weight residual 110.97 115.09 -4.12 1.09e+00 8.42e-01 1.43e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.09 -7.91 2.37e+00 1.78e-01 1.11e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.82 -7.64 2.37e+00 1.78e-01 1.04e+01 angle pdb=" N LEU g 8 " pdb=" CA LEU g 8 " pdb=" C LEU g 8 " ideal model delta sigma weight residual 110.91 114.59 -3.68 1.17e+00 7.31e-01 9.91e+00 angle pdb=" C ALA q 151 " pdb=" N LYS q 152 " pdb=" CA LYS q 152 " ideal model delta sigma weight residual 121.54 127.37 -5.83 1.91e+00 2.74e-01 9.32e+00 ... (remaining 90220 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.64: 40645 34.64 - 69.28: 580 69.28 - 103.92: 69 103.92 - 138.56: 8 138.56 - 173.20: 9 Dihedral angle restraints: 41311 sinusoidal: 16609 harmonic: 24702 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual -60.00 113.20 -173.20 1 2.00e+01 2.50e-03 4.78e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 109.99 -169.99 1 2.00e+01 2.50e-03 4.76e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 130.38 169.62 1 2.00e+01 2.50e-03 4.76e+01 ... (remaining 41308 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 7295 0.034 - 0.068: 2323 0.068 - 0.101: 707 0.101 - 0.135: 415 0.135 - 0.169: 17 Chirality restraints: 10757 Sorted by residual: chirality pdb=" CB ILE G 363 " pdb=" CA ILE G 363 " pdb=" CG1 ILE G 363 " pdb=" CG2 ILE G 363 " both_signs ideal model delta sigma weight residual False 2.64 2.81 -0.17 2.00e-01 2.50e+01 7.13e-01 chirality pdb=" CA ILE b 11 " pdb=" N ILE b 11 " pdb=" C ILE b 11 " pdb=" CB ILE b 11 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" CA GLU a 77 " pdb=" N GLU a 77 " pdb=" C GLU a 77 " pdb=" CB GLU a 77 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 10754 not shown) Planarity restraints: 11514 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG E 14 " -0.053 5.00e-02 4.00e+02 8.12e-02 1.06e+01 pdb=" N PRO E 15 " 0.141 5.00e-02 4.00e+02 pdb=" CA PRO E 15 " -0.043 5.00e-02 4.00e+02 pdb=" CD PRO E 15 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN a 477 " 0.050 5.00e-02 4.00e+02 7.57e-02 9.17e+00 pdb=" N PRO a 478 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO a 478 " 0.040 5.00e-02 4.00e+02 pdb=" CD PRO a 478 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP E 231 " -0.013 2.00e-02 2.50e+03 2.73e-02 7.47e+00 pdb=" CG ASP E 231 " 0.047 2.00e-02 2.50e+03 pdb=" OD1 ASP E 231 " -0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP E 231 " -0.016 2.00e-02 2.50e+03 ... (remaining 11511 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.52: 514 2.52 - 3.12: 49587 3.12 - 3.71: 103339 3.71 - 4.31: 146169 4.31 - 4.90: 252322 Nonbonded interactions: 551931 Sorted by model distance: nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.928 2.120 nonbonded pdb="MG MG B 602 " pdb=" F1 AF3 B 603 " model vdw 1.932 2.120 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.948 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.957 2.120 nonbonded pdb="MG MG G 602 " pdb=" F2 AF3 G 603 " model vdw 1.976 2.120 ... (remaining 551926 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: 1.870 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: 0.090 Extract box with map and model: 2.110 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 123.730 Find NCS groups from input model: 5.990 Set up NCS constraints: 0.450 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:11.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 146.150 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 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 0.162 66816 Z= 0.295 Angle : 0.543 7.910 90225 Z= 0.267 Chirality : 0.041 0.169 10757 Planarity : 0.003 0.081 11514 Dihedral : 13.798 173.199 25313 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.29 % Favored : 96.69 % Rotamer: Outliers : 0.00 % Allowed : 0.14 % Favored : 99.86 % 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: 1.61 (0.09), residues: 8548 helix: 2.26 (0.08), residues: 4378 sheet: 0.36 (0.16), residues: 1169 loop : -0.41 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP q 319 HIS 0.011 0.001 HIS z 161 PHE 0.030 0.001 PHE b 12 TYR 0.017 0.001 TYR G 437 ARG 0.008 0.000 ARG z 270 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 596 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 596 time to evaluate : 6.191 Fit side-chains REVERT: N 223 ASP cc_start: 0.8945 (t70) cc_final: 0.8684 (t70) REVERT: N 268 MET cc_start: 0.8650 (mpp) cc_final: 0.8373 (mpp) REVERT: D 65 LYS cc_start: 0.9322 (ptpp) cc_final: 0.8751 (ptmm) REVERT: D 67 ASP cc_start: 0.8287 (m-30) cc_final: 0.7846 (m-30) REVERT: D 332 ASP cc_start: 0.8782 (m-30) cc_final: 0.8576 (m-30) REVERT: E 21 ASP cc_start: 0.8148 (t70) cc_final: 0.7568 (t0) REVERT: Q 34 GLN cc_start: 0.8168 (tp-100) cc_final: 0.7802 (tp-100) REVERT: e 60 MET cc_start: 0.9014 (ttm) cc_final: 0.8809 (ttp) REVERT: g 182 MET cc_start: 0.8992 (ptp) cc_final: 0.8789 (ptp) REVERT: h 185 MET cc_start: 0.8479 (mtp) cc_final: 0.8123 (mtm) REVERT: h 519 THR cc_start: 0.8876 (m) cc_final: 0.8665 (m) REVERT: q 41 GLN cc_start: 0.8478 (tp-100) cc_final: 0.7937 (tp-100) REVERT: z 415 GLU cc_start: 0.8596 (mp0) cc_final: 0.8353 (mp0) outliers start: 0 outliers final: 2 residues processed: 596 average time/residue: 1.5634 time to fit residues: 1199.7278 Evaluate side-chains 460 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 458 time to evaluate : 6.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 150 ASP Chi-restraints excluded: chain D residue 311 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 718 optimal weight: 10.0000 chunk 645 optimal weight: 2.9990 chunk 357 optimal weight: 9.9990 chunk 220 optimal weight: 8.9990 chunk 435 optimal weight: 5.9990 chunk 344 optimal weight: 8.9990 chunk 667 optimal weight: 8.9990 chunk 258 optimal weight: 0.9980 chunk 405 optimal weight: 10.0000 chunk 496 optimal weight: 7.9990 chunk 772 optimal weight: 3.9990 overall best weight: 4.