Starting phenix.real_space_refine on Tue Jan 21 22:47:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sho_40490/01_2025/8sho_40490.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sho_40490/01_2025/8sho_40490.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sho_40490/01_2025/8sho_40490.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sho_40490/01_2025/8sho_40490.map" model { file = "/net/cci-nas-00/data/ceres_data/8sho_40490/01_2025/8sho_40490.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sho_40490/01_2025/8sho_40490.cif" } resolution = 3.0 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= 0.052 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 422 5.16 5 C 42309 2.51 5 N 11775 2.21 5 O 13107 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 42 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: 67725 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 1101 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1101 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain breaks: 1 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1490 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1490 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 3, 'TRANS': 179} Chain breaks: 9 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 34.28, per 1000 atoms: 0.51 Number of scatterers: 67725 At special positions: 0 Unit cell: (179.86, 176.686, 180.918, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 422 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13107 8.00 N 11775 7.00 C 42309 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 "HETATM67568 O3A ADP e 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67632 O3A ADP h 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67376 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67248 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67504 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=3, symmetry=0 Number of additional bonds: simple=3, symmetry=0 Coordination: Other bonds: Time building additional restraints: 12.96 Conformation dependent library (CDL) restraints added in 7.7 seconds 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16384 Finding SS restraints... Secondary structure from input PDB file: 359 helices and 101 sheets defined 55.8% alpha, 14.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.02 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.721A 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: 3.693A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.660A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.003A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.277A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 258 through 281 removed outlier: 4.378A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 432 through 446 removed outlier: 4.230A pdb=" N LEU A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N LEU A 446 " --> pdb=" O ALA A 442 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 removed outlier: 3.517A pdb=" N ALA A 456 " --> pdb=" O LEU A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 477 removed outlier: 3.608A pdb=" N LEU A 463 " --> pdb=" O ASP A 459 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.664A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N LYS A 484 " --> pdb=" O LYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 118 Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 169 through 174 removed outlier: 6.564A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.604A 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 Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 removed outlier: 3.504A pdb=" N VAL B 341 " --> pdb=" O PRO B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 431 through 454 Proline residue: B 447 - end of helix removed outlier: 3.771A 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: 4.217A 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: 3.833A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.994A 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 172 removed outlier: 3.577A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 293 removed outlier: 3.913A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.075A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.965A 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 442 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.087A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 4.000A 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 30 through 49 removed outlier: 3.638A 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: 3.697A 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: 6.496A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.914A 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: 3.833A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 438 Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.659A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.660A 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: 3.657A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.721A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.533A 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: 4.258A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.652A 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: 3.590A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 Processing helix chain 'H' and resid 36 through 40 Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.579A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.194A pdb=" N THR H 98 " --> pdb=" O THR H 94 " (cutoff:3.500A) Proline residue: H 110 - end of helix removed outlier: 3.560A pdb=" N GLU H 114 " --> pdb=" O PRO H 110 " (cutoff:3.500A) Processing helix chain 'H' and resid 117 through 140 removed outlier: 3.600A 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: 3.725A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.560A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 471 Processing helix chain 'H' and resid 496 through 515 Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.493A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.500A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 168 removed outlier: 4.128A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N SER Q 167 " --> pdb=" O LEU Q 163 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 285 removed outlier: 4.819A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 removed outlier: 3.575A pdb=" N TYR Q 308 " --> pdb=" O TYR Q 304 " (cutoff:3.500A) Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 340 through 344 removed outlier: 3.523A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.955A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.220A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE Q 445 " --> pdb=" O PHE Q 441 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.619A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.704A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.187A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.678A 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 Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 319 through 328 Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.195A 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 removed outlier: 3.774A pdb=" N THR Z 462 " --> pdb=" O ASP Z 458 " (cutoff:3.500A) Processing helix chain 'Z' and resid 498 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.703A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) 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: 4.071A 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 144 removed outlier: 3.829A pdb=" N GLY a 144 " --> pdb=" O ASP a 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 141 through 144' Processing helix chain 'a' and resid 145 through 157 Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.241A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 281 removed outlier: 3.870A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 5.094A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 303 removed outlier: 3.650A pdb=" N TYR a 299 " --> pdb=" O MET a 295 " (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 433 through 445 Processing helix chain 'a' and resid 446 through 456 removed outlier: 3.623A pdb=" N ALA a 456 " --> pdb=" O LEU a 452 " (cutoff:3.500A) Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 removed outlier: 3.583A pdb=" N LYS a 484 " --> pdb=" O LYS a 481 " (cutoff:3.500A) Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 169 removed outlier: 4.419A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.563A 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 Processing helix chain 'b' and resid 297 through 308 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 removed outlier: 3.540A pdb=" N VAL b 341 " --> pdb=" O PRO b 338 " (cutoff:3.500A) Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 428 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.726A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 471 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.681A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.933A 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: 3.632A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N SER d 173 " --> pdb=" O THR d 169 " (cutoff:3.500A) Processing helix chain 'd' and resid 174 through 178 removed outlier: 4.203A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 4.145A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.907A 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 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 