Starting phenix.real_space_refine on Tue Jan 21 23:10:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8shf_40486/01_2025/8shf_40486.cif Found real_map, /net/cci-nas-00/data/ceres_data/8shf_40486/01_2025/8shf_40486.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/8shf_40486/01_2025/8shf_40486.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8shf_40486/01_2025/8shf_40486.map" model { file = "/net/cci-nas-00/data/ceres_data/8shf_40486/01_2025/8shf_40486.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8shf_40486/01_2025/8shf_40486.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= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 8 Type Number sf(0) Gaussians Al 16 5.89 5 P 32 5.49 5 Mg 16 5.21 5 S 420 5.16 5 C 42310 2.51 5 N 11780 2.21 5 O 13108 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): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 67730 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 924 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 2, 'TRANS': 120} 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: 4121 Number of conformers: 1 Conformer: "" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4088 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4088 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "h" Number of atoms: 4032 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4032 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 16, 'TRANS': 508} Chain: "q" Number of atoms: 4053 Number of conformers: 1 Conformer: "" Number of residues, atoms: 533, 4053 Classifications: {'peptide': 533} Link IDs: {'PTRANS': 16, 'TRANS': 516} Chain: "z" Number of atoms: 4033 Number of conformers: 1 Conformer: "" Number of residues, atoms: 527, 4033 Classifications: {'peptide': 527} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 512} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 3 Chain: "P" Number of atoms: 1683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1683 Classifications: {'peptide': 212} Link IDs: {'PTRANS': 6, 'TRANS': 205} Chain breaks: 1 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "G" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "H" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "Z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "a" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 34.34, per 1000 atoms: 0.51 Number of scatterers: 67730 At special positions: 0 Unit cell: (179.86, 177.744, 183.034, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 8 Type Number sf(0) S 420 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13108 8.00 N 11780 7.00 C 42310 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 "HETATM67509 O3A ADP b 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67317 O3A ADP E 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67381 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Atom "HETATM67253 O3A ADP B 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.91 Conformation dependent library (CDL) restraints added in 7.6 seconds 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 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: 366 helices and 99 sheets defined 56.1% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 6.97 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.616A 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: 3.535A pdb=" N LEU A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.610A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N LEU A 107 " --> pdb=" O ASN A 103 " (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: 4.384A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ILE A 149 " --> pdb=" O ARG A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.055A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) removed outlier: 3.631A 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: 3.556A pdb=" N ILE A 263 " --> pdb=" O LYS A 259 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N THR A 281 " --> pdb=" O LYS A 277 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 removed outlier: 3.543A pdb=" N TYR A 299 " --> pdb=" O MET A 295 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE A 300 " --> pdb=" O CYS A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 removed outlier: 3.575A pdb=" N GLU A 387 " --> pdb=" O PHE A 383 " (cutoff:3.500A) 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 445 removed outlier: 4.059A pdb=" N LEU A 436 " --> pdb=" O SER A 432 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA A 437 " --> pdb=" O ARG A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.977A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.421A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N LEU A 483 " --> pdb=" O ARG A 480 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.567A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 145 Processing helix chain 'B' and resid 151 through 169 removed outlier: 4.399A pdb=" N SER B 169 " --> pdb=" O THR B 165 " (cutoff:3.500A) Processing helix chain 'B' and resid 170 through 174 removed outlier: 3.687A pdb=" N HIS B 174 " --> pdb=" O LEU B 171 " (cutoff:3.500A) Processing helix chain 'B' and resid 175 through 189 Processing helix chain 'B' and resid 195 through 197 No H-bonds generated for 'chain 'B' and resid 195 through 197' Processing helix chain 'B' and resid 208 through 212 Processing helix chain 'B' and resid 260 through 284 removed outlier: 3.519A pdb=" N VAL B 264 " --> pdb=" O SER B 260 " (cutoff:3.500A) Processing helix chain 'B' and resid 297 through 308 Processing helix chain 'B' and resid 316 through 328 Processing helix chain 'B' and resid 337 through 341 Processing helix chain 'B' and resid 379 through 403 Processing helix chain 'B' and resid 411 through 426 Processing helix chain 'B' and resid 431 through 453 Proline residue: B 447 - end of helix Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.354A 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: 3.915A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 151 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.752A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N SER D 173 " --> pdb=" O THR D 169 " (cutoff:3.500A) Processing helix chain 'D' and resid 179 through 193 Proline residue: D 185 - end of helix Processing helix chain 'D' and resid 204 through 206 No H-bonds generated for 'chain 'D' and resid 204 through 206' Processing helix chain 'D' and resid 217 through 221 Processing helix chain 'D' and resid 268 through 292 removed outlier: 3.830A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 441 Processing helix chain 'D' and resid 446 through 459 removed outlier: 4.217A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.975A pdb=" N SER D 463 " --> pdb=" O GLU D 459 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 Processing helix chain 'D' and resid 504 through 507 Processing helix chain 'D' and resid 512 through 531 Processing helix chain 'E' and resid 21 through 25 removed outlier: 3.782A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 30 through 49 removed outlier: 3.633A pdb=" N LEU E 34 " --> pdb=" O GLY E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 50 through 52 No H-bonds generated for 'chain 'E' and resid 50 through 52' Processing helix chain 'E' and resid 73 through 81 Processing helix chain 'E' and resid 85 through 102 Processing helix chain 'E' and resid 107 through 126 removed outlier: 3.686A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ARG E 126 " --> pdb=" O GLN E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 129 through 152 Processing helix chain 'E' and resid 162 through 174 Processing helix chain 'E' and resid 175 through 180 removed outlier: 6.624A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.949A 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: 3.753A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 440 removed outlier: 3.763A pdb=" N