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN A 164 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 426 ASN b 498 GLN ** d 301 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 468 ASN ** e 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 320 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** g 396 GLN g 400 ASN h 331 GLN q 303 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 161 HIS z 346 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2842 r_free = 0.2842 target = 0.063439 restraints weight = 159408.191| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 2.75 r_work: 0.2648 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2524 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2524 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2564 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2564 r_free = 0.2564 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2564 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8831 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 66816 Z= 0.393 Angle : 0.621 9.136 90225 Z= 0.310 Chirality : 0.044 0.178 10757 Planarity : 0.004 0.065 11514 Dihedral : 7.840 179.034 9291 Min Nonbonded Distance : 1.801 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.36 % Favored : 96.62 % Rotamer: Outliers : 0.95 % Allowed : 6.13 % Favored : 92.92 % 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: 1.47 (0.09), residues: 8548 helix: 2.15 (0.08), residues: 4444 sheet: 0.22 (0.16), residues: 1143 loop : -0.53 (0.11), residues: 2961 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.012 0.001 HIS z 161 PHE 0.019 0.002 PHE h 455 TYR 0.021 0.002 TYR E 420 ARG 0.008 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 556 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 68 poor density : 488 time to evaluate : 6.387 Fit side-chains REVERT: N 223 ASP cc_start: 0.9058 (t70) cc_final: 0.8622 (t0) REVERT: N 244 ASP cc_start: 0.6857 (t0) cc_final: 0.6568 (t0) REVERT: N 254 PHE cc_start: 0.6706 (t80) cc_final: 0.6431 (t80) REVERT: N 268 MET cc_start: 0.9140 (mpp) cc_final: 0.8721 (mpp) REVERT: A 147 CYS cc_start: 0.9382 (t) cc_final: 0.9179 (t) REVERT: B 245 ASP cc_start: 0.9045 (p0) cc_final: 0.8815 (p0) REVERT: D 65 LYS cc_start: 0.9485 (ptpp) cc_final: 0.8906 (ptmm) REVERT: D 67 ASP cc_start: 0.8758 (m-30) cc_final: 0.8451 (m-30) REVERT: D 332 ASP cc_start: 0.9270 (m-30) cc_final: 0.9051 (m-30) REVERT: E 21 ASP cc_start: 0.8863 (t70) cc_final: 0.8242 (t0) REVERT: E 526 MET cc_start: 0.9356 (OUTLIER) cc_final: 0.9144 (ttm) REVERT: H 185 MET cc_start: 0.8835 (mtp) cc_final: 0.8620 (mtp) REVERT: H 227 MET cc_start: 0.9407 (OUTLIER) cc_final: 0.8447 (mpt) REVERT: Q 34 GLN cc_start: 0.8634 (tp-100) cc_final: 0.8270 (tp40) REVERT: a 156 MET cc_start: 0.9204 (OUTLIER) cc_final: 0.8823 (mtp) REVERT: d 429 GLU cc_start: 0.8850 (mp0) cc_final: 0.8533 (mp0) REVERT: e 4 MET cc_start: 0.3630 (mpp) cc_final: 0.2804 (mmt) REVERT: g 15 LYS cc_start: 0.8847 (mtmm) cc_final: 0.8478 (mtmt) REVERT: h 2 MET cc_start: 0.8291 (OUTLIER) cc_final: 0.7518 (mmp) REVERT: h 30 GLN cc_start: 0.9018 (OUTLIER) cc_final: 0.8331 (mt0) REVERT: h 185 MET cc_start: 0.9021 (mtp) cc_final: 0.8804 (mtp) REVERT: h 227 MET cc_start: 0.9481 (OUTLIER) cc_final: 0.9187 (mtp) REVERT: h 356 GLU cc_start: 0.9145 (OUTLIER) cc_final: 0.8755 (mt-10) REVERT: h 455 PHE cc_start: 0.8277 (m-80) cc_final: 0.7984 (m-80) REVERT: q 41 GLN cc_start: 0.8984 (tp-100) cc_final: 0.8515 (tp-100) REVERT: z 415 GLU cc_start: 0.9143 (mp0) cc_final: 0.8851 (mp0) outliers start: 68 outliers final: 25 residues processed: 513 average time/residue: 1.4728 time to fit residues: 992.5263 Evaluate side-chains 488 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 456 time to evaluate : 6.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 62 MET Chi-restraints excluded: chain D residue 311 ASP Chi-restraints excluded: chain E residue 39 MET Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 20 LEU Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 30 GLN Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 319 ARG Chi-restraints excluded: chain z residue 418 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 684 optimal weight: 9.9990 chunk 615 optimal weight: 4.9990 chunk 428 optimal weight: 7.9990 chunk 11 optimal weight: 40.0000 chunk 107 optimal weight: 3.9990 chunk 666 optimal weight: 5.9990 chunk 159 optimal weight: 10.0000 chunk 93 optimal weight: 1.9990 chunk 151 optimal weight: 9.9990 chunk 170 optimal weight: 0.9980 chunk 503 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN D 502 ASN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 53 ASN d 301 GLN e 122 GLN g 474 ASN g 526 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3067 r_free = 0.3067 target = 0.075715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2847 r_free = 0.2847 target = 0.064025 restraints weight = 138609.521| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.57 r_work: 0.2665 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2543 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2543 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 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 = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8815 moved from start: 0.1052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 66816 Z= 0.332 Angle : 0.590 8.689 90225 Z= 0.293 Chirality : 0.043 0.171 10757 Planarity : 0.003 0.058 11514 Dihedral : 7.677 170.341 9289 Min Nonbonded Distance : 1.836 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.38 % Favored : 96.61 % Rotamer: Outliers : 1.19 % Allowed : 8.31 % Favored : 90.50 % 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: 1.45 (0.09), residues: 8548 helix: 2.17 (0.08), residues: 4444 sheet: 0.18 (0.16), residues: 1114 loop : -0.56 (0.11), residues: 2990 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.019 0.001 PHE h 455 TYR 0.022 0.002 TYR A 181 ARG 0.007 0.000 ARG a 185 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 85 poor density : 501 time to evaluate : 6.187 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.9079 (t70) cc_final: 0.8652 (t0) REVERT: N 244 ASP cc_start: 0.6820 (t0) cc_final: 0.6270 (p0) REVERT: N 254 PHE cc_start: 0.6923 (t80) cc_final: 0.6566 (t80) REVERT: N 267 ASP cc_start: 0.8449 (t0) cc_final: 0.8132 (t0) REVERT: N 268 MET cc_start: 0.9130 (mpp) cc_final: 0.8509 (mpp) REVERT: A 181 TYR cc_start: 0.8933 (p90) cc_final: 0.8651 (p90) REVERT: D 65 LYS cc_start: 0.9484 (ptpp) cc_final: 0.8890 (ptmm) REVERT: D 67 ASP cc_start: 0.8742 (m-30) cc_final: 0.8430 (m-30) REVERT: E 21 ASP cc_start: 0.8830 (t70) cc_final: 0.8112 (t0) REVERT: E 29 MET cc_start: 0.8578 (OUTLIER) cc_final: 0.8376 (mtm) REVERT: E 212 GLU cc_start: 0.8655 (mm-30) cc_final: 0.8431 (mm-30) REVERT: E 526 MET cc_start: 0.9348 (OUTLIER) cc_final: 0.9136 (ttm) REVERT: G 21 LYS cc_start: 0.9145 (mmmm) cc_final: 0.8697 (mmtt) REVERT: G 47 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8943 (mmm) REVERT: Q 34 GLN cc_start: 0.8547 (tp-100) cc_final: 0.8216 (tp40) REVERT: Q 387 ASP cc_start: 0.8937 (t0) cc_final: 0.8444 (m-30) REVERT: Z 415 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: a 77 GLU cc_start: 0.8815 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: a 156 MET cc_start: 0.9122 (OUTLIER) cc_final: 0.8783 (mtp) REVERT: d 429 GLU cc_start: 0.8843 (mp0) cc_final: 0.8497 (mp0) REVERT: e 4 MET cc_start: 0.3865 (mpp) cc_final: 0.2976 (mmt) REVERT: g 15 LYS cc_start: 0.8806 (mtmm) cc_final: 0.8379 (mtmt) REVERT: h 2 MET cc_start: 0.8210 (OUTLIER) cc_final: 0.7367 (mmp) REVERT: h 227 MET cc_start: 0.9483 (mtp) cc_final: 0.9174 (mtp) REVERT: h 455 PHE cc_start: 0.8123 (m-80) cc_final: 0.7797 (m-80) REVERT: q 41 GLN cc_start: 0.8952 (tp-100) cc_final: 0.8476 (tp-100) REVERT: z 244 VAL cc_start: 0.8674 (OUTLIER) cc_final: 0.8185 (t) REVERT: z 364 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8804 (mt-10) REVERT: z 415 GLU cc_start: 0.9118 (mp0) cc_final: 0.8755 (mp0) outliers start: 85 outliers final: 27 residues processed: 541 average time/residue: 1.4470 time to fit residues: 1030.0652 Evaluate side-chains 497 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 462 time to evaluate : 6.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain A residue 5 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 244 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 526 MET Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 685 optimal weight: 1.9990 chunk 519 optimal weight: 4.9990 chunk 785 optimal weight: 1.9990 chunk 239 optimal weight: 5.9990 chunk 715 optimal weight: 0.4980 chunk 825 optimal weight: 3.9990 chunk 219 optimal weight: 0.9990 chunk 295 optimal weight: 6.9990 chunk 485 optimal weight: 4.9990 chunk 607 optimal weight: 9.9990 chunk 694 optimal weight: 9.9990 overall best weight: 1.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.076849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2871 r_free = 0.2871 target = 0.064845 restraints weight = 157908.008| |-----------------------------------------------------------------------------| r_work (start): 0.2827 rms_B_bonded: 2.76 r_work: 0.2683 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2719 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2719 r_free = 0.2719 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2719 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 66816 Z= 0.207 Angle : 0.550 9.274 90225 Z= 0.271 Chirality : 0.042 0.174 10757 Planarity : 0.003 0.056 11514 Dihedral : 7.384 174.957 9287 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.35 % Favored : 96.64 % Rotamer: Outliers : 1.09 % Allowed : 9.62 % Favored : 89.29 % 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: 1.56 (0.09), residues: 8548 helix: 2.32 (0.08), residues: 4428 sheet: 0.08 (0.16), residues: 1114 loop : -0.52 (0.11), residues: 3006 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.018 0.001 PHE A 167 TYR 0.022 0.001 TYR A 181 ARG 0.009 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 78 poor density : 505 time to evaluate : 6.362 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8943 (t70) cc_final: 0.8550 (t0) REVERT: N 244 ASP cc_start: 0.6836 (t0) cc_final: 0.6244 (p0) REVERT: N 254 PHE cc_start: 0.6868 (t80) cc_final: 0.6481 (t80) REVERT: N 268 MET cc_start: 0.9077 (mpp) cc_final: 0.8615 (mpp) REVERT: A 271 THR cc_start: 0.9445 (OUTLIER) cc_final: 0.9172 (t) REVERT: D 65 LYS cc_start: 0.9446 (ptpp) cc_final: 0.8839 (ptmm) REVERT: D 67 ASP cc_start: 0.8608 (m-30) cc_final: 0.8280 (m-30) REVERT: E 21 ASP cc_start: 0.8664 (t70) cc_final: 0.7915 (t0) REVERT: E 212 GLU cc_start: 0.8384 (mm-30) cc_final: 0.8162 (mm-30) REVERT: G 21 LYS cc_start: 0.9040 (mmmm) cc_final: 0.8601 (mmtt) REVERT: G 47 MET cc_start: 0.9084 (OUTLIER) cc_final: 0.8836 (mmm) REVERT: H 227 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.8322 (mpt) REVERT: H 370 CYS cc_start: 0.8924 (m) cc_final: 0.8658 (m) REVERT: H 394 MET cc_start: 0.9193 (mmm) cc_final: 0.8867 (mmm) REVERT: Q 34 GLN cc_start: 0.8367 (tp-100) cc_final: 0.8031 (tp40) REVERT: Q 61 GLU cc_start: 0.9066 (OUTLIER) cc_final: 0.8655 (mp0) REVERT: Q 387 ASP cc_start: 0.8809 (t0) cc_final: 0.8319 (m-30) REVERT: Z 415 GLU cc_start: 0.9007 (OUTLIER) cc_final: 0.8253 (mp0) REVERT: a 77 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.7878 (mp0) REVERT: a 156 MET cc_start: 0.8887 (OUTLIER) cc_final: 0.8581 (mtp) REVERT: d 429 GLU cc_start: 0.8626 (mp0) cc_final: 0.8307 (mp0) REVERT: e 4 MET cc_start: 0.3942 (mpp) cc_final: 0.3003 (mmt) REVERT: e 60 MET cc_start: 0.9343 (ttm) cc_final: 0.9079 (ttp) REVERT: g 15 LYS cc_start: 0.8739 (mtmm) cc_final: 0.8316 (mtmt) REVERT: g 527 LYS cc_start: 0.8954 (mmmt) cc_final: 0.8660 (mmmm) REVERT: h 2 MET cc_start: 0.8185 (OUTLIER) cc_final: 0.7364 (mmp) REVERT: q 41 GLN cc_start: 0.8841 (tp-100) cc_final: 0.8304 (tp-100) REVERT: z 210 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8958 (mp) REVERT: z 244 VAL cc_start: 0.8478 (OUTLIER) cc_final: 0.8093 (t) REVERT: z 364 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8583 (mt-10) REVERT: z 415 GLU cc_start: 0.8929 (mp0) cc_final: 0.8558 (mp0) outliers start: 78 outliers final: 20 residues processed: 544 average time/residue: 1.4569 time to fit residues: 1037.0594 Evaluate side-chains 504 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 474 time to evaluate : 6.