removed outlier: 3.624A pdb=" N THR d 442 " --> pdb=" O GLU d 438 " (cutoff:3.500A) Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.870A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.787A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 5.014A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 Processing helix chain 'e' and resid 50 through 52 No H-bonds generated for 'chain 'e' and resid 50 through 52' Processing helix chain 'e' and resid 73 through 81 Processing helix chain 'e' and resid 85 through 102 Processing helix chain 'e' and resid 105 through 125 removed outlier: 4.249A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 152 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.629A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.946A 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: 3.824A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 438 Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.563A pdb=" N GLN e 445 " --> pdb=" O PRO e 441 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) 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: 3.756A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.827A 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: 3.740A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.610A pdb=" N VAL g 122 " --> pdb=" O HIS g 118 " (cutoff:3.500A) Processing helix chain 'g' and resid 148 through 161 Processing helix chain 'g' and resid 163 through 167 removed outlier: 3.860A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 426 Processing helix chain 'g' and resid 427 through 429 No H-bonds generated for 'chain 'g' and resid 427 through 429' Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.519A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) Processing helix chain 'h' and resid 36 through 40 removed outlier: 3.580A 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 75 through 90 removed outlier: 4.227A pdb=" N LEU h 79 " --> pdb=" O ALA h 75 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.153A 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: 3.567A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.826A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 4.072A 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 259 through 284 removed outlier: 3.527A 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 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 4.143A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.212A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.775A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.684A 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 121 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 157 through 168 removed outlier: 3.618A pdb=" N SER q 161 " --> pdb=" O ILE q 157 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER q 167 " --> pdb=" O LEU q 163 " (cutoff:3.500A) Processing helix chain 'q' and resid 175 through 190 removed outlier: 4.297A pdb=" N LEU q 179 " --> pdb=" O ASN q 175 " (cutoff:3.500A) Processing helix chain 'q' and resid 198 through 200 No H-bonds generated for 'chain 'q' and resid 198 through 200' Processing helix chain 'q' and resid 211 through 215 Processing helix chain 'q' and resid 261 through 285 removed outlier: 3.548A pdb=" N LEU q 265 " --> pdb=" O THR q 261 " (cutoff:3.500A) removed outlier: 4.768A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.832A pdb=" N LYS q 270 " --> pdb=" O MET q 266 " (cutoff:3.500A) Processing helix chain 'q' and resid 298 through 308 Processing helix chain 'q' and resid 317 through 329 Processing helix chain 'q' and resid 381 through 405 Processing helix chain 'q' and resid 413 through 430 removed outlier: 3.643A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.304A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.533A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 66 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.562A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.793A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.112A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.661A 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 Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.630A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.734A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.281A 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: 4.222A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 58 through 61 Processing helix chain 'P' and resid 62 through 88 removed outlier: 3.737A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ARG P 86 " --> pdb=" O ARG P 82 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N ILE P 88 " --> pdb=" O MET P 84 " (cutoff:3.500A) Processing helix chain 'P' and resid 140 through 151 removed outlier: 4.334A pdb=" N ARG P 144 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 167 through 176 removed outlier: 3.560A pdb=" N ILE P 174 " --> pdb=" O PHE P 170 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N LYS P 176 " --> pdb=" O ASP P 172 " (cutoff:3.500A) Processing helix chain 'P' and resid 195 through 209 removed outlier: 3.839A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 227 through 231 Processing helix chain 'P' and resid 260 through 271 removed outlier: 3.983A pdb=" N PHE P 271 " --> pdb=" O PHE P 267 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'N' and resid 198 through 203 removed outlier: 4.512A pdb=" N ALA N 200 " --> pdb=" O ALA N 213 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA N 213 " --> pdb=" O ALA N 200 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N THR N 212 " --> pdb=" O ALA N 220 " (cutoff:3.500A) removed outlier: 6.574A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 240 through 243 removed outlier: 6.371A pdb=" N VAL N 265 " --> pdb=" O VAL N 274 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 284 through 289 removed outlier: 3.592A pdb=" N PHE N 296 " --> pdb=" O TYR N 308 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N ARG N 306 " --> pdb=" O SER N 298 " (cutoff:3.500A) removed outlier: 3.806A pdb=" N THR N 304 " --> pdb=" O SER N 300 " (cutoff:3.500A) removed outlier: 7.619A pdb=" N LEU N 307 " --> pdb=" O VAL N 316 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 13 removed outlier: 6.222A pdb=" N ASP D 58 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 4.070A pdb=" N ASP A 529 " --> pdb=" O ASP D 58 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 52 through 55 removed outlier: 5.784A 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 181 through 182 Processing sheet with id=AA8, first strand: chain 'A' and resid 196 through 199 removed outlier: 6.368A pdb=" N ASN A 196 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N LEU A 377 " --> pdb=" O ASN A 196 " (cutoff:3.500A) removed outlier: 6.794A pdb=" N LEU A 198 " --> pdb=" O LEU A 377 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.511A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.511A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.165A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.297A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.643A pdb=" N ARG A 496 " --> pdb=" O GLY A 487 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.269A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.741A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.899A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.982A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.790A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB7, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.975A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.431A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.363A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.753A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AC1, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AC2, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.279A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.462A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.471A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.314A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.217A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.591A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.591A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.476A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.004A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 5.773A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.530A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.612A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 28 through 29 removed outlier: 4.670A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.489A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.602A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.444A pdb=" N ARG E 534 " --> pdb=" O VAL H 50 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC8, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.794A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.640A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.640A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 8.502A pdb=" N VAL E 342 " --> pdb=" O ILE E 248 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N ILE E 250 " --> pdb=" O VAL E 342 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 57 through 60 removed outlier: 7.781A pdb=" N MET G 47 " --> pdb=" O GLU Z 520 " (cutoff:3.500A) removed outlier: 8.974A pdb=" N MET Z 522 " --> pdb=" O MET G 47 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N MET G 49 " --> pdb=" O MET Z 522 