LYS E 439 " --> pdb=" O GLN E 435 " (cutoff:3.500A) Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.655A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.711A 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 510 through 529 Processing helix chain 'G' and resid 19 through 38 removed outlier: 3.692A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 39 through 41 No H-bonds generated for 'chain 'G' and resid 39 through 41' Processing helix chain 'G' and resid 62 through 69 Processing helix chain 'G' and resid 74 through 91 Processing helix chain 'G' and resid 94 through 114 removed outlier: 3.723A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.952A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 141 removed outlier: 3.636A 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: 4.168A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 306 Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 removed outlier: 3.564A pdb=" N LYS G 427 " --> pdb=" O THR G 423 " (cutoff:3.500A) Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 removed outlier: 3.631A pdb=" N LEU G 462 " --> pdb=" O SER G 458 " (cutoff:3.500A) Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 519 removed outlier: 3.597A pdb=" N ILE G 519 " --> pdb=" O LEU G 515 " (cutoff:3.500A) Processing helix chain 'H' and resid 18 through 36 removed outlier: 3.592A pdb=" N ALA H 35 " --> pdb=" O VAL H 31 " (cutoff:3.500A) removed outlier: 4.099A pdb=" N VAL H 36 " --> pdb=" O ILE H 32 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 40 removed outlier: 3.827A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 37 through 40' Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.754A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.233A 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: 3.754A 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 Processing helix chain 'H' and resid 191 through 193 No H-bonds generated for 'chain 'H' and resid 191 through 193' Processing helix chain 'H' and resid 204 through 208 Processing helix chain 'H' and resid 224 through 228 Processing helix chain 'H' and resid 259 through 284 removed outlier: 3.543A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 342 removed outlier: 3.530A pdb=" N LEU H 342 " --> pdb=" O ALA H 339 " (cutoff:3.500A) Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.983A pdb=" N LEU H 434 " --> pdb=" O LYS H 430 " (cutoff:3.500A) Processing helix chain 'H' and resid 443 through 454 Processing helix chain 'H' and resid 456 through 471 Processing helix chain 'H' and resid 496 through 516 removed outlier: 3.535A pdb=" N VAL H 516 " --> pdb=" O LEU H 512 " (cutoff:3.500A) Processing helix chain 'Q' and resid 10 through 15 Processing helix chain 'Q' and resid 24 through 45 removed outlier: 4.309A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.757A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 75 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 Processing helix chain 'Q' and resid 156 through 166 removed outlier: 4.505A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) Processing helix chain 'Q' and resid 176 through 190 Processing helix chain 'Q' and resid 198 through 200 No H-bonds generated for 'chain 'Q' and resid 198 through 200' Processing helix chain 'Q' and resid 211 through 215 Processing helix chain 'Q' and resid 261 through 286 removed outlier: 4.943A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 5.012A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N THR Q 286 " --> pdb=" O ALA Q 282 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.874A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 445 removed outlier: 4.135A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) removed outlier: 3.756A 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 removed outlier: 3.979A pdb=" N LEU Z 7 " --> pdb=" O ALA Z 3 " (cutoff:3.500A) Processing helix chain 'Z' and resid 16 through 35 removed outlier: 3.825A pdb=" N LEU Z 20 " --> pdb=" O ALA Z 16 " (cutoff:3.500A) Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 66 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 92 through 111 removed outlier: 3.621A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.767A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 4.106A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.647A pdb=" N GLU Z 170 " --> pdb=" O ASP Z 166 " (cutoff:3.500A) Processing helix chain 'Z' and resid 187 through 189 No H-bonds generated for 'chain 'Z' and resid 187 through 189' Processing helix chain 'Z' and resid 200 through 204 removed outlier: 3.555A pdb=" N THR Z 204 " --> pdb=" O GLU Z 201 " (cutoff:3.500A) Processing helix chain 'Z' and resid 252 through 263 Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.611A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 308 removed outlier: 3.791A pdb=" N GLU Z 308 " --> pdb=" O ALA Z 304 " (cutoff:3.500A) Processing helix chain 'Z' and resid 317 through 329 removed outlier: 3.801A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 removed outlier: 3.627A pdb=" N ASP Z 404 " --> pdb=" O ASN Z 400 " (cutoff:3.500A) Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.210A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.711A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 Processing helix chain 'Z' and resid 488 through 493 Processing helix chain 'Z' and resid 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.572A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 144 through 157 removed outlier: 4.343A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.273A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N ILE a 179 " --> pdb=" O ALA a 175 " (cutoff:3.500A) Processing helix chain 'a' and resid 184 through 186 No H-bonds generated for 'chain 'a' and resid 184 through 186' Processing helix chain 'a' and resid 204 through 208 Processing helix chain 'a' and resid 256 through 258 No H-bonds generated for 'chain 'a' and resid 256 through 258' Processing helix chain 'a' and resid 259 through 280 removed outlier: 3.882A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 4.983A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 removed outlier: 3.519A pdb=" N ALA a 303 " --> pdb=" O TYR a 299 " (cutoff:3.500A) Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 427 Processing helix chain 'a' and resid 428 through 430 No H-bonds generated for 'chain 'a' and resid 428 through 430' Processing helix chain 'a' and resid 433 through 445 Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 478 through 484 removed outlier: 3.884A pdb=" N LYS a 481 " --> pdb=" O PRO a 478 " (cutoff:3.500A) removed outlier: 5.327A pdb=" N ASN a 482 " --> pdb=" O GLU a 479 " (cutoff:3.500A) removed outlier: 3.650A 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: 4.448A pdb=" N SER b 169 " --> pdb=" O THR b 165 " (cutoff:3.500A) Processing helix chain 'b' and resid 170 through 174 removed outlier: 3.571A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 195 through 197 No H-bonds generated for 'chain 'b' and resid 195 through 197' Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.571A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 426 Processing helix chain 'b' and resid 431 through 454 Proline residue: b 447 - end of helix removed outlier: 3.771A 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 48 Processing helix chain 'd' and resid 73 through 81 removed outlier: 3.615A pdb=" N MET d 81 " --> pdb=" O ILE d 77 " (cutoff:3.500A) Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.658A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 152 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.586A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.723A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 194 Proline residue: d 185 - end of helix removed outlier: 3.566A pdb=" N VAL d 194 " --> pdb=" O ALA d 190 " (cutoff:3.500A) Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 292 Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 442 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.725A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.809A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 487 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.941A 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 126 removed outlier: 4.192A pdb=" N VAL e 110 " --> pdb=" O THR e 106 " (cutoff:3.500A) removed outlier: 3.575A 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: 6.440A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.839A 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: 3.895A pdb=" N THR e 295 " --> pdb=" O GLN e 291 " (cutoff:3.500A) Processing helix chain 'e' and resid 307 through 317 Processing helix chain 'e' and resid 326 through 338 Processing helix chain 'e' and resid 344 through 348 Processing helix chain 'e' and resid 349 through 353 Processing helix chain 'e' and resid 391 through 415 Processing helix chain 'e' and resid 423 through 440 removed outlier: 3.820A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.638A pdb=" N GLN e 445 " --> pdb=" O PRO e 441 " (cutoff:3.500A) removed outlier: 4.000A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.579A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.758A 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: 3.796A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.820A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 140 removed outlier: 3.624A 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: 3.921A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 removed outlier: 3.553A pdb=" N ALA g 172 " --> pdb=" O TRP g 168 " (cutoff:3.500A) Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 306 Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 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 removed outlier: 3.525A pdb=" N LEU g 462 " --> pdb=" O SER g 458 " (cutoff:3.500A) Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 35 removed outlier: 3.591A pdb=" N ALA h 35 " --> pdb=" O VAL h 31 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.666A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 3.956A 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: 3.686A pdb=" N ILE h 121 " --> pdb=" O HIS h 117 " (cutoff:3.500A) Processing helix chain 'h' and resid 147 through 164 Processing helix chain 'h' and resid 168 through 170 No H-bonds generated for 'chain 'h' and resid 168 through 170' Processing helix chain 'h' and resid 171 through 186 removed outlier: 3.706A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N LEU h 186 " --> pdb=" O ALA h 182 " (cutoff:3.500A) Processing helix chain 'h' and resid 191 through 193 No H-bonds generated for 'chain 'h' and resid 191 through 193' Processing helix chain 'h' and resid 204 through 208 Processing helix chain 'h' and resid 224 through 228 Processing helix chain 'h' and resid 259 through 284 Processing helix chain 'h' and resid 296 through 306 Processing helix chain 'h' and resid 315 through 327 Processing helix chain 'h' and resid 338 through 342 Processing helix chain 'h' and resid 378 through 402 Processing helix chain 'h' and resid 410 through 425 Processing helix chain 'h' and resid 429 through 442 removed outlier: 3.574A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 454 Processing helix chain 'h' and resid 456 through 471 Processing helix chain 'h' and resid 496 through 515 Processing helix chain 'q' and resid 10 through 15 Processing helix chain 'q' and resid 24 through 45 removed outlier: 4.365A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.813A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.536A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 75 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 Processing helix chain 'q' and resid 156 through 168 removed outlier: 3.645A pdb=" N VAL q 160 " --> pdb=" O ASP q 156 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.516A 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: 4.850A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.702A 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: 3.810A pdb=" N THR q 429 " --> pdb=" O SER q 425 " (cutoff:3.500A) Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.265A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.794A 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 Processing helix chain 'z' and resid 16 through 35 removed outlier: 3.656A pdb=" N LEU z 20 " --> pdb=" O ALA z 16 " (cutoff:3.500A) Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.545A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.765A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 3.597A pdb=" N LEU z 148 " --> pdb=" O ASP z 144 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.657A pdb=" N GLU z 170 " --> pdb=" O ASP z 166 " (cutoff:3.500A) Processing helix chain 'z' and resid 187 through 191 Processing helix chain 'z' and resid 200 through 204 removed outlier: 3.708A pdb=" N THR z 204 " --> pdb=" O GLU z 201 " (cutoff:3.500A) Processing helix chain 'z' and resid 252 through 263 Processing helix chain 'z' and resid 264 through 282 removed outlier: 3.629A 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 318 through 328 removed outlier: 4.198A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 removed outlier: 3.563A pdb=" N ASP z 404 " --> pdb=" O ASN z 400 " (cutoff:3.500A) Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.135A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.596A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 498 through 517 Processing helix chain 'P' and resid 57 through 62 Processing helix chain 'P' and resid 62 through 85 removed outlier: 3.699A pdb=" N PHE P 69 " --> pdb=" O ASP P 65 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N GLU P 79 " --> pdb=" O GLU P 75 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 139 Processing helix chain 'P' and resid 140 through 151 removed outlier: 4.445A pdb=" N ARG P 144 " --> pdb=" O TYR P 140 " (cutoff:3.500A) removed outlier: 4.585A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLN P 151 " --> pdb=" O GLU P 147 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 175 Processing helix chain 'P' and resid 195 through 209 removed outlier: 3.764A pdb=" N ALA P 207 " --> pdb=" O ILE P 203 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N GLU P 208 " --> pdb=" O CYS P 204 " (cutoff:3.500A) Processing helix chain 'P' and resid 219 through 223 Processing helix chain 'P' and resid 225 through 232 Processing helix chain 'P' and resid 250 through 256 removed outlier: 4.031A pdb=" N GLN P 254 " --> pdb=" O ARG P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 271 removed outlier: 3.768A 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: 7.505A pdb=" N ALA N 213 " --> pdb=" O SER N 199 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N CYS N 201 " --> pdb=" O LEU N 211 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N LEU N 211 " --> pdb=" O CYS N 201 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N PHE N 203 " --> pdb=" O GLN N 209 " (cutoff:3.500A) removed outlier: 7.795A pdb=" N GLN N 209 " --> pdb=" O PHE N 203 " (cutoff:3.500A) removed outlier: 6.166A pdb=" N CYS N 219 " --> pdb=" O SER N 232 " (cutoff:3.500A) removed outlier: 4.513A pdb=" N SER N 232 " --> pdb=" O CYS N 219 " (cutoff:3.500A) removed outlier: 6.828A 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 245 removed outlier: 6.688A pdb=" N GLY N 257 " --> pdb=" O LEU N 241 " (cutoff:3.500A) removed outlier: 4.436A pdb=" N LEU N 243 " --> pdb=" O VAL N 255 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N VAL N 255 " --> pdb=" O LEU N 243 " (cutoff:3.500A) removed outlier: 5.212A pdb=" N LEU N 245 " --> pdb=" O THR N 253 " (cutoff:3.500A) removed outlier: 7.422A pdb=" N THR N 253 " --> pdb=" O LEU