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 227 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 385 MET Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 275 optimal weight: 10.0000 chunk 359 optimal weight: 5.9990 chunk 307 optimal weight: 0.0870 chunk 263 optimal weight: 7.9990 chunk 258 optimal weight: 7.9990 chunk 684 optimal weight: 10.0000 chunk 214 optimal weight: 0.9980 chunk 520 optimal weight: 9.9990 chunk 267 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 774 optimal weight: 6.9990 overall best weight: 4.4164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** H 21 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN Q 309 ASN a 135 ASN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2823 r_free = 0.2823 target = 0.062500 restraints weight = 155698.207| |-----------------------------------------------------------------------------| r_work (start): 0.2775 rms_B_bonded: 2.71 r_work: 0.2631 rms_B_bonded: 3.07 restraints_weight: 0.5000 r_work: 0.2507 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.2507 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2548 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2548 r_free = 0.2548 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2548 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8839 moved from start: 0.1272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.070 66816 Z= 0.401 Angle : 0.616 12.248 90225 Z= 0.304 Chirality : 0.044 0.172 10757 Planarity : 0.004 0.055 11514 Dihedral : 7.444 175.356 9287 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.76 % Favored : 96.22 % Rotamer: Outliers : 1.41 % Allowed : 10.43 % Favored : 88.16 % 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: 1.45 (0.09), residues: 8548 helix: 2.21 (0.08), residues: 4425 sheet: 0.07 (0.16), residues: 1117 loop : -0.58 (0.11), residues: 3006 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 0.002 PHE A 167 TYR 0.020 0.002 TYR E 420 ARG 0.007 0.000 ARG a 480 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 474 time to evaluate : 6.081 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.9125 (t70) cc_final: 0.8693 (t0) REVERT: N 244 ASP cc_start: 0.7008 (t0) cc_final: 0.6418 (p0) REVERT: N 254 PHE cc_start: 0.7263 (t80) cc_final: 0.6865 (t80) REVERT: N 268 MET cc_start: 0.9145 (mpp) cc_final: 0.8511 (mpp) REVERT: A 271 THR cc_start: 0.9492 (OUTLIER) cc_final: 0.9206 (t) REVERT: B 245 ASP cc_start: 0.8978 (p0) cc_final: 0.8769 (p0) REVERT: D 65 LYS cc_start: 0.9503 (ptpp) cc_final: 0.8909 (ptmm) REVERT: D 67 ASP cc_start: 0.8764 (m-30) cc_final: 0.8473 (m-30) REVERT: E 21 ASP cc_start: 0.8921 (t70) cc_final: 0.8192 (t0) REVERT: E 212 GLU cc_start: 0.8675 (mm-30) cc_final: 0.8449 (mm-30) REVERT: E 426 GLU cc_start: 0.9211 (OUTLIER) cc_final: 0.8811 (mm-30) REVERT: G 21 LYS cc_start: 0.9163 (mmmm) cc_final: 0.8732 (mmtt) REVERT: G 47 MET cc_start: 0.9181 (OUTLIER) cc_final: 0.8968 (mmm) REVERT: H 394 MET cc_start: 0.9326 (mmm) cc_final: 0.8982 (mmm) REVERT: Q 34 GLN cc_start: 0.8553 (tp-100) cc_final: 0.8249 (tp40) REVERT: Q 61 GLU cc_start: 0.9152 (OUTLIER) cc_final: 0.8593 (mp0) REVERT: Z 415 GLU cc_start: 0.9178 (OUTLIER) cc_final: 0.8435 (mp0) REVERT: a 77 GLU cc_start: 0.8844 (OUTLIER) cc_final: 0.8149 (mp0) REVERT: a 156 MET cc_start: 0.9116 (OUTLIER) cc_final: 0.8774 (mtp) REVERT: d 429 GLU cc_start: 0.8877 (mp0) cc_final: 0.8514 (mp0) REVERT: e 4 MET cc_start: 0.3781 (mpp) cc_final: 0.2972 (mmt) REVERT: g 15 LYS cc_start: 0.8810 (mtmm) cc_final: 0.8384 (mtmt) REVERT: g 71 GLN cc_start: 0.9065 (tp40) cc_final: 0.8430 (tp40) REVERT: g 527 LYS cc_start: 0.9007 (mmmt) cc_final: 0.8725 (mmmm) REVERT: h 2 MET cc_start: 0.8281 (OUTLIER) cc_final: 0.7537 (mmp) REVERT: h 57 THR cc_start: 0.9177 (OUTLIER) cc_final: 0.8808 (p) REVERT: q 41 GLN cc_start: 0.8979 (tp-100) cc_final: 0.8529 (tp-100) REVERT: z 244 VAL cc_start: 0.8685 (OUTLIER) cc_final: 0.8198 (t) REVERT: z 364 GLU cc_start: 0.9099 (mt-10) cc_final: 0.8876 (mt-10) REVERT: z 415 GLU cc_start: 0.9118 (mp0) cc_final: 0.8800 (mp0) outliers start: 101 outliers final: 43 residues processed: 528 average time/residue: 1.4351 time to fit residues: 995.4974 Evaluate side-chains 511 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 458 time to evaluate : 6.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 492 MET Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 390 LEU Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 80 MET Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 121 ILE Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 741 optimal weight: 0.6980 chunk 724 optimal weight: 4.9990 chunk 820 optimal weight: 0.9990 chunk 470 optimal weight: 3.9990 chunk 168 optimal weight: 2.9990 chunk 83 optimal weight: 7.9990 chunk 206 optimal weight: 10.0000 chunk 324 optimal weight: 1.9990 chunk 240 optimal weight: 0.9990 chunk 722 optimal weight: 3.9990 chunk 403 optimal weight: 2.9990 overall best weight: 1.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 228 GLN N 272 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN G 481 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 233 HIS z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.078357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.065805 restraints weight = 160695.465| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 2.83 r_work: 0.2685 rms_B_bonded: 3.19 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2721 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2721 r_free = 0.2721 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2721 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 66816 Z= 0.187 Angle : 0.541 12.595 90225 Z= 0.265 Chirality : 0.041 0.156 10757 Planarity : 0.003 0.055 11514 Dihedral : 7.185 177.632 9287 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.19 % Favored : 96.79 % Rotamer: Outliers : 1.17 % Allowed : 11.12 % Favored : 87.71 % 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: 1.62 (0.09), residues: 8548 helix: 2.37 (0.08), residues: 4422 sheet: 0.09 (0.16), residues: 1094 loop : -0.51 (0.11), residues: 3032 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 222 HIS 0.014 0.001 HIS z 161 PHE 0.018 0.001 PHE A 167 TYR 0.019 0.001 TYR N 174 ARG 0.010 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 583 