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD4, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD5, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.705A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 7.857A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.320A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD7, first strand: chain 'G' and resid 238 through 241 removed outlier: 3.527A pdb=" N THR G 292 " --> pdb=" O ILE G 312 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD9, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.254A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE2, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.638A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE4, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE5, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE6, first strand: chain 'Q' and resid 20 through 23 removed outlier: 6.768A pdb=" N MET Z 44 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N GLN Q 523 " --> pdb=" O MET Z 44 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.857A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.705A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AF1, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AF2, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF3, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF4, first strand: chain 'Z' and resid 192 through 196 removed outlier: 6.388A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF6, first strand: chain 'Z' and resid 310 through 313 Processing sheet with id=AF7, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id=AF8, first strand: chain 'a' and resid 9 through 13 removed outlier: 6.046A pdb=" N ASP d 58 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ASP a 529 " --> pdb=" O ASP d 58 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.264A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AG2, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG3, first strand: chain 'a' and resid 196 through 199 Processing sheet with id=AG4, first strand: chain 'a' and resid 213 through 216 removed outlier: 3.509A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 213 through 216 removed outlier: 3.509A pdb=" N GLU a 350 " --> pdb=" O LYS a 365 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.019A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.167A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG8, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.200A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.360A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.587A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.889A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AH2, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.690A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.356A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N LEU b 348 " --> pdb=" O GLU b 233 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N GLU b 233 " --> pdb=" O LEU b 348 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'b' and resid 476 through 479 removed outlier: 3.516A pdb=" N GLY b 477 " --> pdb=" O GLY b 486 " (cutoff:3.500A) 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: 3.965A 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: 6.610A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.610A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.690A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.968A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 5.903A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.562A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.465A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.786A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AI1, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.522A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.404A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.322A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.776A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AI3, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.422A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.437A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.482A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.976A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.380A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N LEU e 299 " --> pdb=" O ASP e 245 " (cutoff:3.500A) removed outlier: 5.771A pdb=" N LYS e 247 " --> pdb=" O LEU e 299 " (cutoff:3.500A) removed outlier: 7.330A pdb=" N ILE e 301 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ALA e 249 " --> pdb=" O ILE e 301 " (cutoff:3.500A) removed outlier: 6.707A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.332A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.687A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI7, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI8, first strand: chain 'g' and resid 200 through 203 removed outlier: 6.916A pdb=" N ARG g 200 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 7.605A pdb=" N LEU g 376 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N GLU g 202 " --> pdb=" O LEU g 376 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AJ1, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.372A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'g' and resid 478 through 480 Processing sheet with id=AJ3, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.499A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.666A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ5, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ6, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ7, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ8, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ9, first strand: chain 'q' and resid 20 through 23 removed outlier: 4.985A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.352A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.799A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AK2, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.569A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.122A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK4, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK5, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK6, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK7, first strand: chain 'z' and resid 192 through 196 removed outlier: 6.197A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.016A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.557A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK9, first strand: chain 'z' and resid 310 through 313 removed outlier: 9.132A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 8.011A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.281A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 6.992A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 5.882A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.273A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AL1, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AL2, first strand: chain 'P' and resid 162 through 163 removed outlier: 5.719A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.756A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.687A pdb=" N VAL P 182 " --> pdb=" O LYS P 213 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 5.809A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.584A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) 4114 hydrogen bonds defined for protein. 11736 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 35.66 Time building geometry restraints manager: 15.29 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: 22659 1.34 - 1.46: 8286 1.46 - 1.58: 36757 1.58 - 1.70: 48 1.70 - 1.82: 744 Bond restraints: 68494 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.798 -0.161 2.00e-02 2.50e+03 6.48e+01 bond pdb=" F2 AF3 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 6.43e+01 bond pdb=" F2 AF3 G 603 " pdb="AL AF3 G 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.36e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.32e+01 bond pdb=" F2 AF3 E 603 " pdb="AL AF3 E 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.28e+01 ... (remaining 68489 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 90761 1.67 - 3.35: 1293 3.35 - 5.02: 259 5.02 - 6.69: 148 6.69 - 8.37: 8 Bond angle restraints: 92469 Sorted by residual: angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 121.55 -8.37 2.37e+00 1.78e-01 1.25e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 121.48 -8.30 2.37e+00 1.78e-01 1.23e+01 angle pdb=" N VAL Z 160 " pdb=" CA VAL Z 160 " pdb=" C VAL Z 160 " ideal model delta sigma weight residual 108.53 112.63 -4.10 1.22e+00 6.72e-01 1.13e+01 angle pdb=" N ILE G 165 " pdb=" CA ILE G 165 " pdb=" C ILE G 165 " ideal model delta sigma weight residual 112.80 109.35 3.45 1.15e+00 7.56e-01 8.99e+00 angle pdb=" C THR Z 158 " pdb=" N LYS Z 159 " pdb=" CA LYS Z 159 " ideal model delta sigma weight residual 122.53 116.80 5.73 1.92e+00 2.71e-01 8.91e+00 ... (remaining 92464 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.65: 41576 35.65 - 71.31: 671 71.31 - 106.96: 73 106.96 - 142.62: 11 142.62 - 178.27: 5 Dihedral angle restraints: 42336 sinusoidal: 17044 harmonic: 25292 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual 300.00 121.73 178.27 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP q 601 " pdb=" O3A ADP q 601 " pdb=" PA ADP q 601 " pdb=" PB ADP q 601 " ideal model delta sinusoidal sigma weight residual 300.00 124.92 175.08 1 2.00e+01 2.50e-03 