N 245 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N ALA N 263 " --> pdb=" O PHE N 277 " (cutoff:3.500A) removed outlier: 7.306A pdb=" N ASP N 267 " --> pdb=" O CYS N 273 " (cutoff:3.500A) removed outlier: 6.536A pdb=" N CYS N 273 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'N' and resid 286 through 289 Processing sheet with id=AA4, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.692A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.482A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.891A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 54 through 55 removed outlier: 5.794A 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 Processing sheet with id=AA9, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.725A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.745A 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: 6.725A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N VAL A 285 " --> pdb=" O LYS A 233 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.295A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.272A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N GLU H 254 " --> pdb=" O ILE Q 259 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 486 through 489 removed outlier: 3.511A pdb=" N LYS A 494 " --> pdb=" O ASP A 489 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.491A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.612A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.334A 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: 3.580A pdb=" N MET B 62 " --> pdb=" O LEU B 52 " (cutoff:3.500A) removed outlier: 6.889A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 7.870A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 5.813A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (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: 3.732A 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: 6.504A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.356A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.745A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.984A pdb=" N GLU B 350 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 7.263A pdb=" N ARG B 231 " --> pdb=" O GLU B 350 " (cutoff:3.500A) removed outlier: 6.343A pdb=" N PHE B 290 " --> pdb=" O ILE B 312 " (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: 6.419A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.378A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.224A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.151A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.317A 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: 6.812A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.079A 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: 6.812A pdb=" N LYS D 372 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N ASN D 366 " --> pdb=" O LYS D 372 " (cutoff:3.500A) removed outlier: 6.601A pdb=" N LEU D 374 " --> pdb=" O GLU D 364 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N GLU D 364 " --> pdb=" O LEU D 374 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N ILE D 376 " --> pdb=" O ALA D 362 " (cutoff:3.500A) removed outlier: 6.571A pdb=" N ALA D 362 " --> pdb=" O ILE D 376 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N GLY D 378 " --> pdb=" O GLU D 360 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.445A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.247A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.451A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.533A 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: 3.570A 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: 4.440A pdb=" N ILE E 530 " --> pdb=" O ASP H 46 " (cutoff:3.500A) removed outlier: 7.327A pdb=" N LEU H 48 " --> pdb=" O ILE E 530 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N ASP E 532 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N VAL H 50 " --> pdb=" O ASP E 532 " (cutoff:3.500A) removed outlier: 6.422A 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: 3.857A 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: 6.545A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LYS E 247 " --> pdb=" O PHE E 355 " (cutoff:3.500A) removed outlier: 6.546A pdb=" N GLY E 357 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.847A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.475A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.590A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.405A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.274A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AD3, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD4, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.942A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.429A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N THR G 373 " --> pdb=" O LEU G 215 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD6, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD7, first strand: chain 'G' and resid 478 through 480 Processing sheet with id=AD8, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.595A pdb=" N GLU H 518 " --> pdb=" O MET Q 55 " (cutoff:3.500A) removed outlier: 7.879A pdb=" N ILE Q 57 " --> pdb=" O GLU H 518 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N ILE H 520 " --> pdb=" O ILE Q 57 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AE1, first strand: chain 'H' and resid 195 through 201 removed outlier: 6.257A pdb=" N GLY H 196 " --> pdb=" O PHE H 372 " (cutoff:3.500A) removed outlier: 7.346A pdb=" N LEU H 374 " --> pdb=" O GLY H 196 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N LYS H 198 " --> pdb=" O LEU H 374 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N GLY H 376 " --> pdb=" O LYS H 198 " (cutoff:3.500A) removed outlier: 6.725A pdb=" N VAL H 200 " --> pdb=" O GLY H 376 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AE2, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AE3, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE4, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE5, first strand: chain 'Q' and resid 20 through 23 removed outlier: 5.019A pdb=" N VAL Q 521 " --> pdb=" O MET Z 44 " (cutoff:3.500A) removed outlier: 7.150A pdb=" N MET Z 46 " --> pdb=" O VAL Q 521 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N GLN Q 523 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.744A pdb=" N VAL Z 48 " --> pdb=" O GLN Q 523 " (cutoff:3.500A) removed outlier: 6.564A pdb=" N ILE Q 525 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE6, first strand: chain 'Q' and resid 202 through 206 removed outlier: 6.446A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.293A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.458A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE8, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AE9, first strand: chain 'Q' and resid 408 through 410 Processing sheet with id=AF1, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AF2, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AF3, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.645A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.408A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) Processing sheet with id=AF4, first strand: chain 'Z' and resid 210 through 212 removed outlier: 6.425A pdb=" N CYS Z 366 " --> pdb=" O ALA Z 347 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA Z 347 " --> pdb=" O CYS Z 366 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'Z' and resid 210 through 212 removed outlier: 6.425A pdb=" N CYS Z 366 " --> pdb=" O ALA Z 347 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N ALA Z 347 " --> pdb=" O CYS Z 366 " (cutoff:3.500A) removed outlier: 6.399A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.192A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.218A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 9 