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 84 poor density : 499 time to evaluate : 6.313 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8945 (t70) cc_final: 0.8568 (t0) REVERT: N 244 ASP cc_start: 0.6932 (t0) cc_final: 0.6360 (p0) REVERT: N 254 PHE cc_start: 0.6940 (t80) cc_final: 0.6564 (t80) REVERT: N 264 MET cc_start: 0.7126 (mmt) cc_final: 0.6638 (mmm) REVERT: N 268 MET cc_start: 0.9093 (mpp) cc_final: 0.8624 (mpp) REVERT: A 271 THR cc_start: 0.9431 (OUTLIER) cc_final: 0.9140 (t) REVERT: A 344 MET cc_start: 0.9269 (OUTLIER) cc_final: 0.8568 (mtp) REVERT: B 408 TYR cc_start: 0.9173 (m-80) cc_final: 0.8877 (m-80) REVERT: D 65 LYS cc_start: 0.9483 (ptpp) cc_final: 0.8901 (ptmm) REVERT: D 67 ASP cc_start: 0.8631 (m-30) cc_final: 0.8336 (m-30) REVERT: E 21 ASP cc_start: 0.8593 (t70) cc_final: 0.7797 (t0) REVERT: E 426 GLU cc_start: 0.9095 (OUTLIER) cc_final: 0.8653 (mm-30) REVERT: G 21 LYS cc_start: 0.9057 (mmmm) cc_final: 0.8626 (mmtt) REVERT: H 394 MET cc_start: 0.9225 (mmm) cc_final: 0.8915 (mmm) REVERT: Q 34 GLN cc_start: 0.8282 (tp-100) cc_final: 0.7963 (tp40) REVERT: Q 61 GLU cc_start: 0.9073 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: Q 387 ASP cc_start: 0.8802 (t0) cc_final: 0.8378 (m-30) REVERT: Z 415 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8245 (mp0) REVERT: a 246 MET cc_start: 0.9011 (mmm) cc_final: 0.8806 (mmt) REVERT: d 429 GLU cc_start: 0.8642 (mp0) cc_final: 0.8323 (mp0) REVERT: e 4 MET cc_start: 0.3886 (mpp) cc_final: 0.2972 (mmt) REVERT: e 60 MET cc_start: 0.9326 (ttm) cc_final: 0.9063 (ttp) REVERT: g 15 LYS cc_start: 0.8755 (mtmm) cc_final: 0.8352 (mtmt) REVERT: g 71 GLN cc_start: 0.8940 (tp40) cc_final: 0.8336 (tp40) REVERT: g 527 LYS cc_start: 0.8969 (mmmt) cc_final: 0.8662 (mmmm) REVERT: h 2 MET cc_start: 0.8233 (OUTLIER) cc_final: 0.7618 (mmp) REVERT: h 57 THR cc_start: 0.9120 (OUTLIER) cc_final: 0.8697 (p) REVERT: h 227 MET cc_start: 0.9401 (OUTLIER) cc_final: 0.9102 (mtp) REVERT: h 455 PHE cc_start: 0.8159 (m-10) cc_final: 0.7843 (m-10) REVERT: q 41 GLN cc_start: 0.8854 (tp-100) cc_final: 0.8324 (tp-100) REVERT: q 462 GLU cc_start: 0.9164 (mp0) cc_final: 0.8746 (mp0) REVERT: z 210 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8946 (mp) REVERT: z 244 VAL cc_start: 0.8508 (OUTLIER) cc_final: 0.8096 (t) REVERT: z 415 GLU cc_start: 0.8928 (mp0) cc_final: 0.8618 (mp0) outliers start: 84 outliers final: 35 residues processed: 546 average time/residue: 1.4929 time to fit residues: 1070.7460 Evaluate side-chains 512 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 467 time to evaluate : 6.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 206 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 45 optimal weight: 8.9990 chunk 612 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 632 optimal weight: 2.9990 chunk 805 optimal weight: 2.9990 chunk 462 optimal weight: 0.9980 chunk 47 optimal weight: 7.9990 chunk 832 optimal weight: 10.0000 chunk 358 optimal weight: 3.9990 chunk 782 optimal weight: 10.0000 chunk 286 optimal weight: 3.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN N 272 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 331 GLN q 303 HIS z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3073 r_free = 0.3073 target = 0.076935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.064679 restraints weight = 147705.529| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.69 r_work: 0.2670 rms_B_bonded: 3.01 restraints_weight: 0.5000 r_work: 0.2546 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.2546 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2583 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2583 r_free = 0.2583 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 = 0.2583 r_free = 0.2583 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2583 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8813 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 66816 Z= 0.284 Angle : 0.572 13.933 90225 Z= 0.280 Chirality : 0.042 0.161 10757 Planarity : 0.003 0.054 11514 Dihedral : 7.184 179.216 9287 Min Nonbonded Distance : 1.845 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.49 % Favored : 96.50 % Rotamer: Outliers : 1.22 % Allowed : 11.56 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.09), residues: 8548 helix: 2.34 (0.08), residues: 4426 sheet: 0.12 (0.16), residues: 1103 loop : -0.53 (0.11), residues: 3019 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.019 0.001 PHE A 167 TYR 0.020 0.001 TYR N 174 ARG 0.008 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 470 time to evaluate : 6.251 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.9091 (t70) cc_final: 0.8678 (t0) REVERT: N 244 ASP cc_start: 0.6994 (t0) cc_final: 0.6413 (p0) REVERT: N 254 PHE cc_start: 0.7194 (t80) cc_final: 0.6807 (t80) REVERT: N 264 MET cc_start: 0.7202 (mmt) cc_final: 0.6909 (mmt) REVERT: N 268 MET cc_start: 0.9182 (mpp) cc_final: 0.8646 (mpp) REVERT: A 271 THR cc_start: 0.9468 (OUTLIER) cc_final: 0.9164 (t) REVERT: A 344 MET cc_start: 0.9364 (OUTLIER) cc_final: 0.8686 (mtp) REVERT: D 65 LYS cc_start: 0.9497 (ptpp) cc_final: 0.8897 (ptmm) REVERT: D 67 ASP cc_start: 0.8769 (m-30) cc_final: 0.8480 (m-30) REVERT: E 21 ASP cc_start: 0.8753 (t70) cc_final: 0.7994 (t0) REVERT: E 426 GLU cc_start: 0.9239 (OUTLIER) cc_final: 0.9026 (mp0) REVERT: G 21 LYS cc_start: 0.9149 (mmmm) cc_final: 0.8727 (mmtt) REVERT: H 394 MET cc_start: 0.9328 (mmm) cc_final: 0.8983 (mmm) REVERT: Q 34 GLN cc_start: 0.8500 (tp-100) cc_final: 0.8191 (tp40) REVERT: Q 61 GLU cc_start: 0.9144 (OUTLIER) cc_final: 0.8685 (mp0) REVERT: Q 249 MET cc_start: 0.8749 (OUTLIER) cc_final: 0.8449 (pmm) REVERT: Q 387 ASP cc_start: 0.8957 (t0) cc_final: 0.8536 (m-30) REVERT: Z 415 GLU cc_start: 0.9136 (OUTLIER) cc_final: 0.8443 (mp0) REVERT: a 156 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8727 (mtp) REVERT: d 429 GLU cc_start: 0.8840 (mp0) cc_final: 0.8461 (mp0) REVERT: e 4 MET cc_start: 0.3785 (mpp) cc_final: 0.2939 (mmt) REVERT: g 15 LYS cc_start: 0.8776 (mtmm) cc_final: 0.8370 (mtmt) REVERT: g 71 GLN cc_start: 0.9051 (tp40) cc_final: 0.8421 (tp40) REVERT: g 527 LYS cc_start: 0.8995 (mmmt) cc_final: 0.8695 (mmmm) REVERT: h 2 MET cc_start: 0.8278 (OUTLIER) cc_final: 0.7625 (mmp) REVERT: h 57 THR cc_start: 0.9145 (OUTLIER) cc_final: 0.8791 (p) REVERT: h 455 PHE cc_start: 0.8290 (m-10) cc_final: 0.7956 (m-10) REVERT: q 41 GLN cc_start: 0.8973 (tp-100) cc_final: 0.8475 (tp-100) REVERT: q 462 GLU cc_start: 0.9286 (mp0) cc_final: 0.8881 (mp0) REVERT: z 210 LEU cc_start: 0.9312 (OUTLIER) cc_final: 0.9023 (mp) REVERT: z 415 GLU cc_start: 0.9111 (mp0) cc_final: 0.8741 (mp0) outliers start: 87 outliers final: 51 residues processed: 524 average time/residue: 1.4188 time to fit residues: 987.2724 Evaluate side-chains 520 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 459 time to evaluate : 6.