4.79e+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 -60.00 107.19 -167.19 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 42333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 8092 0.042 - 0.084: 2104 0.084 - 0.127: 751 0.127 - 0.169: 53 0.169 - 0.211: 3 Chirality restraints: 11003 Sorted by residual: chirality pdb=" CB VAL H 36 " pdb=" CA VAL H 36 " pdb=" CG1 VAL H 36 " pdb=" CG2 VAL H 36 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE d 325 " pdb=" N ILE d 325 " pdb=" C ILE d 325 " pdb=" CB ILE d 325 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.15e-01 ... (remaining 11000 not shown) Planarity restraints: 11805 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP b 245 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.28e+00 pdb=" CG ASP b 245 " -0.040 2.00e-02 2.50e+03 pdb=" OD1 ASP b 245 " 0.014 2.00e-02 2.50e+03 pdb=" OD2 ASP b 245 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO e 441 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE b 11 " -0.009 2.00e-02 2.50e+03 1.76e-02 3.11e+00 pdb=" C ILE b 11 " 0.030 2.00e-02 2.50e+03 pdb=" O ILE b 11 " -0.011 2.00e-02 2.50e+03 pdb=" N PHE b 12 " -0.010 2.00e-02 2.50e+03 ... (remaining 11802 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 559 2.52 - 3.11: 51236 3.11 - 3.71: 105457 3.71 - 4.30: 149364 4.30 - 4.90: 257490 Nonbonded interactions: 564106 Sorted by model distance: nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.924 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.933 2.120 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.937 2.120 nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.944 2.120 nonbonded pdb=" OD1 ASP b 97 " pdb="MG MG b 602 " model vdw 1.951 2.170 ... (remaining 564101 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: 2.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.080 Extract box with map and model: 2.080 Check model and map are aligned: 0.400 Set scattering table: 0.470 Process input model: 132.740 Find NCS groups from input model: 5.840 Set up NCS constraints: 0.460 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:11.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8607 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 : 0.006 0.161 68494 Z= 0.351 Angle : 0.572 8.368 92469 Z= 0.282 Chirality : 0.042 0.211 11003 Planarity : 0.003 0.047 11805 Dihedral : 14.699 178.273 25952 Min Nonbonded Distance : 1.924 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.01 % Allowed : 0.29 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.09), residues: 8741 helix: 2.25 (0.08), residues: 4425 sheet: 0.27 (0.16), residues: 1137 loop : -0.45 (0.11), residues: 3179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.007 0.001 HIS Z 161 PHE 0.028 0.001 PHE N 254 TYR 0.017 0.001 TYR N 289 ARG 0.007 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 603 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 602 time to evaluate : 6.098 Fit side-chains revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6899 (t) cc_final: 0.6582 (t) REVERT: B 221 ASP cc_start: 0.8107 (t0) cc_final: 0.7890 (t70) REVERT: B 415 MET cc_start: 0.8876 (tpp) cc_final: 0.8653 (tpp) REVERT: E 456 GLU cc_start: 0.8432 (mm-30) cc_final: 0.8074 (mm-30) REVERT: G 415 GLU cc_start: 0.8006 (mp0) cc_final: 0.7751 (mp0) REVERT: H 45 MET cc_start: 0.9278 (mmm) cc_final: 0.8921 (mmt) REVERT: H 451 ASP cc_start: 0.8391 (m-30) cc_final: 0.7949 (m-30) REVERT: Z 53 ASP cc_start: 0.7945 (m-30) cc_final: 0.7595 (m-30) REVERT: e 39 MET cc_start: 0.8507 (ttm) cc_final: 0.8277 (ttm) REVERT: e 460 MET cc_start: 0.9037 (mtm) cc_final: 0.8743 (mtm) REVERT: g 52 ASP cc_start: 0.8019 (m-30) cc_final: 0.7798 (m-30) REVERT: h 130 GLN cc_start: 0.7994 (tp40) cc_final: 0.7614 (tp-100) REVERT: h 497 MET cc_start: 0.7980 (ptm) cc_final: 0.7760 (tmm) REVERT: h 524 ARG cc_start: 0.7497 (tmt170) cc_final: 0.7091 (tmm-80) REVERT: q 26 GLU cc_start: 0.8082 (mp0) cc_final: 0.7838 (mp0) REVERT: P 145 MET cc_start: 0.7921 (mmp) cc_final: 0.7401 (ptm) REVERT: P 163 GLU cc_start: 0.6666 (tt0) cc_final: 0.5842 (tp30) REVERT: P 173 MET cc_start: 0.8025 (tmm) cc_final: 0.7815 (tmm) REVERT: P 213 LYS cc_start: 0.6509 (tmtt) cc_final: 0.5846 (tmtm) outliers start: 1 outliers final: 1 residues processed: 602 average time/residue: 1.5755 time to fit residues: 1226.8457 Evaluate side-chains 493 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 492 time to evaluate : 6.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain d residue 503 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 735 optimal weight: 1.9990 chunk 660 optimal weight: 6.9990 chunk 366 optimal weight: 0.9990 chunk 225 optimal weight: 9.9990 chunk 445 optimal weight: 3.9990 chunk 352 optimal weight: 3.9990 chunk 682 optimal weight: 0.9980 chunk 264 optimal weight: 0.0870 chunk 415 optimal weight: 4.9990 chunk 508 optimal weight: 10.0000 chunk 790 optimal weight: 4.9990 overall best weight: 1.6164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 103 ASN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 502 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 274 ASN Z 23 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 73 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 116 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** z 115 HIS ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.081623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2906 r_free = 0.2906 target = 0.067331 restraints weight = 167063.977| |-----------------------------------------------------------------------------| r_work (start): 0.2878 rms_B_bonded: 2.80 r_work: 0.2739 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2748 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2748 r_free = 0.2748 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2748 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8705 moved from start: 0.0783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 68494 Z= 0.194 Angle : 0.555 8.861 92469 Z= 0.279 Chirality : 0.042 0.177 11003 Planarity : 0.003 0.048 11805 Dihedral : 7.598 177.377 9505 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.71 % Allowed : 6.01 % Favored : 93.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.57 (0.09), residues: 8741 helix: 2.29 (0.08), residues: 4477 sheet: 0.21 (0.16), residues: 1153 loop : -0.46 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.010 0.001 HIS Z 161 PHE 0.031 0.001 PHE P 69 TYR 0.014 0.001 TYR E 420 ARG 0.011 0.000 ARG g 228 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 548 time to evaluate : 6.127 Fit side-chains REVERT: N 208 MET cc_start: 0.8492 (ppp) cc_final: 0.8193 (ppp) REVERT: N 242 CYS cc_start: 0.6958 (t) cc_final: 0.6390 (t) REVERT: A 214 TYR cc_start: 0.8813 (t80) cc_final: 0.8457 (t80) REVERT: B 221 ASP cc_start: 0.8646 (t0) cc_final: 0.8284 (t70) REVERT: B 415 MET cc_start: 0.9216 (tpp) cc_final: 0.8971 (tpp) REVERT: B 488 MET cc_start: 0.9076 (mmm) cc_final: 0.8781 (mmm) REVERT: D 24 TYR cc_start: 0.8703 (t80) cc_final: 0.8499 (t80) REVERT: E 29 MET cc_start: 0.8352 (OUTLIER) cc_final: 0.7897 (tmm) REVERT: E 32 GLU cc_start: 0.7723 (mp0) cc_final: 0.7425 (mp0) REVERT: G 415 GLU cc_start: 0.8581 (mp0) cc_final: 0.8364 (mp0) REVERT: H 70 ASP cc_start: 0.7906 (m-30) cc_final: 0.7682 (t0) REVERT: H 194 MET cc_start: 0.9462 (mmp) cc_final: 0.9260 (mmp) REVERT: H 283 HIS cc_start: 0.8770 (OUTLIER) cc_final: 0.8463 (m90) REVERT: H 451 ASP cc_start: 0.8759 (m-30) cc_final: 0.8327 (m-30) REVERT: Q 416 GLU cc_start: 0.8718 (mp0) cc_final: 0.8490 (mp0) REVERT: Z 53 ASP cc_start: 0.8414 (m-30) cc_final: 0.8038 (m-30) REVERT: d 28 ASP cc_start: 0.8441 (OUTLIER) cc_final: 0.8182 (OUTLIER) REVERT: d 458 MET cc_start: 0.8862 (mmm) cc_final: 0.8661 (mmp) REVERT: e 39 MET cc_start: 0.9044 (ttm) cc_final: 0.8790 (ttm) REVERT: e 460 MET cc_start: 0.9248 (mtm) cc_final: 0.9008 (mtm) REVERT: g 52 ASP cc_start: 0.8210 (m-30) cc_final: 0.7994 (m-30) REVERT: g 415 GLU cc_start: 0.8969 (mp0) cc_final: 0.8700 (mp0) REVERT: h 81 ASP cc_start: 0.8569 (m-30) cc_final: 0.8368 (m-30) REVERT: h 103 GLU cc_start: 0.8596 (tp30) cc_final: 0.8298 (tp30) REVERT: h 130 GLN cc_start: 0.8420 (tp40) cc_final: 0.7926 (tp-100) REVERT: h 524 ARG cc_start: 0.7614 (tmt170) cc_final: 0.7118 (tmm-80) REVERT: q 26 GLU cc_start: 0.8470 (mp0) cc_final: 0.8203 (mp0) REVERT: q 443 GLU cc_start: 0.8942 (tt0) cc_final: 0.8697 (mt-10) REVERT: z 415 GLU cc_start: 0.8665 (OUTLIER) cc_final: 0.8436 (mp0) REVERT: P 163 GLU cc_start: 0.6512 (tt0) cc_final: 0.5685 (tp30) REVERT: P 259 PHE cc_start: 0.5974 (p90) cc_final: 0.5620 (p90) outliers start: 52 outliers final: 10 residues processed: 569 average time/residue: 1.5624 time to fit residues: 1161.5638 Evaluate side-chains 506 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 493 time to evaluate : 5.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 362 ILE Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 28 ASP Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 415 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 776 optimal weight: 9.9990 chunk 686 optimal weight: 2.9990 chunk 381 optimal weight: 6.9990 chunk 649 optimal weight: 10.0000 chunk 68 optimal weight: 8.9990 chunk 44 optimal weight: 7.9990 chunk 424 optimal weight: 4.9990 chunk 216 optimal weight: 0.3980 chunk 802 optimal weight: 5.9990 chunk 191 optimal weight: 3.9990 chunk 332 optimal weight: 0.9980 overall best weight: 2.