through 13 removed outlier: 6.182A pdb=" N ASP d 58 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N ASP a 529 " --> pdb=" O ASP d 58 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.329A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N VAL g 523 " --> pdb=" O MET a 44 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AF9, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AG1, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.427A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.428A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.718A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.962A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 7.361A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.461A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.461A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.518A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'g' and resid 254 through 256 removed outlier: 8.983A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.190A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.434A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N LYS e 263 " --> pdb=" O ALA h 253 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG6, first strand: chain 'b' and resid 17 through 19 removed outlier: 6.222A pdb=" N ASP e 58 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 4.007A pdb=" N ASN b 519 " --> pdb=" O ASP e 58 " (cutoff:3.500A) Processing sheet with id=AG7, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.959A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.129A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.027A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG9, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.674A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AH1, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.455A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.106A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N CYS b 289 " --> pdb=" O LYS b 236 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH3, first strand: chain 'd' and resid 153 through 154 Processing sheet with id=AH4, first strand: chain 'd' and resid 208 through 214 removed outlier: 4.023A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH5, first strand: chain 'd' and resid 227 through 229 removed outlier: 3.569A pdb=" N LEU d 227 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.644A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.124A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N LEU d 361 " --> pdb=" O GLU d 242 " (cutoff:3.500A) removed outlier: 6.983A pdb=" N GLU d 242 " --> pdb=" O LEU d 361 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL d 297 " --> pdb=" O LYS d 245 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH7, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.527A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.863A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH8, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH9, first strand: chain 'e' and resid 209 through 215 removed outlier: 6.293A pdb=" N LYS e 210 " --> pdb=" O ILE e 385 " (cutoff:3.500A) removed outlier: 7.491A pdb=" N ILE e 387 " --> pdb=" O LYS e 210 " (cutoff:3.500A) removed outlier: 6.917A pdb=" N GLU e 212 " --> pdb=" O ILE e 387 " (cutoff:3.500A) removed outlier: 8.784A pdb=" N GLY e 389 " --> pdb=" O GLU e 212 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS e 214 " --> pdb=" O GLY e 389 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.475A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'e' and resid 300 through 301 removed outlier: 6.533A pdb=" N ALA e 300 " --> pdb=" O VAL e 322 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI2 Processing sheet with id=AI3, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.348A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.755A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLU z 12 " --> pdb=" O ARG z 523 " (cutoff:3.500A) Processing sheet with id=AI4, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI5, first strand: chain 'g' and resid 200 through 205 removed outlier: 3.964A pdb=" N GLY g 378 " --> pdb=" O ILE g 204 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI7, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.465A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) removed outlier: 6.218A pdb=" N VAL g 290 " --> pdb=" O ILE g 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AI7 Processing sheet with id=AI8, first strand: chain 'g' and resid 407 through 409 Processing sheet with id=AI9, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.755A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.519A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.176A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 195 through 201 removed outlier: 3.609A pdb=" N GLY h 376 " --> pdb=" O VAL h 200 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N THR h 371 " --> pdb=" O VAL h 211 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ4, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ5, first strand: chain 'h' and resid 405 through 407 Processing sheet with id=AJ6, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ7, first strand: chain 'q' and resid 20 through 23 removed outlier: 5.327A pdb=" N VAL q 521 " --> pdb=" O MET z 44 " (cutoff:3.500A) removed outlier: 7.148A pdb=" N MET z 46 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN q 523 " --> pdb=" O MET z 46 " (cutoff:3.500A) removed outlier: 7.738A pdb=" N VAL z 48 " --> pdb=" O GLN q 523 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE q 525 " --> pdb=" O VAL z 48 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.690A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ9, first strand: chain 'q' and resid 202 through 206 removed outlier: 6.738A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) Processing sheet with id=AK1, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AK2, first strand: chain 'q' and resid 239 through 242 removed outlier: 3.579A pdb=" N VAL q 292 " --> pdb=" O ALA q 240 " (cutoff:3.500A) Processing sheet with id=AK3, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK4, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK5, first strand: chain 'z' and resid 192 through 196 removed outlier: 6.409A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.037A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.734A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK7, first strand: chain 'z' and resid 310 through 313 removed outlier: 9.001A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.841A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.249A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) Processing sheet with id=AK8, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK9, first strand: chain 'P' and resid 162 through 164 removed outlier: 5.891A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.816A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.808A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.868A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU P 236 " --> pdb=" O ASN P 247 " (cutoff:3.500A) removed outlier: 5.119A pdb=" N ASN P 247 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 6.603A pdb=" N ILE P 238 " --> pdb=" O ILE P 245 " (cutoff:3.500A) 4084 hydrogen bonds defined for protein. 