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 156 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 29 MET Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 564 optimal weight: 3.9990 chunk 524 optimal weight: 7.9990 chunk 156 optimal weight: 4.9990 chunk 805 optimal weight: 4.9990 chunk 796 optimal weight: 7.9990 chunk 543 optimal weight: 1.9990 chunk 172 optimal weight: 6.9990 chunk 135 optimal weight: 1.9990 chunk 626 optimal weight: 8.9990 chunk 4 optimal weight: 9.9990 chunk 288 optimal weight: 0.7980 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN N 272 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** z 71 HIS ** 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 = 0.3075 r_free = 0.3075 target = 0.075739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2853 r_free = 0.2853 target = 0.063868 restraints weight = 155604.598| |-----------------------------------------------------------------------------| r_work (start): 0.2809 rms_B_bonded: 2.72 r_work: 0.2666 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work: 0.2541 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2541 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 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 = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8812 moved from start: 0.1336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 66816 Z= 0.268 Angle : 0.568 14.404 90225 Z= 0.278 Chirality : 0.042 0.158 10757 Planarity : 0.003 0.054 11514 Dihedral : 7.153 178.795 9287 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.44 % Favored : 96.55 % Rotamer: Outliers : 1.13 % Allowed : 11.80 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.09), residues: 8548 helix: 2.34 (0.08), residues: 4425 sheet: 0.13 (0.16), residues: 1102 loop : -0.54 (0.11), residues: 3021 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.018 0.001 PHE A 167 TYR 0.018 0.001 TYR N 174 ARG 0.009 0.000 ARG a 185 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 81 poor density : 464 time to evaluate : 6.331 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.9108 (t70) cc_final: 0.8691 (t0) REVERT: N 244 ASP cc_start: 0.7042 (t0) cc_final: 0.6474 (p0) REVERT: N 254 PHE cc_start: 0.7257 (t80) cc_final: 0.6808 (t80) REVERT: N 264 MET cc_start: 0.7190 (mmt) cc_final: 0.6855 (mmt) REVERT: N 268 MET cc_start: 0.9191 (mpp) cc_final: 0.8642 (mpp) REVERT: A 271 THR cc_start: 0.9471 (OUTLIER) cc_final: 0.9162 (t) REVERT: A 344 MET cc_start: 0.9365 (OUTLIER) cc_final: 0.8679 (mtp) REVERT: D 65 LYS cc_start: 0.9498 (ptpp) cc_final: 0.8912 (ptmm) REVERT: D 67 ASP cc_start: 0.8763 (m-30) cc_final: 0.8491 (m-30) REVERT: E 21 ASP cc_start: 0.8698 (t70) cc_final: 0.7925 (t0) REVERT: E 426 GLU cc_start: 0.9252 (OUTLIER) cc_final: 0.9041 (mp0) REVERT: G 21 LYS cc_start: 0.9159 (mmmm) cc_final: 0.8729 (mmtt) REVERT: H 394 MET cc_start: 0.9334 (mmm) cc_final: 0.8982 (mmm) REVERT: Q 34 GLN cc_start: 0.8503 (tp-100) cc_final: 0.8195 (tp40) REVERT: Q 61 GLU cc_start: 0.9158 (OUTLIER) cc_final: 0.8694 (mp0) REVERT: Q 249 MET cc_start: 0.8729 (OUTLIER) cc_final: 0.8432 (pmm) REVERT: Q 276 MET cc_start: 0.9169 (tpt) cc_final: 0.8292 (tpt) REVERT: Q 387 ASP cc_start: 0.8959 (t0) cc_final: 0.8529 (m-30) REVERT: Z 415 GLU cc_start: 0.9143 (OUTLIER) cc_final: 0.8450 (mp0) REVERT: d 429 GLU cc_start: 0.8843 (mp0) cc_final: 0.8458 (mp0) REVERT: e 4 MET cc_start: 0.3911 (mpp) cc_final: 0.3019 (mmt) REVERT: g 15 LYS cc_start: 0.8750 (mtmm) cc_final: 0.8360 (mtmt) REVERT: g 71 GLN cc_start: 0.9042 (tp40) cc_final: 0.8430 (tp40) REVERT: g 527 LYS cc_start: 0.9009 (mmmt) cc_final: 0.8694 (mmmm) REVERT: h 2 MET cc_start: 0.8285 (OUTLIER) cc_final: 0.7629 (mmp) REVERT: h 57 THR cc_start: 0.9141 (OUTLIER) cc_final: 0.8786 (p) REVERT: h 227 MET cc_start: 0.9495 (OUTLIER) cc_final: 0.9188 (mtp) REVERT: h 455 PHE cc_start: 0.8277 (m-10) cc_final: 0.7928 (m-10) REVERT: q 41 GLN cc_start: 0.8967 (tp-100) cc_final: 0.8465 (tp-100) REVERT: z 210 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9047 (mp) REVERT: z 415 GLU cc_start: 0.9129 (mp0) cc_final: 0.8812 (mp0) outliers start: 81 outliers final: 51 residues processed: 512 average time/residue: 1.4334 time to fit residues: 971.0316 Evaluate side-chains 522 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 461 time to evaluate : 6.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 255 VAL Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 480 MET Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 206 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 256 THR Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 210 LEU Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 308 optimal weight: 5.9990 chunk 105 optimal weight: 6.9990 chunk 566 optimal weight: 10.0000 chunk 399 optimal weight: 9.9990 chunk 265 optimal weight: 0.5980 chunk 365 optimal weight: 3.9990 chunk 114 optimal weight: 4.9990 chunk 621 optimal weight: 10.0000 chunk 675 optimal weight: 5.9990 chunk 493 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 overall best weight: 4.3188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN N 272 GLN ** G 226 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN h 501 ASN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.074311 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.062662 restraints weight = 146861.511| |-----------------------------------------------------------------------------| r_work (start): 0.2779 rms_B_bonded: 2.62 r_work: 0.2639 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2517 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2517 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8833 moved from start: 0.1405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 66816 Z= 0.388 Angle : 0.623 14.038 90225 Z= 0.306 Chirality : 0.044 0.170 10757 Planarity : 0.004 0.054 11514 Dihedral : 7.284 174.136 9287 Min Nonbonded Distance : 1.816 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.79 % Favored : 96.18 % Rotamer: Outliers : 1.20 % Allowed : 12.03 % Favored : 86.