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 231 GLN A 20 GLN ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 61 ASN G 390 ASN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3160 r_free = 0.3160 target = 0.082677 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.067429 restraints weight = 189880.054| |-----------------------------------------------------------------------------| r_work (start): 0.2852 rms_B_bonded: 3.11 r_work: 0.2704 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2704 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2712 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2712 r_free = 0.2712 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 = 0.2712 r_free = 0.2712 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2712 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.0890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 68494 Z= 0.255 Angle : 0.551 7.938 92469 Z= 0.275 Chirality : 0.042 0.184 11003 Planarity : 0.003 0.048 11805 Dihedral : 7.365 179.797 9503 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.90 % Allowed : 8.29 % Favored : 90.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.56 (0.09), residues: 8741 helix: 2.29 (0.08), residues: 4477 sheet: 0.17 (0.16), residues: 1154 loop : -0.49 (0.11), residues: 3110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP N 222 HIS 0.011 0.001 HIS Z 161 PHE 0.024 0.001 PHE P 136 TYR 0.014 0.001 TYR E 446 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 570 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 504 time to evaluate : 6.123 Fit side-chains REVERT: N 208 MET cc_start: 0.8465 (ppp) cc_final: 0.8078 (ppp) REVERT: N 242 CYS cc_start: 0.6935 (t) cc_final: 0.6286 (t) REVERT: N 264 MET cc_start: 0.6598 (mtm) cc_final: 0.6380 (mtm) REVERT: A 105 ASP cc_start: 0.9157 (t70) cc_final: 0.8956 (t0) REVERT: A 384 MET cc_start: 0.9098 (ttt) cc_final: 0.8879 (ttt) REVERT: B 221 ASP cc_start: 0.8694 (t0) cc_final: 0.8326 (t70) REVERT: B 488 MET cc_start: 0.9084 (mmm) cc_final: 0.8832 (mmm) REVERT: D 360 GLU cc_start: 0.8625 (tp30) cc_final: 0.8270 (tm-30) REVERT: E 29 MET cc_start: 0.8360 (OUTLIER) cc_final: 0.8011 (tmm) REVERT: E 32 GLU cc_start: 0.7828 (mp0) cc_final: 0.7536 (mp0) REVERT: G 415 GLU cc_start: 0.8667 (mp0) cc_final: 0.8383 (mp0) REVERT: H 70 ASP cc_start: 0.7907 (m-30) cc_final: 0.7689 (t0) REVERT: H 283 HIS cc_start: 0.8794 (OUTLIER) cc_final: 0.8482 (m90) REVERT: H 451 ASP cc_start: 0.8787 (m-30) cc_final: 0.8358 (m-30) REVERT: Q 416 GLU cc_start: 0.8759 (mp0) cc_final: 0.8521 (mp0) REVERT: Z 53 ASP cc_start: 0.8393 (m-30) cc_final: 0.7991 (m-30) REVERT: e 39 MET cc_start: 0.9065 (ttm) cc_final: 0.8788 (ttm) REVERT: h 81 ASP cc_start: 0.8629 (m-30) cc_final: 0.8414 (m-30) REVERT: h 130 GLN cc_start: 0.8457 (tp40) cc_final: 0.7968 (tp-100) REVERT: h 524 ARG cc_start: 0.7636 (tmt170) cc_final: 0.7092 (tmm-80) REVERT: q 26 GLU cc_start: 0.8542 (mp0) cc_final: 0.8265 (mp0) REVERT: z 415 GLU cc_start: 0.8707 (OUTLIER) cc_final: 0.8494 (mp0) REVERT: P 145 MET cc_start: 0.7690 (mmp) cc_final: 0.7192 (ptm) REVERT: P 163 GLU cc_start: 0.6339 (tt0) cc_final: 0.5598 (tp30) REVERT: P 173 MET cc_start: 0.7954 (tmm) cc_final: 0.7668 (tmm) REVERT: P 250 ARG cc_start: 0.2138 (mmm160) cc_final: 0.1928 (mmp80) outliers start: 66 outliers final: 24 residues processed: 543 average time/residue: 1.5252 time to fit residues: 1076.6214 Evaluate side-chains 521 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 494 time to evaluate : 5.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 228 optimal weight: 10.0000 chunk 258 optimal weight: 9.9990 chunk 514 optimal weight: 9.9990 chunk 512 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 190 optimal weight: 4.9990 chunk 60 optimal weight: 5.9990 chunk 176 optimal weight: 1.9990 chunk 303 optimal weight: 5.9990 chunk 394 optimal weight: 0.8980 chunk 476 optimal weight: 4.9990 overall best weight: 1.9944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 353 GLN A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.083706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2921 r_free = 0.2921 target = 0.068796 restraints weight = 164491.430| |-----------------------------------------------------------------------------| r_work (start): 0.2875 rms_B_bonded: 2.90 r_work: 0.2733 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.2733 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2741 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2741 r_free = 0.2741 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2741 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 68494 Z= 0.205 Angle : 0.529 7.491 92469 Z= 0.263 Chirality : 0.042 0.185 11003 Planarity : 0.003 0.048 11805 Dihedral : 7.132 174.044 9503 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 0.89 % Allowed : 9.57 % Favored : 89.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.09), residues: 8741 helix: 2.35 (0.08), residues: 4469 sheet: 0.15 (0.16), residues: 1150 loop : -0.45 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP P 66 HIS 0.012 0.001 HIS Z 161 PHE 0.017 0.001 PHE P 136 TYR 0.014 0.001 TYR z 353 ARG 0.007 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 595 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 530 time to evaluate : 6.144 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 208 MET cc_start: 0.8493 (ppp) cc_final: 0.8270 (ppp) REVERT: N 242 CYS cc_start: 0.6877 (t) cc_final: 0.6164 (t) REVERT: N 264 MET cc_start: 0.6618 (mtm) cc_final: 0.6397 (mtm) REVERT: A 105 ASP cc_start: 0.9143 (t70) cc_final: 0.8918 (t0) REVERT: A 384 MET cc_start: 0.9116 (ttt) cc_final: 0.8881 (ttt) REVERT: B 221 ASP cc_start: 0.8730 (t0) cc_final: 0.8334 (t70) REVERT: D 360 GLU cc_start: 0.8560 (tp30) cc_final: 0.8208 (tm-30) REVERT: E 426 GLU cc_start: 0.8466 (OUTLIER) cc_final: 0.8241 (mp0) REVERT: E 474 MET cc_start: 0.8831 (OUTLIER) cc_final: 0.7842 (ttp) REVERT: G 415 GLU cc_start: 0.8635 (mp0) cc_final: 0.8327 (mp0) REVERT: H 70 ASP cc_start: 0.7855 (m-30) cc_final: 0.7380 (t70) REVERT: H 220 PHE cc_start: 0.8954 (t80) cc_final: 0.8540 (t80) REVERT: H 283 HIS cc_start: 0.8751 (OUTLIER) cc_final: 0.8466 (m90) REVERT: H 451 ASP cc_start: 0.8752 (m-30) cc_final: 0.8321 (m-30) REVERT: Q 416 GLU cc_start: 0.8704 (mp0) cc_final: 0.8461 (mp0) REVERT: Z 53 ASP cc_start: 0.8368 (m-30) cc_final: 0.7963 (m-30) REVERT: a 430 MET cc_start: 0.7829 (mmm) cc_final: 0.7457 (mpp) REVERT: a 473 GLU cc_start: 0.8493 (tm-30) cc_final: 0.8198 (tm-30) REVERT: e 21 ASP cc_start: 0.8930 (m-30) cc_final: 0.8600 (t70) REVERT: e 39 MET cc_start: 0.9028 (ttm) cc_final: 0.8748 (ttm) REVERT: g 229 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8341 (mmt) REVERT: h 81 ASP cc_start: 0.8602 (m-30) cc_final: 0.8360 (m-30) REVERT: h 103 GLU cc_start: 0.8586 (tp30) cc_final: 0.8280 (tp30) REVERT: h 130 GLN cc_start: 0.8415 (tp40) cc_final: 0.7932 (tp-100) REVERT: h 524 ARG cc_start: 0.7601 (tmt170) cc_final: 0.7123 (tmm-80) REVERT: q 26 GLU cc_start: 0.8558 (mp0) cc_final: 0.8280 (mp0) REVERT: z 415 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.8379 (mp0) REVERT: P 173 MET cc_start: 0.8075 (tmm) cc_final: 0.7774 (tmm) REVERT: P 259 PHE cc_start: 0.5761 (p90) cc_final: 0.5503 (p90) outliers start: 65 outliers final: 28 residues processed: 567 average time/residue: 1.5147 time to fit residues: 1124.0090 Evaluate side-chains 528 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 495 time to evaluate : 5.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 272 MET Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 426 GLU Chi-restraints excluded: chain E residue 474 MET Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 73 LEU Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 229 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain P residue 69 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 399 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 513 optimal weight: 2.9990 chunk 437 optimal weight: 3.9990 chunk 411 optimal weight: 10.0000 chunk 687 optimal weight: 5.9990 chunk 320 optimal weight: 6.9990 chunk 702 optimal weight: 1.9990 chunk 577 optimal weight: 4.9990 chunk 427 optimal weight: 6.9990 chunk 169 optimal weight: 7.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 20 GLN ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** g 71 GLN h 130 GLN ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3133 r_free = 0.3133 target = 0.081158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.066387 restraints weight = 160788.674| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 2.83 r_work: 0.2692 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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 = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8743 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 68494 Z= 0.352 Angle : 0.587 8.422 92469 Z= 0.292 Chirality : 0.044 0.184 11003 Planarity : 0.003 0.048 11805 Dihedral : 7.200 174.961 9503 Min Nonbonded Distance : 1.870 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 1.35 % Allowed : 10.28 % Favored : 88.37 % 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: 8741 helix: 2.23 (0.08), residues: 4484 sheet: 0.05 (0.16), residues: 1162 loop : -0.53 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.013 0.001 HIS Z 161 PHE 0.018 0.001 PHE a 167 TYR 0.017 0.001 TYR E 446 ARG 0.009 0.000 ARG G 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 597 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 498 time to evaluate : 6.205 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6896 (t) cc_final: 0.6086 (t) REVERT: N 264 MET cc_start: 0.6880 (mtm) cc_final: 0.6492 (mtm) REVERT: A 105 ASP cc_start: 0.9158 (t70) cc_final: 0.8932 (t0) REVERT: A 384 MET cc_start: 0.9170 (ttt) cc_final: 0.8914 (ttt) REVERT: B 221 ASP cc_start: 