11664 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: 31.39 Time building geometry restraints manager: 16.08 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: 22794 1.34 - 1.46: 10354 1.46 - 1.58: 34568 1.58 - 1.69: 48 1.69 - 1.81: 742 Bond restraints: 68506 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 6.50e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 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 6.35e+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 6.35e+01 bond pdb=" F2 AF3 a 603 " pdb="AL AF3 a 603 " ideal model delta sigma weight residual 1.637 1.796 -0.159 2.00e-02 2.50e+03 6.33e+01 ... (remaining 68501 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.51: 91676 2.51 - 5.03: 675 5.03 - 7.54: 135 7.54 - 10.06: 8 10.06 - 12.57: 2 Bond angle restraints: 92496 Sorted by residual: angle pdb=" C MET P 148 " pdb=" N ARG P 149 " pdb=" CA ARG P 149 " ideal model delta sigma weight residual 122.38 112.61 9.77 1.81e+00 3.05e-01 2.91e+01 angle pdb=" CA ARG P 149 " pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " ideal model delta sigma weight residual 114.10 122.91 -8.81 2.00e+00 2.50e-01 1.94e+01 angle pdb=" CB MET P 148 " pdb=" CG MET P 148 " pdb=" SD MET P 148 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.76e+01 angle pdb=" C ASP a 47 " pdb=" N ASP a 48 " pdb=" CA ASP a 48 " ideal model delta sigma weight residual 121.54 129.45 -7.91 1.91e+00 2.74e-01 1.72e+01 angle pdb=" CG MET h 497 " pdb=" SD MET h 497 " pdb=" CE MET h 497 " ideal model delta sigma weight residual 100.90 92.04 8.86 2.20e+00 2.07e-01 1.62e+01 ... (remaining 92491 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.49: 41659 35.49 - 70.99: 615 70.99 - 106.48: 55 106.48 - 141.98: 12 141.98 - 177.47: 6 Dihedral angle restraints: 42347 sinusoidal: 17044 harmonic: 25303 Sorted by residual: dihedral pdb=" O2A ADP z 601 " pdb=" O3A ADP z 601 " pdb=" PA ADP z 601 " pdb=" PB ADP z 601 " ideal model delta sinusoidal sigma weight residual 300.00 122.53 177.47 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP g 601 " pdb=" O3A ADP g 601 " pdb=" PA ADP g 601 " pdb=" PB ADP g 601 " ideal model delta sinusoidal sigma weight residual -60.00 113.94 -173.94 1 2.00e+01 2.50e-03 4.79e+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 300.00 132.72 167.28 1 2.00e+01 2.50e-03 4.74e+01 ... (remaining 42344 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 8094 0.041 - 0.081: 2056 0.081 - 0.122: 794 0.122 - 0.162: 55 0.162 - 0.203: 4 Chirality restraints: 11003 Sorted by residual: chirality pdb=" CA MET P 148 " pdb=" N MET P 148 " pdb=" C MET P 148 " pdb=" CB MET P 148 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.03e+00 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 2.47 0.17 2.00e-01 2.50e+01 7.56e-01 chirality pdb=" CA GLU a 77 " pdb=" N GLU a 77 " pdb=" C GLU a 77 " pdb=" CB GLU a 77 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.26e-01 ... (remaining 11000 not shown) Planarity restraints: 11814 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP a 47 " -0.010 2.00e-02 2.50e+03 2.06e-02 4.23e+00 pdb=" C ASP a 47 " 0.036 2.00e-02 2.50e+03 pdb=" O ASP a 47 " -0.013 2.00e-02 2.50e+03 pdb=" N ASP a 48 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO e 441 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TRP P 66 " 0.015 2.00e-02 2.50e+03 1.20e-02 3.62e+00 pdb=" CG TRP P 66 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP P 66 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP P 66 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP P 66 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP P 66 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP P 66 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP P 66 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP P 66 " 0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP P 66 " 0.003 2.00e-02 2.50e+03 ... (remaining 11811 not shown) Histogram of nonbonded interaction distances: 1.93 - 2.53: 601 2.53 - 3.12: 51665 3.12 - 3.71: 106279 3.71 - 4.31: 148861 4.31 - 4.90: 256473 Nonbonded interactions: 563879 Sorted by model distance: nonbonded pdb="MG MG h 602 " pdb=" F1 AF3 h 603 " model vdw 1.934 2.120 nonbonded pdb="MG MG z 602 " pdb=" F1 AF3 z 603 " model vdw 1.940 2.120 nonbonded pdb=" O1A ADP z 601 " pdb="MG MG z 602 " model vdw 1.946 2.170 nonbonded pdb=" O3A ADP B 601 " pdb="MG MG B 602 " model vdw 1.953 2.170 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.962 2.120 ... (remaining 563874 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: 0.060 Extract box with map and model: 2.260 Check model and map are aligned: 0.410 Set scattering table: 0.490 Process input model: 130.510 Find NCS groups from input model: 6.180 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:11.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 154.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8674 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.161 68506 Z= 0.292 Angle : 0.549 12.572 92496 Z= 0.272 Chirality : 0.041 0.203 11003 Planarity : 0.003 0.049 11814 Dihedral : 14.209 177.469 25963 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 8760 helix: 2.29 (0.08), residues: 4470 sheet: 0.15 (0.16), residues: 1157 loop : -0.42 (0.11), residues: 3133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP P 66 HIS 0.012 0.001 HIS Z 161 PHE 0.026 0.001 PHE P 136 TYR 0.022 0.001 TYR q 132 ARG 0.007 0.000 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 634 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 634 time to evaluate : 6.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: N 225 GLU cc_start: 0.8368 (tp30) cc_final: 0.8116 (mm-30) REVERT: N 228 GLN cc_start: 0.8687 (mp10) cc_final: 0.8433 (mp10) REVERT: N 259 CYS cc_start: 0.8515 (m) cc_final: 0.7946 (m) REVERT: A 293 ASP cc_start: 0.8091 (m-30) cc_final: 0.7854 (m-30) REVERT: B 160 MET cc_start: 0.9138 (mmm) cc_final: 0.8867 (mmt) REVERT: D 399 GLU cc_start: 0.7928 (mp0) cc_final: 0.7590 (mp0) REVERT: D 429 GLU cc_start: 0.8796 (mp0) cc_final: 0.8460 (mp0) REVERT: G 15 LYS cc_start: 0.8786 (mmmt) cc_final: 0.8551 (mmpt) REVERT: H 524 ARG cc_start: 0.7162 (tpm170) cc_final: 0.6815 (tpm170) REVERT: Z 66 GLU cc_start: 0.7923 (mp0) cc_final: 0.7665 (mp0) REVERT: Z 86 ASP cc_start: 0.8333 (m-30) cc_final: 0.8098 (m-30) REVERT: Z 415 GLU cc_start: 0.8325 (mp0) cc_final: 0.8040 (mp0) REVERT: d 60 MET cc_start: 0.9248 (ttp) cc_final: 0.8992 (ttp) REVERT: e 61 MET cc_start: 0.9243 (mmm) cc_final: 0.8819 (mmm) REVERT: g 12 GLN cc_start: 0.8429 (mp10) cc_final: 0.8095 (mp10) REVERT: g 415 GLU cc_start: 0.8353 (mp0) cc_final: 0.8002 (mp0) REVERT: h 81 ASP cc_start: 0.8214 (m-30) cc_final: 0.7542 (m-30) REVERT: h 324 MET cc_start: 0.9274 (mmm) cc_final: 0.9012 (mmm) REVERT: q 41 GLN cc_start: 0.8432 (tp40) cc_final: 0.7870 (tp-100) REVERT: P 84 MET cc_start: 0.7117 (ttt) cc_final: 0.6636 (tmm) REVERT: P 86 ARG cc_start: 0.8019 (tpm170) cc_final: 0.7294 (tpm170) REVERT: P 145 MET cc_start: 0.8809 (ptp) cc_final: 0.8453 (mpp) REVERT: P 230 ARG cc_start: 0.8388 (ptm-80) cc_final: 0.8141 (ppp80) outliers start: 0 outliers final: 2 residues processed: 634 average time/residue: 1.5580 time to fit residues: 1284.9006 Evaluate side-chains 490 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 488 time to evaluate : 6.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 282 ILE Chi-restraints excluded: chain Z residue 183 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 736 optimal weight: 5.9990 chunk 660 optimal weight: 5.9990 chunk 366 optimal weight: 9.9990 chunk 225 optimal weight: 4.9990 chunk 445 optimal weight: 0.9980 chunk 353 optimal weight: 9.9990 chunk 683 optimal weight: 2.9990 chunk 264 optimal weight: 1.9990 chunk 415 optimal weight: 6.9990 chunk 508 optimal weight: 9.9990 chunk 791 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 469 HIS D 235 ASN E 435 GLN G 73 GLN G 111 HIS Z 84 GLN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 453 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** e 435 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** e 516 GLN g 526 HIS q 316 ASN z 65 HIS z 84 GLN z 161 HIS z 382 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 151 GLN ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.067746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.055406 restraints weight = 181970.966| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.89 r_work: 0.2544 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2549 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2549 r_free = 0.2549 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2549 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8776 moved from start: 0.0833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 68506 Z= 0.302 Angle : 0.596 10.581 92496 Z= 0.298 Chirality : 0.043 0.172 11003 Planarity : 0.003 0.052 11814 Dihedral : 7.814 174.389 9517 Min Nonbonded Distance : 1.830 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 0.83 % Allowed : 6.63 % Favored : 92.