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.45 (0.09), residues: 8548 helix: 2.23 (0.08), residues: 4428 sheet: 0.04 (0.16), residues: 1119 loop : -0.61 (0.11), residues: 3001 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.013 0.001 HIS z 161 PHE 0.019 0.002 PHE A 167 TYR 0.020 0.002 TYR E 420 ARG 0.010 0.000 ARG a 185 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 550 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 464 time to evaluate : 6.400 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.9173 (t70) cc_final: 0.8733 (t70) REVERT: N 244 ASP cc_start: 0.7094 (t0) cc_final: 0.6747 (p0) REVERT: N 254 PHE cc_start: 0.7286 (t80) cc_final: 0.6813 (t80) REVERT: N 264 MET cc_start: 0.7186 (mmt) cc_final: 0.6777 (mmt) REVERT: N 268 MET cc_start: 0.9198 (mpp) cc_final: 0.8641 (mpp) REVERT: A 271 THR cc_start: 0.9490 (OUTLIER) cc_final: 0.9198 (t) REVERT: A 344 MET cc_start: 0.9341 (OUTLIER) cc_final: 0.8621 (mtp) REVERT: D 65 LYS cc_start: 0.9493 (ptpp) cc_final: 0.8882 (ptmm) REVERT: D 67 ASP cc_start: 0.8747 (m-30) cc_final: 0.8477 (m-30) REVERT: E 21 ASP cc_start: 0.8711 (t70) cc_final: 0.7940 (t0) REVERT: E 426 GLU cc_start: 0.9237 (OUTLIER) cc_final: 0.9033 (mp0) REVERT: Q 34 GLN cc_start: 0.8529 (tp-100) cc_final: 0.8228 (tp40) REVERT: Q 41 GLN cc_start: 0.9184 (tm-30) cc_final: 0.8947 (tp-100) REVERT: Q 61 GLU cc_start: 0.9161 (OUTLIER) cc_final: 0.8575 (mp0) REVERT: Q 249 MET cc_start: 0.8732 (OUTLIER) cc_final: 0.8444 (pmm) REVERT: Q 276 MET cc_start: 0.9236 (tpt) cc_final: 0.8479 (tpt) REVERT: Q 387 ASP cc_start: 0.8988 (t0) cc_final: 0.8530 (m-30) REVERT: Z 415 GLU cc_start: 0.9168 (OUTLIER) cc_final: 0.8414 (mp0) REVERT: a 77 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8070 (mp0) REVERT: d 429 GLU cc_start: 0.8839 (mp0) cc_final: 0.8329 (mp0) REVERT: e 4 MET cc_start: 0.3760 (mpp) cc_final: 0.2949 (mmt) REVERT: g 15 LYS cc_start: 0.8737 (mtmm) cc_final: 0.8347 (mtmt) REVERT: g 71 GLN cc_start: 0.9058 (tp40) cc_final: 0.8431 (tp40) REVERT: g 527 LYS cc_start: 0.9022 (mmmt) cc_final: 0.8700 (mmmm) REVERT: h 2 MET cc_start: 0.8276 (OUTLIER) cc_final: 0.7599 (mmp) REVERT: h 57 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8786 (p) REVERT: h 356 GLU cc_start: 0.9120 (OUTLIER) cc_final: 0.8355 (mm-30) REVERT: h 455 PHE cc_start: 0.8456 (m-10) cc_final: 0.7633 (m-80) REVERT: h 482 GLU cc_start: 0.8729 (tp30) cc_final: 0.8463 (tp30) REVERT: q 41 GLN cc_start: 0.8965 (tp-100) cc_final: 0.8473 (tp-100) REVERT: z 415 GLU cc_start: 0.9087 (mp0) cc_final: 0.8760 (mp0) outliers start: 86 outliers final: 55 residues processed: 518 average time/residue: 1.5045 time to fit residues: 1021.6600 Evaluate side-chains 516 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 451 time to evaluate : 6.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 4 MET Chi-restraints excluded: chain E residue 109 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 230 VAL Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain E residue 443 LEU Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain G residue 83 ILE Chi-restraints excluded: chain G residue 86 THR Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Q residue 296 LYS Chi-restraints excluded: chain Q residue 358 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain Z residue 374 LEU Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 206 MET Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 77 ASP Chi-restraints excluded: chain b residue 153 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 91 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 125 GLN Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 398 ILE Chi-restraints excluded: chain e residue 229 ILE Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain g residue 18 SER Chi-restraints excluded: chain h residue 2 MET Chi-restraints excluded: chain h residue 32 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 117 GLU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 463 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 294 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 436 optimal weight: 1.9990 chunk 69 optimal weight: 0.8980 chunk 267 optimal weight: 0.2980 chunk 397 optimal weight: 0.9990 chunk 203 optimal weight: 0.4980 chunk 398 optimal weight: 8.9990 chunk 793 optimal weight: 10.0000 chunk 275 optimal weight: 0.9990 chunk 434 optimal weight: 0.5980 overall best weight: 0.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN N 272 GLN G 390 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.078588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.066610 restraints weight = 155438.799| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 2.76 r_work: 0.2721 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2721 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2759 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2759 r_free = 0.2759 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2759 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.1442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 66816 Z= 0.153 Angle : 0.543 13.357 90225 Z= 0.266 Chirality : 0.041 0.159 10757 Planarity : 0.003 0.054 11514 Dihedral : 6.987 174.145 9287 Min Nonbonded Distance : 1.964 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.01 % Favored : 96.98 % Rotamer: Outliers : 0.70 % Allowed : 12.66 % Favored : 86.