0.8724 (t0) cc_final: 0.8312 (t70) REVERT: D 24 TYR cc_start: 0.8774 (t80) cc_final: 0.8557 (t80) REVERT: D 360 GLU cc_start: 0.8566 (tp30) cc_final: 0.8224 (tm-30) REVERT: G 415 GLU cc_start: 0.8649 (mp0) cc_final: 0.8334 (mp0) REVERT: H 283 HIS cc_start: 0.8757 (OUTLIER) cc_final: 0.8422 (m90) REVERT: H 316 GLU cc_start: 0.8179 (tp30) cc_final: 0.7946 (tp30) REVERT: H 451 ASP cc_start: 0.8782 (m-30) cc_final: 0.8353 (m-30) REVERT: Q 416 GLU cc_start: 0.8736 (mp0) cc_final: 0.8492 (mp0) REVERT: Z 53 ASP cc_start: 0.8392 (m-30) cc_final: 0.7988 (m-30) REVERT: Z 357 GLU cc_start: 0.8362 (mm-30) cc_final: 0.7749 (tp30) REVERT: a 473 GLU cc_start: 0.8458 (tm-30) cc_final: 0.7984 (tm-30) REVERT: b 415 MET cc_start: 0.9461 (tpp) cc_final: 0.9186 (mmp) REVERT: e 21 ASP cc_start: 0.8929 (m-30) cc_final: 0.8578 (t70) REVERT: e 39 MET cc_start: 0.9068 (ttm) cc_final: 0.8773 (ttm) REVERT: h 57 THR cc_start: 0.9375 (OUTLIER) cc_final: 0.9046 (p) REVERT: h 81 ASP cc_start: 0.8603 (m-30) cc_final: 0.8357 (m-30) REVERT: h 130 GLN cc_start: 0.8387 (tp-100) cc_final: 0.7879 (tp-100) REVERT: q 26 GLU cc_start: 0.8567 (mp0) cc_final: 0.8268 (mp0) REVERT: z 415 GLU cc_start: 0.8698 (OUTLIER) cc_final: 0.8413 (mp0) REVERT: P 145 MET cc_start: 0.7687 (mmp) cc_final: 0.7206 (ptm) REVERT: P 163 GLU cc_start: 0.6648 (tt0) cc_final: 0.6446 (tt0) REVERT: P 218 LYS cc_start: 0.5638 (OUTLIER) cc_final: 0.5417 (mptt) REVERT: P 259 PHE cc_start: 0.5675 (p90) cc_final: 0.5356 (p90) outliers start: 99 outliers final: 42 residues processed: 558 average time/residue: 1.5385 time to fit residues: 1123.6704 Evaluate side-chains 543 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 497 time to evaluate : 6.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain e residue 118 GLU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 250 ILE Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 218 LYS Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 159 optimal weight: 5.9990 chunk 824 optimal weight: 9.9990 chunk 322 optimal weight: 7.9990 chunk 30 optimal weight: 7.9990 chunk 547 optimal weight: 0.6980 chunk 754 optimal weight: 7.9990 chunk 742 optimal weight: 8.9990 chunk 867 optimal weight: 7.9990 chunk 530 optimal weight: 0.8980 chunk 656 optimal weight: 2.9990 chunk 590 optimal weight: 10.0000 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 469 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.081519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.066695 restraints weight = 164267.779| |-----------------------------------------------------------------------------| r_work (start): 0.2833 rms_B_bonded: 2.86 r_work: 0.2693 rms_B_bonded: 3.20 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2701 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2701 r_free = 0.2701 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 = 0.2701 r_free = 0.2701 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2701 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 68494 Z= 0.328 Angle : 0.580 9.320 92469 Z= 0.288 Chirality : 0.043 0.171 11003 Planarity : 0.003 0.047 11805 Dihedral : 7.182 174.022 9503 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 1.17 % Allowed : 11.35 % Favored : 87.47 % 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: 8741 helix: 2.22 (0.08), residues: 4481 sheet: 0.03 (0.16), residues: 1152 loop : -0.54 (0.11), residues: 3108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP N 266 HIS 0.013 0.001 HIS Z 161 PHE 0.042 0.001 PHE N 254 TYR 0.017 0.001 TYR E 446 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 86 poor density : 502 time to evaluate : 6.307 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6952 (t) cc_final: 0.6186 (t) REVERT: N 264 MET cc_start: 0.6937 (mtm) cc_final: 0.6528 (mtm) REVERT: A 105 ASP cc_start: 0.9215 (t70) cc_final: 0.8992 (t0) REVERT: A 384 MET cc_start: 0.9171 (ttm) cc_final: 0.8919 (ttt) REVERT: B 221 ASP cc_start: 0.8727 (t0) cc_final: 0.8322 (t70) REVERT: D 24 TYR cc_start: 0.8769 (t80) cc_final: 0.8560 (t80) REVERT: D 360 GLU cc_start: 0.8533 (tp30) cc_final: 0.8191 (tm-30) REVERT: E 32 GLU cc_start: 0.7764 (mp0) cc_final: 0.7522 (pm20) REVERT: G 20 ARG cc_start: 0.8501 (ttm-80) cc_final: 0.8205 (ttm170) REVERT: G 415 GLU cc_start: 0.8645 (mp0) cc_final: 0.8327 (mp0) REVERT: H 283 HIS cc_start: 0.8785 (OUTLIER) cc_final: 0.8457 (m90) REVERT: H 451 ASP cc_start: 0.8790 (m-30) cc_final: 0.8357 (m-30) REVERT: Q 52 MET cc_start: 0.9326 (mmp) cc_final: 0.8960 (mmt) REVERT: Q 416 GLU cc_start: 0.8726 (mp0) cc_final: 0.8492 (mp0) REVERT: Z 53 ASP cc_start: 0.8398 (m-30) cc_final: 0.8010 (m-30) REVERT: Z 357 GLU cc_start: 0.8382 (mm-30) cc_final: 0.7773 (tp30) REVERT: a 225 MET cc_start: 0.9435 (ptp) cc_final: 0.9198 (mtt) REVERT: a 430 MET cc_start: 0.7841 (mmm) cc_final: 0.7463 (mpp) REVERT: a 473 GLU cc_start: 0.8437 (tm-30) cc_final: 0.7929 (tm-30) REVERT: e 21 ASP cc_start: 0.8931 (m-30) cc_final: 0.8582 (t70) REVERT: e 39 MET cc_start: 0.9062 (ttm) cc_final: 0.8755 (ttm) REVERT: e 526 MET cc_start: 0.9215 (ttt) cc_final: 0.8835 (ttt) REVERT: g 59 MET cc_start: 0.9160 (OUTLIER) cc_final: 0.8739 (tmm) REVERT: h 57 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9045 (p) REVERT: h 81 ASP cc_start: 0.8623 (m-30) cc_final: 0.8353 (m-30) REVERT: h 130 GLN cc_start: 0.8364 (tp-100) cc_final: 0.7823 (tp-100) REVERT: h 524 ARG cc_start: 0.7613 (tmt170) cc_final: 0.7091 (tmm-80) REVERT: q 26 GLU cc_start: 0.8602 (mp0) cc_final: 0.8297 (mp0) REVERT: z 161 HIS cc_start: 0.7483 (OUTLIER) cc_final: 0.6897 (t70) REVERT: z 415 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8466 (mp0) REVERT: P 145 MET cc_start: 0.7701 (mmp) cc_final: 0.7312 (ptm) REVERT: P 173 MET cc_start: 0.7990 (tmm) cc_final: 0.7714 (tmm) REVERT: P 259 PHE cc_start: 0.5555 (p90) cc_final: 0.5265 (p90) outliers start: 86 outliers final: 40 residues processed: 556 average time/residue: 1.5753 time to fit residues: 1148.6471 Evaluate side-chains 535 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 490 time to evaluate : 6.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain A residue 248 LEU Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain e residue 118 GLU Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 204 THR Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 212 optimal weight: 1.9990 chunk 223 optimal weight: 4.9990 chunk 122 optimal weight: 7.9990 chunk 245 optimal weight: 2.9990 chunk 804 optimal weight: 4.9990 chunk 722 optimal weight: 1.9990 chunk 806 optimal weight: 9.9990 chunk 668 optimal weight: 9.9990 chunk 76 optimal weight: 10.0000 chunk 468 optimal weight: 2.9990 chunk 206 optimal weight: 7.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS B 469 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 219 HIS ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 71 HIS ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.082018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2881 r_free = 0.2881 target = 0.066674 restraints weight = 197032.256| |-----------------------------------------------------------------------------| r_work (start): 0.2834 rms_B_bonded: 3.17 r_work: 0.2683 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 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 = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.057 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8746 moved from start: 0.1100 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 68494 Z= 0.277 Angle : 0.564 9.948 92469 Z= 0.279 Chirality : 0.042 0.177 11003 Planarity : 0.003 0.047 11805 Dihedral : 7.118 173.892 9503 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 1.20 % Allowed : 12.02 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.47 (0.09), residues: 8741 helix: 2.25 (0.08), residues: 4482 sheet: 0.02 (0.16), residues: 1150 loop : -0.53 (0.11), residues: 3109 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 0.032 0.001 PHE N 254 TYR 0.021 0.001 TYR z 498 ARG 0.009 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 88 poor density : 500 time to evaluate : 6.211 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6908 (t) cc_final: 0.6128 (t) REVERT: N 264 MET cc_start: 0.7055 (mtm) cc_final: 0.6571 (mtm) REVERT: A 384 MET cc_start: 0.9166 (ttm) cc_final: 0.8908 (ttt) REVERT: B 221 ASP cc_start: 0.8793 (t0) cc_final: 0.8391 (t70) REVERT: D 360 GLU cc_start: 0.8551 (tp30) cc_final: 0.8197 (tm-30) REVERT: E 32 GLU cc_start: 0.7869 (mp0) cc_final: 0.7631 (pm20) REVERT: G 20 ARG cc_start: 0.8529 (ttm-80) cc_final: 0.8231 (ttm170) REVERT: G 415 GLU cc_start: 0.8674 (mp0) cc_final: 0.8358 (mp0) REVERT: H 53 ARG cc_start: 0.8352 (OUTLIER) cc_final: 0.7601 (mmm160) REVERT: H 70 ASP cc_start: 0.7811 (t0) cc_final: 0.7396 (t70) REVERT: H 283 HIS cc_start: 0.8826 (OUTLIER) cc_final: 0.8498 (m90) REVERT: H 323 MET cc_start: 0.9118 (ttm) cc_final: 0.8907 (ttt) REVERT: H 451 ASP cc_start: 0.8744 (m-30) cc_final: 0.8328 (m-30) REVERT: Q 416 GLU cc_start: 0.8740 (mp0) cc_final: 0.8511 (mp0) REVERT: Z 53 ASP cc_start: 0.8435 (m-30) cc_final: 0.8043 (m-30) REVERT: Z 357 GLU cc_start: 0.8480 (mm-30) cc_final: 0.7797 (tp30) REVERT: a 225 MET cc_start: 0.9450 (ptp) cc_final: 0.9203 (mtt) REVERT: a 430 MET cc_start: 0.7818 (mmm) cc_final: 0.7385 (mpp) REVERT: a 473 GLU cc_start: 0.8396 (tm-30) cc_final: 0.7875 (tm-30) REVERT: e 21 ASP cc_start: 0.8968 (m-30) cc_final: 0.8594 (t70) REVERT: e 39 MET cc_start: 0.9079 (ttm) cc_final: 0.8771 (ttm) REVERT: e 526 MET cc_start: 0.9207 (ttt) cc_final: 0.8805 (ttt) REVERT: h 57 THR cc_start: 0.9372 (OUTLIER) cc_final: 0.9035 (p) REVERT: h 81 ASP cc_start: 0.8649 (m-30) cc_final: 