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 8760 helix: 2.27 (0.08), residues: 4521 sheet: 0.16 (0.16), residues: 1119 loop : -0.53 (0.11), residues: 3120 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP N 266 HIS 0.013 0.001 HIS Z 161 PHE 0.015 0.001 PHE a 167 TYR 0.021 0.001 TYR G 437 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 599 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 538 time to evaluate : 6.377 Fit side-chains REVERT: N 228 GLN cc_start: 0.8871 (mp10) cc_final: 0.8491 (mp10) REVERT: N 259 CYS cc_start: 0.8542 (m) cc_final: 0.8147 (m) REVERT: A 293 ASP cc_start: 0.8336 (m-30) cc_final: 0.7734 (m-30) REVERT: A 354 GLU cc_start: 0.8721 (tp30) cc_final: 0.8345 (tp30) REVERT: B 160 MET cc_start: 0.9255 (mmm) cc_final: 0.9040 (mmt) REVERT: D 67 ASP cc_start: 0.8855 (m-30) cc_final: 0.8442 (m-30) REVERT: D 399 GLU cc_start: 0.8297 (mp0) cc_final: 0.8004 (mp0) REVERT: D 429 GLU cc_start: 0.9178 (mp0) cc_final: 0.8806 (mp0) REVERT: G 17 GLU cc_start: 0.8427 (OUTLIER) cc_final: 0.7714 (mp0) REVERT: G 47 MET cc_start: 0.9255 (mtm) cc_final: 0.8914 (mtp) REVERT: Z 66 GLU cc_start: 0.8375 (mp0) cc_final: 0.7597 (mp0) REVERT: Z 86 ASP cc_start: 0.8816 (m-30) cc_final: 0.8579 (m-30) REVERT: Z 143 MET cc_start: 0.8135 (OUTLIER) cc_final: 0.7848 (mtp) REVERT: Z 161 HIS cc_start: 0.7705 (OUTLIER) cc_final: 0.7265 (t-170) REVERT: d 307 ASP cc_start: 0.8602 (t0) cc_final: 0.8393 (t0) REVERT: e 21 ASP cc_start: 0.9116 (OUTLIER) cc_final: 0.8860 (t0) REVERT: e 61 MET cc_start: 0.9492 (mmm) cc_final: 0.9146 (mmm) REVERT: e 199 MET cc_start: 0.7301 (tmm) cc_final: 0.7079 (tmm) REVERT: e 460 MET cc_start: 0.9189 (OUTLIER) cc_final: 0.8648 (mmm) REVERT: e 474 MET cc_start: 0.9240 (OUTLIER) cc_final: 0.8657 (ttm) REVERT: g 12 GLN cc_start: 0.8660 (mp10) cc_final: 0.8299 (mp10) REVERT: g 47 MET cc_start: 0.9169 (OUTLIER) cc_final: 0.8382 (mtp) REVERT: g 152 MET cc_start: 0.9418 (mmm) cc_final: 0.9176 (mmm) REVERT: g 415 GLU cc_start: 0.8844 (mp0) cc_final: 0.8554 (mp0) REVERT: h 81 ASP cc_start: 0.8707 (m-30) cc_final: 0.8065 (m-30) REVERT: h 185 MET cc_start: 0.8572 (mtm) cc_final: 0.8259 (mtm) REVERT: h 324 MET cc_start: 0.9496 (mmm) cc_final: 0.9180 (mmm) REVERT: q 41 GLN cc_start: 0.8830 (tp40) cc_final: 0.8225 (tp-100) REVERT: z 244 VAL cc_start: 0.8546 (OUTLIER) cc_final: 0.8239 (t) REVERT: P 64 ASN cc_start: 0.8443 (p0) cc_final: 0.8044 (p0) REVERT: P 77 ARG cc_start: 0.5210 (ptt-90) cc_final: 0.4998 (ptt180) REVERT: P 145 MET cc_start: 0.8736 (ptp) cc_final: 0.8351 (mpp) outliers start: 61 outliers final: 17 residues processed: 560 average time/residue: 1.4917 time to fit residues: 1096.9209 Evaluate side-chains 520 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 495 time to evaluate : 6.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 244 ASP Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 68 VAL Chi-restraints excluded: chain e residue 460 MET Chi-restraints excluded: chain e residue 474 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain q residue 316 ASN Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 44 optimal weight: 9.9990 chunk 424 optimal weight: 10.0000 chunk 216 optimal weight: 3.9990 chunk 803 optimal weight: 4.9990 chunk 191 optimal weight: 5.9990 chunk 333 optimal weight: 10.0000 chunk 843 optimal weight: 5.9990 chunk 229 optimal weight: 6.9990 chunk 592 optimal weight: 8.9990 chunk 572 optimal weight: 20.0000 chunk 440 optimal weight: 0.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 28 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 250 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS z 218 HIS ** P 56 ASN ** 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 = 0.2934 r_free = 0.2934 target = 0.066801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2669 r_free = 0.2669 target = 0.054463 restraints weight = 186266.007| |-----------------------------------------------------------------------------| r_work (start): 0.2664 rms_B_bonded: 2.90 r_work: 0.2520 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2520 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2521 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2521 r_free = 0.2521 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2521 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8796 moved from start: 0.1012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 68506 Z= 0.369 Angle : 0.606 9.526 92496 Z= 0.301 Chirality : 0.044 0.171 11003 Planarity : 0.003 0.055 11814 Dihedral : 7.689 177.036 9513 Min Nonbonded Distance : 1.834 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 1.08 % Allowed : 8.37 % Favored : 90.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 8760 helix: 2.26 (0.08), residues: 4523 sheet: 0.06 (0.16), residues: 1112 loop : -0.59 (0.11), residues: 3125 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP e 304 HIS 0.014 0.001 HIS Z 161 PHE 0.018 0.001 PHE A 167 TYR 0.024 0.001 TYR A 181 ARG 0.012 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 79 poor density : 512 time to evaluate : 6.449 Fit side-chains revert: symmetry clash REVERT: N 208 MET cc_start: 0.8539 (pmt) cc_final: 0.8266 (pmm) REVERT: N 228 GLN cc_start: 0.8901 (mp10) cc_final: 0.8095 (mp10) REVERT: N 259 CYS cc_start: 0.8836 (m) cc_final: 0.8374 (m) REVERT: A 203 ARG cc_start: 0.8605 (OUTLIER) cc_final: 0.7884 (mmm-85) REVERT: A 354 GLU cc_start: 0.8729 (tp30) cc_final: 0.8437 (tp30) REVERT: B 160 MET cc_start: 0.9263 (mmm) cc_final: 0.9029 (mmt) REVERT: D 429 GLU cc_start: 0.9177 (mp0) cc_final: 0.8839 (mp0) REVERT: E 29 MET cc_start: 0.8569 (mmm) cc_final: 0.8364 (mmm) REVERT: E 533 ILE cc_start: 0.9176 (mm) cc_final: 0.8920 (mm) REVERT: G 17 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7737 (mp0) REVERT: G 47 MET cc_start: 0.9259 (OUTLIER) cc_final: 0.8885 (mtp) REVERT: H 160 MET cc_start: 0.9287 (mtp) cc_final: 0.9060 (mtp) REVERT: Z 66 GLU cc_start: 0.8440 (mp0) cc_final: 0.8162 (mm-30) REVERT: Z 86 ASP cc_start: 0.8851 (m-30) cc_final: 0.8574 (m-30) REVERT: Z 143 MET cc_start: 0.8202 (OUTLIER) cc_final: 0.7937 (mmm) REVERT: Z 161 HIS cc_start: 0.7842 (OUTLIER) cc_final: 0.7440 (t-170) REVERT: b 195 ASN cc_start: 0.9233 (OUTLIER) cc_final: 0.8987 (p0) REVERT: b 414 GLU cc_start: 0.9081 (mp0) cc_final: 0.8317 (mp0) REVERT: d 48 ILE cc_start: 0.9180 (OUTLIER) cc_final: 0.8896 (pp) REVERT: d 307 ASP cc_start: 0.8696 (t0) cc_final: 0.8476 (t0) REVERT: e 21 ASP cc_start: 0.9159 (OUTLIER) cc_final: 0.8934 (t0) REVERT: e 61 MET cc_start: 0.9518 (mmm) cc_final: 0.9267 (mmm) REVERT: e 474 MET cc_start: 0.9276 (OUTLIER) cc_final: 0.8841 (ttm) REVERT: g 12 GLN cc_start: 0.8639 (mp10) cc_final: 0.8275 (mp10) REVERT: g 47 MET cc_start: 0.9155 (OUTLIER) cc_final: 0.8308 (mtp) REVERT: g 152 MET cc_start: 0.9411 (mmm) cc_final: 0.9145 (mmm) REVERT: g 415 GLU cc_start: 0.8929 (mp0) cc_final: 0.8641 (mp0) REVERT: g 528 LYS cc_start: 0.9017 (tmtt) cc_final: 0.8782 (tmmt) REVERT: h 7 ILE cc_start: 0.8527 (OUTLIER) cc_final: 0.8259 (pp) REVERT: h 11 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8798 (mp0) REVERT: h 81 ASP cc_start: 0.8716 (m-30) cc_final: 0.8073 (m-30) REVERT: h 160 MET cc_start: 0.9128 (mtp) cc_final: 0.8876 (mtm) REVERT: h 185 MET cc_start: 0.8623 (mtm) cc_final: 0.8319 (mtm) REVERT: h 227 MET cc_start: 0.9362 (OUTLIER) cc_final: 0.8981 (mtp) REVERT: h 324 MET cc_start: 0.9491 (mmm) cc_final: 0.9197 (mmm) REVERT: q 41 GLN cc_start: 0.8855 (tp40) cc_final: 0.8267 (tp-100) REVERT: q 65 VAL cc_start: 0.9042 (OUTLIER) cc_final: 0.8804 (m) REVERT: z 351 TYR cc_start: 0.9083 (p90) cc_final: 0.8712 (p90) REVERT: z 364 GLU cc_start: 0.9005 (mt-10) cc_final: 0.8681 (mt-10) REVERT: P 77 ARG cc_start: 0.5197 (ptt-90) cc_final: 0.4968 (ptt180) REVERT: P 86 ARG cc_start: 0.8304 (tpm170) cc_final: 0.7408 (tpm170) REVERT: P 145 MET cc_start: 0.8771 (ptp) cc_final: 0.8371 (mpp) outliers start: 79 outliers final: 26 residues processed: 553 average time/residue: 1.5524 time to fit residues: 1122.8131 Evaluate side-chains 536 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 497 time to evaluate : 6.