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.09), residues: 8548 helix: 2.42 (0.08), residues: 4429 sheet: 0.09 (0.16), residues: 1074 loop : -0.52 (0.11), residues: 3045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.016 0.001 PHE A 167 TYR 0.020 0.001 TYR N 174 ARG 0.011 0.000 ARG a 185 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17096 Ramachandran restraints generated. 8548 Oldfield, 0 Emsley, 8548 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 559 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 509 time to evaluate : 6.271 Fit side-chains revert: symmetry clash REVERT: N 223 ASP cc_start: 0.8965 (t70) cc_final: 0.8618 (t0) REVERT: N 244 ASP cc_start: 0.7023 (t0) cc_final: 0.6330 (p0) REVERT: N 254 PHE cc_start: 0.6818 (t80) cc_final: 0.6430 (t80) REVERT: N 264 MET cc_start: 0.7266 (mmt) cc_final: 0.6981 (mmt) REVERT: N 267 ASP cc_start: 0.8295 (t0) cc_final: 0.8046 (t0) REVERT: N 268 MET cc_start: 0.9115 (mpp) cc_final: 0.8785 (mpp) REVERT: A 271 THR cc_start: 0.9417 (OUTLIER) cc_final: 0.9110 (t) REVERT: A 344 MET cc_start: 0.9256 (OUTLIER) cc_final: 0.8535 (mtp) REVERT: B 408 TYR cc_start: 0.9124 (m-80) cc_final: 0.8786 (m-80) REVERT: D 65 LYS cc_start: 0.9464 (ptpp) cc_final: 0.8867 (ptmm) REVERT: D 67 ASP cc_start: 0.8626 (m-30) cc_final: 0.8324 (m-30) REVERT: D 120 CYS cc_start: 0.9206 (m) cc_final: 0.8856 (m) REVERT: E 426 GLU cc_start: 0.9107 (OUTLIER) cc_final: 0.8858 (mp0) REVERT: G 21 LYS cc_start: 0.9051 (mmmm) cc_final: 0.8547 (mmtm) REVERT: G 415 GLU cc_start: 0.9013 (mp0) cc_final: 0.8751 (mp0) REVERT: H 11 GLU cc_start: 0.8691 (tp30) cc_final: 0.8429 (tp30) REVERT: H 382 MET cc_start: 0.9171 (mtm) cc_final: 0.8956 (mtm) REVERT: H 394 MET cc_start: 0.9228 (mmm) cc_final: 0.8836 (mmm) REVERT: Q 34 GLN cc_start: 0.8236 (tp-100) cc_final: 0.7922 (tp40) REVERT: Q 61 GLU cc_start: 0.9101 (OUTLIER) cc_final: 0.8651 (mp0) REVERT: Q 249 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8247 (pmm) REVERT: Q 276 MET cc_start: 0.8917 (tpt) cc_final: 0.8101 (tpt) REVERT: Q 387 ASP cc_start: 0.8837 (t0) cc_final: 0.8500 (m-30) REVERT: Q 428 GLU cc_start: 0.8680 (mm-30) cc_final: 0.8444 (mm-30) REVERT: Z 415 GLU cc_start: 0.8950 (OUTLIER) cc_final: 0.8248 (mp0) REVERT: a 77 GLU cc_start: 0.8633 (OUTLIER) cc_final: 0.7870 (mp0) REVERT: a 206 MET cc_start: 0.9288 (OUTLIER) cc_final: 0.9055 (mmp) REVERT: d 27 ARG cc_start: 0.8297 (mmm-85) cc_final: 0.8089 (mmm-85) REVERT: d 429 GLU cc_start: 0.8627 (mp0) cc_final: 0.8201 (mp0) REVERT: e 4 MET cc_start: 0.3733 (mpp) cc_final: 0.2832 (mmt) REVERT: e 84 ASP cc_start: 0.9120 (t70) cc_final: 0.8666 (m-30) REVERT: g 15 LYS cc_start: 0.8675 (mtmm) cc_final: 0.8300 (mtmt) REVERT: g 71 GLN cc_start: 0.8885 (tp40) cc_final: 0.8288 (tp40) REVERT: g 527 LYS cc_start: 0.8973 (mmmt) cc_final: 0.8648 (mmmm) REVERT: h 227 MET cc_start: 0.9406 (mtp) cc_final: 0.9079 (mtp) REVERT: q 41 GLN cc_start: 0.8825 (tp-100) cc_final: 0.8284 (tp-100) REVERT: q 473 GLU cc_start: 0.8348 (tm-30) cc_final: 0.8118 (tm-30) REVERT: z 210 LEU cc_start: 0.9247 (tp) cc_final: 0.9012 (mp) REVERT: z 415 GLU cc_start: 0.8915 (mp0) cc_final: 0.8540 (mp0) outliers start: 50 outliers final: 28 residues processed: 543 average time/residue: 1.4749 time to fit residues: 1055.9940 Evaluate side-chains 519 residues out of total 7151 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 483 time to evaluate : 6.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 176 LEU Chi-restraints excluded: chain A residue 230 VAL Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain A residue 271 THR Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 344 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 395 LYS Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 322 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 435 GLN Chi-restraints excluded: chain G residue 8 LEU Chi-restraints excluded: chain H residue 81 ASP Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 61 GLU Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 249 MET Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 415 GLU Chi-restraints excluded: chain a residue 67 VAL Chi-restraints excluded: chain a residue 77 GLU Chi-restraints excluded: chain a residue 206 MET Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 53 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 217 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 9 VAL Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 851 random chunks: chunk 261 optimal weight: 0.9990 chunk 73 optimal weight: 6.9990 chunk 228 optimal weight: 0.9990 chunk 65 optimal weight: 6.9990 chunk 502 optimal weight: 8.9990 chunk 620 optimal weight: 1.9990 chunk 477 optimal weight: 9.9990 chunk 506 optimal weight: 0.7980 chunk 582 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 4 optimal weight: 8.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 228 GLN N 231 GLN N 272 GLN A 251 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN ** a 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.078922 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.066292 restraints weight = 168312.336| |-----------------------------------------------------------------------------| r_work (start): 0.2843 rms_B_bonded: 2.91 r_work: 0.2693 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2729 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2729 r_free = 0.2729 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2729 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8721 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 66816 Z= 0.188 Angle : 0.555 13.696 90225 Z= 0.269 Chirality : 0.041 0.183 10757 Planarity : 0.003 0.053 11514 Dihedral : 6.913 169.763 9287 Min Nonbonded Distance : 1.881 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.22 % Favored : 96.77 % Rotamer: Outliers : 0.63 % Allowed : 12.96 % Favored : 86.41 % 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: 8548 helix: 2.46 (0.08), residues: 4433 sheet: 0.10 (0.16), residues: 1086 loop : -0.50 (0.11), residues: 3029 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.016 0.001 HIS z 161 PHE 0.021 0.001 PHE h 455 TYR 0.020 0.001 TYR N 174 ARG 0.014 0.000 ARG a 185 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 33782.54 seconds wall clock time: 581 minutes 9.26 seconds (34869.26 seconds total)