0.8369 (m-30) REVERT: h 130 GLN cc_start: 0.8370 (tp-100) cc_final: 0.7879 (tp-100) REVERT: h 524 ARG cc_start: 0.7563 (tmt170) cc_final: 0.7073 (tmm-80) REVERT: q 26 GLU cc_start: 0.8620 (mp0) cc_final: 0.8322 (mp0) REVERT: z 161 HIS cc_start: 0.7488 (OUTLIER) cc_final: 0.6917 (t70) REVERT: z 415 GLU cc_start: 0.8666 (OUTLIER) cc_final: 0.8411 (mp0) REVERT: P 145 MET cc_start: 0.7748 (mmp) cc_final: 0.7338 (ptm) REVERT: P 173 MET cc_start: 0.8029 (tmm) cc_final: 0.7745 (tmm) REVERT: P 259 PHE cc_start: 0.5595 (p90) cc_final: 0.5345 (p90) REVERT: P 276 GLU cc_start: 0.5661 (tp30) cc_final: 0.4751 (pp20) outliers start: 88 outliers final: 40 residues processed: 554 average time/residue: 1.5620 time to fit residues: 1133.7021 Evaluate side-chains 540 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 495 time to evaluate : 6.051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 219 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain d residue 395 LYS Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 483 GLU Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 221 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 741 optimal weight: 7.9990 chunk 857 optimal weight: 30.0000 chunk 18 optimal weight: 3.9990 chunk 523 optimal weight: 2.9990 chunk 546 optimal weight: 8.9990 chunk 494 optimal weight: 0.9990 chunk 558 optimal weight: 6.9990 chunk 684 optimal weight: 3.9990 chunk 309 optimal weight: 2.9990 chunk 759 optimal weight: 3.9990 chunk 188 optimal weight: 0.7980 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 170 ASN A 534 HIS B 469 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.082528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.067588 restraints weight = 170452.249| |-----------------------------------------------------------------------------| r_work (start): 0.2855 rms_B_bonded: 2.94 r_work: 0.2713 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2713 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2722 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2722 r_free = 0.2722 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 = 0.2722 r_free = 0.2722 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2722 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8725 moved from start: 0.1158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 68494 Z= 0.232 Angle : 0.553 11.491 92469 Z= 0.273 Chirality : 0.042 0.180 11003 Planarity : 0.003 0.048 11805 Dihedral : 7.022 176.293 9503 Min Nonbonded Distance : 1.905 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 1.04 % Allowed : 12.54 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.09), residues: 8741 helix: 2.31 (0.08), residues: 4483 sheet: 0.03 (0.16), residues: 1156 loop : -0.51 (0.11), residues: 3102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 222 HIS 0.015 0.001 HIS Z 161 PHE 0.024 0.001 PHE P 214 TYR 0.023 0.001 TYR z 498 ARG 0.008 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 512 time to evaluate : 6.202 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6878 (t) cc_final: 0.6094 (t) REVERT: N 264 MET cc_start: 0.7018 (mtm) cc_final: 0.6699 (mtm) REVERT: A 384 MET cc_start: 0.9147 (ttm) cc_final: 0.8906 (ttt) REVERT: B 221 ASP cc_start: 0.8758 (t0) cc_final: 0.8359 (t70) REVERT: D 360 GLU cc_start: 0.8503 (tp30) cc_final: 0.8155 (tm-30) REVERT: E 32 GLU cc_start: 0.7792 (mp0) cc_final: 0.7549 (pm20) REVERT: G 20 ARG cc_start: 0.8464 (ttm-80) cc_final: 0.8125 (ttm170) REVERT: G 415 GLU cc_start: 0.8650 (mp0) cc_final: 0.8329 (mp0) REVERT: H 53 ARG cc_start: 0.8372 (OUTLIER) cc_final: 0.7601 (mmm160) REVERT: H 70 ASP cc_start: 0.7805 (t0) cc_final: 0.7378 (t70) REVERT: H 220 PHE cc_start: 0.9001 (t80) cc_final: 0.8611 (t80) REVERT: H 283 HIS cc_start: 0.8780 (OUTLIER) cc_final: 0.8447 (m90) REVERT: H 451 ASP cc_start: 0.8722 (m-30) cc_final: 0.8304 (m-30) REVERT: Q 416 GLU cc_start: 0.8708 (mp0) cc_final: 0.8474 (mp0) REVERT: Z 53 ASP cc_start: 0.8412 (m-30) cc_final: 0.8011 (m-30) REVERT: Z 357 GLU cc_start: 0.8400 (mm-30) cc_final: 0.7728 (tp30) REVERT: a 225 MET cc_start: 0.9443 (ptp) cc_final: 0.9181 (mtt) REVERT: a 430 MET cc_start: 0.7847 (mmm) cc_final: 0.7394 (mpp) REVERT: a 473 GLU cc_start: 0.8391 (tm-30) cc_final: 0.7857 (tm-30) REVERT: d 524 GLU cc_start: 0.8770 (tt0) cc_final: 0.8521 (mm-30) REVERT: e 21 ASP cc_start: 0.8944 (m-30) cc_final: 0.8563 (t70) REVERT: e 39 MET cc_start: 0.9046 (ttm) cc_final: 0.8737 (ttm) REVERT: e 526 MET cc_start: 0.9199 (ttt) cc_final: 0.8789 (ttt) REVERT: g 59 MET cc_start: 0.9194 (OUTLIER) cc_final: 0.8789 (tmm) REVERT: h 57 THR cc_start: 0.9349 (OUTLIER) cc_final: 0.8996 (p) REVERT: h 81 ASP cc_start: 0.8624 (m-30) cc_final: 0.8341 (m-30) REVERT: h 130 GLN cc_start: 0.8340 (tp-100) cc_final: 0.7858 (tp-100) REVERT: h 524 ARG cc_start: 0.7530 (tmt170) cc_final: 0.7085 (tmm-80) REVERT: q 26 GLU cc_start: 0.8600 (mp0) cc_final: 0.8313 (mp0) REVERT: q 249 MET cc_start: 0.8449 (OUTLIER) cc_final: 0.8034 (pmm) REVERT: z 161 HIS cc_start: 0.7395 (OUTLIER) cc_final: 0.6836 (t70) REVERT: z 337 ASP cc_start: 0.8324 (t0) cc_final: 0.8116 (t0) REVERT: z 415 GLU cc_start: 0.8624 (OUTLIER) cc_final: 0.8372 (mp0) REVERT: P 145 MET cc_start: 0.7656 (mmp) cc_final: 0.7319 (ptm) REVERT: P 173 MET cc_start: 0.8075 (tmm) cc_final: 0.7758 (tmm) REVERT: P 250 ARG cc_start: 0.2722 (mmm160) cc_final: 0.2378 (mmp80) REVERT: P 259 PHE cc_start: 0.5549 (p90) cc_final: 0.5304 (p90) outliers start: 76 outliers final: 46 residues processed: 560 average time/residue: 1.5400 time to fit residues: 1128.2654 Evaluate side-chains 546 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 493 time to evaluate : 6.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 43 THR Chi-restraints excluded: chain q residue 249 MET Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 483 GLU Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 69 PHE Chi-restraints excluded: chain P residue 164 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 105 optimal weight: 7.9990 chunk 723 optimal weight: 2.9990 chunk 708 optimal weight: 6.9990 chunk 182 optimal weight: 4.9990 chunk 332 optimal weight: 4.9990 chunk 705 optimal weight: 1.9990 chunk 852 optimal weight: 4.9990 chunk 510 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 758 optimal weight: 1.9990 chunk 95 optimal weight: 4.9990 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 359 GLN ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.082378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2889 r_free = 0.2889 target = 0.067043 restraints weight = 196416.405| |-----------------------------------------------------------------------------| r_work (start): 0.2842 rms_B_bonded: 3.17 r_work: 0.2691 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2691 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 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 = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8741 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 68494 Z= 0.264 Angle : 0.568 11.821 92469 Z= 0.280 Chirality : 0.042 0.185 11003 Planarity : 0.003 0.048 11805 Dihedral : 6.987 179.138 9503 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.72 % Favored : 96.28 % Rotamer: Outliers : 1.04 % Allowed : 12.68 % Favored : 86.29 % 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: 1.51 (0.09), residues: 8741 helix: 2.29 (0.08), residues: 4485 sheet: 0.04 (0.16), residues: 1138 loop : -0.52 (0.11), residues: 3118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.015 0.001 HIS Z 161 PHE 0.016 0.001 PHE H 174 TYR 0.022 0.001 TYR z 498 ARG 0.009 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 574 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 76 poor density : 498 time to evaluate : 6.160 Fit side-chains revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6861 (t) cc_final: 0.6082 (t) REVERT: N 264 MET cc_start: 0.7008 (mtm) cc_final: 0.6762 (mtm) REVERT: A 384 MET cc_start: 0.9153 (ttm) cc_final: 0.8917 (ttt) REVERT: B 221 ASP cc_start: 0.8790 (t0) cc_final: 0.8388 (t70) REVERT: D 360 GLU cc_start: 0.8535 (tp30) cc_final: 0.8181 (tm-30) REVERT: E 32 GLU cc_start: 0.7880 (mp0) cc_final: 0.7636 (pm20) REVERT: G 20 ARG cc_start: 0.8509 (ttm-80) cc_final: 0.8164 (ttm170) REVERT: G 415 GLU cc_start: 0.8674 (mp0) cc_final: 0.8350 (mp0) REVERT: H 53 ARG cc_start: 0.8357 (OUTLIER) cc_final: 0.7577 (mmm160) REVERT: H 70 ASP cc_start: 0.7808 (t0) cc_final: 0.7354 (t70) REVERT: H 283 HIS cc_start: 0.8809 (OUTLIER) cc_final: 0.8473 (m90) REVERT: H 323 MET cc_start: 0.9121 (ttt) cc_final: 0.8834 (ttt) REVERT: H 451 ASP cc_start: 0.8757 (m-30) cc_final: 0.8334 (m-30) REVERT: Q 416 GLU cc_start: 0.8736 (mp0) cc_final: 0.8524 (mp0) REVERT: Z 53 ASP cc_start: 0.8423 (m-30) cc_final: 0.8022 (m-30) REVERT: Z 357 GLU cc_start: 0.8414 (mm-30) cc_final: 0.7762 (tp30) REVERT: a 225 MET cc_start: 0.9448 (ptp) cc_final: 0.9194 (mtt) REVERT: a 430 MET cc_start: 0.7862 (mmm) cc_final: 0.7522 (mpp) REVERT: a 473 GLU cc_start: 0.8398 (tm-30) cc_final: 0.7858 (tm-30) REVERT: d 524 GLU cc_start: 0.8796 (tt0) cc_final: 0.8531 (mm-30) REVERT: e 21 ASP cc_start: 0.8962 (m-30) cc_final: 0.8579 (t70) REVERT: e 39 MET cc_start: 0.9071 (ttm) cc_final: 0.8762 (ttm) REVERT: e 371 MET cc_start: 0.9151 (mtp) cc_final: 0.8926 (ttm) REVERT: e 526 MET cc_start: 0.9196 (ttt) cc_final: 0.8805 (ttt) REVERT: g 59 MET cc_start: 0.9212 (OUTLIER) cc_final: 0.8770 (tmm) REVERT: h 57 THR cc_start: 0.9354 (OUTLIER) cc_final: 0.9014 (p) REVERT: h 81 ASP cc_start: 0.8638 (m-30) cc_final: 0.8376 (m-30) REVERT: h 130 GLN cc_start: 0.8356 (tp-100) cc_final: 0.7805 (tp-100) REVERT: q 26 GLU cc_start: 0.8626 (mp0) cc_final: 0.8329 (mp0) REVERT: z 161 HIS cc_start: 0.7471 (OUTLIER) cc_final: 0.6962 (t70) REVERT: z 337 ASP cc_start: 0.8362 (t0) cc_final: 0.8144 (t0) REVERT: z 415 GLU cc_start: 0.8662 (OUTLIER) cc_final: 0.8410 (mp0) REVERT: P 88 ILE cc_start: 0.5573 (OUTLIER) cc_final: 0.5296 (pp) REVERT: P 173 MET cc_start: 0.8084 (tmm) cc_final: 0.7758 (tmm) outliers start: 76 outliers final: 48 residues processed: 546 average time/residue: 1.5896 time to fit residues: 1134.4899 Evaluate side-chains 537 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 482 time to evaluate : 5.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain N residue 289 TYR Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain B residue 414 GLU Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain G residue 332 VAL Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 101 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 483 GLU Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 145 MET Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 187 optimal weight: 1.9990 chunk 619 optimal weight: 10.0000 chunk 325 optimal weight: 3.9990 chunk 362 optimal weight: 3.9990 chunk 689 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 746 optimal weight: 1.9990 chunk 636 optimal weight: 8.9990 chunk 758 optimal weight: 2.9990 chunk 188 optimal weight: 0.9980 chunk 817 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.083190 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2910 r_free = 0.2910 target = 0.068153 restraints weight = 175080.618| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 2.99 r_work: 0.2718 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2718 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2727 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2727 r_free = 0.2727 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 = 0.2727 r_free = 0.2727 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2727 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8720 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 68494 Z= 0.209 Angle : 0.559 12.500 92469 Z= 0.275 Chirality : 0.042 0.187 11003 Planarity : 0.003 0.057 11805 Dihedral : 6.899 177.692 9503 Min Nonbonded Distance : 1.903 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.85 % Allowed : 12.99 % Favored : 86.16 % 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: 1.55 (0.09), residues: 8741 helix: 2.33 (0.08), residues: 4482 sheet: 0.03 (0.16), residues: 1158 loop : -0.50 (0.11), residues: 3101 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP P 66 HIS 0.016 0.001 HIS Z 161 PHE 0.026 0.001 PHE P 214 TYR 0.022 0.001 TYR z 498 ARG 0.013 0.000 ARG P 250 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17482 Ramachandran restraints generated. 8741 Oldfield, 0 Emsley, 8741 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 562 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 500 time to evaluate : 6.066 Fit side-chains revert: symmetry clash REVERT: N 242 CYS cc_start: 0.6803 (t) cc_final: 0.5970 (t) REVERT: N 264 MET cc_start: 0.6994 (mtm) cc_final: 0.6652 (mtm) REVERT: N 306 ARG cc_start: 0.6922 (ptp-170) cc_final: 0.6334 (ptp-170) REVERT: A 384 MET cc_start: 0.9120 (ttm) cc_final: 0.8885 (ttt) REVERT: B 221 ASP cc_start: 0.8762 (t0) cc_final: 0.8359 (t70) REVERT: D 360 GLU cc_start: 0.8501 (tp30) cc_final: 0.8147 (tm-30) REVERT: E 32 GLU cc_start: 0.7839 (mp0) cc_final: 0.7588 (pm20) REVERT: G 20 ARG cc_start: 0.8468 (ttm-80) cc_final: 0.8120 (ttm170) REVERT: G 415 GLU cc_start: 0.8654 (mp0) cc_final: 0.8326 (mp0) REVERT: H 53 ARG cc_start: 0.8345 (OUTLIER) cc_final: 0.7574 (mmm160) REVERT: H 70 ASP cc_start: 0.7787 (t0) cc_final: 0.7333 (t70) REVERT: H 220 PHE cc_start: 0.8986 (t80) cc_final: 0.8607 (t80) REVERT: H 283 HIS cc_start: 0.8776 (OUTLIER) cc_final: 0.8471 (m90) REVERT: H 451 ASP cc_start: 0.8734 (m-30) cc_final: 0.8312 (m-30) REVERT: Q 14 MET cc_start: 0.9209 (mtp) cc_final: 0.8958 (mtp) REVERT: Q 416 GLU cc_start: 0.8705 (mp0) cc_final: 0.8504 (mp0) REVERT: Z 53 ASP cc_start: 0.8410 (m-30) cc_final: 0.8012 (m-30) REVERT: Z 95 ASN cc_start: 0.8849 (t0) cc_final: 0.8535 (m-40) REVERT: Z 357 GLU cc_start: 0.8392 (mm-30) cc_final: 0.7745 (tp30) REVERT: a 430 MET cc_start: 0.7920 (mmm) cc_final: 0.7465 (mpp) REVERT: a 473 GLU cc_start: 0.8386 (tm-30) cc_final: 0.7840 (tm-30) REVERT: d 458 MET cc_start: 0.8994 (mmm) cc_final: 0.8765 (mmp) REVERT: d 524 GLU cc_start: 0.8773 (tt0) cc_final: 0.8519 (mm-30) REVERT: e 21 ASP cc_start: 0.8951 (m-30) cc_final: 0.8572 (t70) REVERT: e 39 MET cc_start: 0.9048 (ttm) cc_final: 0.8713 (ttm) REVERT: e 139 GLN cc_start: 0.8790 (tt0) cc_final: 0.8476 (tt0) REVERT: e 371 MET cc_start: 0.9118 (mtp) cc_final: 0.8875 (ttm) REVERT: e 448 MET cc_start: 0.9140 (mtm) cc_final: 0.8572 (mtm) REVERT: e 474 MET cc_start: 0.8657 (tmm) cc_final: 0.8156 (ttm) REVERT: e 526 MET cc_start: 0.9184 (ttt) cc_final: 0.8784 (ttt) REVERT: g 59 MET cc_start: 0.9201 (OUTLIER) cc_final: 0.8764 (tmm) REVERT: h 57 THR cc_start: 0.9338 (OUTLIER) cc_final: 0.8991 (p) REVERT: h 81 ASP cc_start: 0.8615 (m-30) cc_final: 0.8348 (m-30) REVERT: h 130 GLN cc_start: 0.8335 (tp-100) cc_final: 0.7855 (tp-100) REVERT: h 524 ARG cc_start: 0.7552 (tmt170) cc_final: 0.7132 (tmm-80) REVERT: q 26 GLU cc_start: 0.8609 (mp0) cc_final: 0.8325 (mp0) REVERT: z 337 ASP cc_start: 0.8326 (t0) cc_final: 0.8115 (t0) REVERT: z 415 GLU cc_start: 0.8626 (OUTLIER) cc_final: 0.8378 (mp0) REVERT: P 88 ILE cc_start: 0.5532 (OUTLIER) cc_final: 0.5284 (pp) REVERT: P 173 MET cc_start: 0.8116 (tmm) cc_final: 0.7776 (tmm) outliers start: 62 outliers final: 42 residues processed: 542 average time/residue: 1.5657 time to fit residues: 1111.4481 Evaluate side-chains 538 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 490 time to evaluate : 6.029 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 173 VAL Chi-restraints excluded: chain N residue 201 CYS Chi-restraints excluded: chain A residue 244 THR Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 346 CYS Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain D residue 352 THR Chi-restraints excluded: chain D residue 397 VAL Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain G residue 96 THR Chi-restraints excluded: chain H residue 36 VAL Chi-restraints excluded: chain H residue 53 ARG Chi-restraints excluded: chain H residue 283 HIS Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 105 LEU Chi-restraints excluded: chain Q residue 502 LEU Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 210 LEU Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 166 ASP Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 242 THR Chi-restraints excluded: chain b residue 371 CYS Chi-restraints excluded: chain b residue 446 LEU Chi-restraints excluded: chain d residue 83 VAL Chi-restraints excluded: chain d residue 121 THR Chi-restraints excluded: chain g residue 52 ASP Chi-restraints excluded: chain g residue 59 MET Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 480 VAL Chi-restraints excluded: chain h residue 38 THR Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 293 LEU Chi-restraints excluded: chain q residue 42 THR Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 372 ILE Chi-restraints excluded: chain q residue 483 GLU Chi-restraints excluded: chain q residue 513 ASN Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 415 GLU Chi-restraints excluded: chain z residue 477 VAL Chi-restraints excluded: chain P residue 88 ILE Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 221 VAL Chi-restraints excluded: chain P residue 249 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 871 random chunks: chunk 138 optimal weight: 2.9990 chunk 611 optimal weight: 0.8980 chunk 423 optimal weight: 7.9990 chunk 329 optimal weight: 9.9990 chunk 789 optimal weight: 6.9990 chunk 463 optimal weight: 4.9990 chunk 695 optimal weight: 10.0000 chunk 837 optimal weight: 3.9990 chunk 616 optimal weight: 3.9990 chunk 184 optimal weight: 4.9990 chunk 615 optimal weight: 4.9990 overall best weight: 3.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 164 ASN A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 71 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 161 HIS ** Z 514 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 302 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.081967 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2892 r_free = 0.2892 target = 0.067259 restraints weight = 157092.563| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 2.78 r_work: 0.2709 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2718 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2718 r_free = 0.2718 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 = 0.2718 r_free = 0.2718 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2718 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.1185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 68494 Z= 0.302 Angle : 0.585 12.700 92469 Z= 0.288 Chirality : 0.043 0.180 11003 Planarity : 0.003 0.047 11805 Dihedral : 6.863 173.798 9503 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 0.93 % Allowed : 13.07 % Favored : 86.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.09), residues: 8741 helix: 2.28 (0.08), residues: 4485 sheet: 0.02 (0.16), residues: 1145 loop : -0.54 (0.11), residues: 3111 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP G 168 HIS 0.015 0.001 HIS Z 161 PHE 0.024 0.001 PHE P 214 TYR 0.021 0.001 TYR z 498 ARG 0.009 0.000 ARG g 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 30723.13 seconds wall clock time: 530 minutes 23.85 seconds (31823.85 seconds total)