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 143 MET Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 474 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 227 MET Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 246 SER Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 476 optimal weight: 20.0000 chunk 714 optimal weight: 8.9990 chunk 407 optimal weight: 8.9990 chunk 136 optimal weight: 1.9990 chunk 34 optimal weight: 4.9990 chunk 207 optimal weight: 0.9990 chunk 771 optimal weight: 0.6980 chunk 497 optimal weight: 6.9990 chunk 89 optimal weight: 3.9990 chunk 108 optimal weight: 6.9990 chunk 15 optimal weight: 7.9990 overall best weight: 2.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 23 ASN ** Z 161 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 250 GLN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.068381 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2709 r_free = 0.2709 target = 0.056716 restraints weight = 174506.570| |-----------------------------------------------------------------------------| r_work (start): 0.2692 rms_B_bonded: 2.75 r_work: 0.2554 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2556 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2556 r_free = 0.2556 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2556 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8771 moved from start: 0.1086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 68506 Z= 0.235 Angle : 0.560 10.104 92496 Z= 0.276 Chirality : 0.042 0.172 11003 Planarity : 0.003 0.053 11814 Dihedral : 7.488 178.858 9513 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.55 % Favored : 96.45 % Rotamer: Outliers : 1.02 % Allowed : 9.82 % Favored : 89.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 8760 helix: 2.34 (0.08), residues: 4518 sheet: 0.04 (0.16), residues: 1111 loop : -0.57 (0.11), residues: 3131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP G 168 HIS 0.014 0.001 HIS z 161 PHE 0.015 0.001 PHE P 158 TYR 0.021 0.001 TYR A 181 ARG 0.012 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 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: 75 poor density : 525 time to evaluate : 6.468 Fit side-chains REVERT: N 208 MET cc_start: 0.8595 (pmt) cc_final: 0.8319 (pmm) REVERT: N 228 GLN cc_start: 0.8907 (mp10) cc_final: 0.8559 (mp10) REVERT: N 259 CYS cc_start: 0.8673 (m) cc_final: 0.8104 (m) REVERT: A 203 ARG cc_start: 0.8630 (OUTLIER) cc_final: 0.7910 (mmm-85) REVERT: A 344 MET cc_start: 0.9287 (mpp) cc_final: 0.8866 (mmm) REVERT: A 354 GLU cc_start: 0.8738 (tp30) cc_final: 0.8406 (tp30) REVERT: D 429 GLU cc_start: 0.9162 (mp0) cc_final: 0.8840 (mp0) REVERT: G 17 GLU cc_start: 0.8424 (OUTLIER) cc_final: 0.7721 (mp0) REVERT: G 47 MET cc_start: 0.9222 (OUTLIER) cc_final: 0.8876 (mtp) REVERT: H 1 MET cc_start: 0.6114 (mmm) cc_final: 0.5851 (tpp) REVERT: H 22 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.9005 (tp) REVERT: H 524 ARG cc_start: 0.7633 (tpm170) cc_final: 0.7292 (tpm170) REVERT: Z 86 ASP cc_start: 0.8758 (m-30) cc_final: 0.8506 (m-30) REVERT: Z 161 HIS cc_start: 0.7712 (OUTLIER) cc_final: 0.7287 (t-170) REVERT: b 195 ASN cc_start: 0.9306 (OUTLIER) cc_final: 0.9091 (p0) REVERT: d 48 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8703 (pp) REVERT: d 307 ASP cc_start: 0.8722 (t0) cc_final: 0.8501 (t0) REVERT: e 21 ASP cc_start: 0.9160 (OUTLIER) cc_final: 0.8920 (t0) REVERT: g 12 GLN cc_start: 0.8635 (mp10) cc_final: 0.8267 (mp10) REVERT: g 47 MET cc_start: 0.9095 (OUTLIER) cc_final: 0.8270 (mtp) REVERT: g 59 MET cc_start: 0.9239 (ttm) cc_final: 0.8959 (ttp) REVERT: g 152 MET cc_start: 0.9410 (mmm) cc_final: 0.9157 (mmm) REVERT: g 415 GLU cc_start: 0.8942 (mp0) cc_final: 0.8680 (mp0) REVERT: g 528 LYS cc_start: 0.9000 (tmtt) cc_final: 0.8777 (tmmt) REVERT: h 7 ILE cc_start: 0.8593 (OUTLIER) cc_final: 0.8234 (pp) REVERT: h 11 GLU cc_start: 0.9155 (mm-30) cc_final: 0.8755 (mp0) REVERT: h 81 ASP cc_start: 0.8700 (m-30) cc_final: 0.8056 (m-30) REVERT: h 185 MET cc_start: 0.8599 (mtm) cc_final: 0.8349 (mtm) REVERT: h 324 MET cc_start: 0.9480 (mmm) cc_final: 0.9191 (mmm) REVERT: q 41 GLN cc_start: 0.8846 (tp40) cc_final: 0.8273 (tp-100) REVERT: z 244 VAL cc_start: 0.8539 (OUTLIER) cc_final: 0.8221 (t) REVERT: z 351 TYR cc_start: 0.9048 (p90) cc_final: 0.8641 (p90) REVERT: z 364 GLU cc_start: 0.8961 (mt-10) cc_final: 0.8649 (mt-10) REVERT: P 77 ARG cc_start: 0.5201 (ptt-90) cc_final: 0.4938 (ptt180) REVERT: P 86 ARG cc_start: 0.8186 (tpm170) cc_final: 0.7375 (tpm170) REVERT: P 145 MET cc_start: 0.8817 (ptp) cc_final: 0.8440 (mpp) REVERT: P 149 ARG cc_start: 0.8308 (ptt-90) cc_final: 0.7975 (ptt-90) outliers start: 75 outliers final: 30 residues processed: 569 average time/residue: 1.5288 time to fit residues: 1153.0112 Evaluate side-chains 531 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 490 time to evaluate : 6.381 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 488 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 34 LEU Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain H residue 22 LEU Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain d residue 48 ILE Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 374 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 84 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 378 optimal weight: 5.9990 chunk 150 optimal weight: 9.9990 chunk 221 optimal weight: 3.9990 chunk 536 optimal weight: 10.0000 chunk 262 optimal weight: 7.9990 chunk 472 optimal weight: 10.0000 chunk 777 optimal weight: 0.5980 chunk 17 optimal weight: 9.9990 chunk 600 optimal weight: 2.9990 chunk 838 optimal weight: 0.8980 chunk 800 optimal weight: 2.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 475 GLN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** q 53 ASN z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2966 r_free = 0.2966 target = 0.068384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2711 r_free = 0.2711 target = 0.056284 restraints weight = 164334.232| |-----------------------------------------------------------------------------| r_work (start): 0.2699 rms_B_bonded: 2.74 r_work: 0.2562 rms_B_bonded: 3.21 restraints_weight: 0.5000 r_work (final): 0.2562 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2569 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2569 r_free = 0.2569 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2569 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8764 moved from start: 0.1177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 68506 Z= 0.220 Angle : 0.554 11.246 92496 Z= 0.272 Chirality : 0.042 0.176 11003 Planarity : 0.003 0.053 11814 Dihedral : 7.347 179.904 9513 Min Nonbonded Distance : 1.863 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.28 % Allowed : 10.80 % Favored : 87.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.09), residues: 8760 helix: 2.39 (0.08), residues: 4520 sheet: 0.04 (0.16), residues: 1106 loop : -0.54 (0.11), residues: 3134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP P 66 HIS 0.013 0.001 HIS Z 161 PHE 0.018 0.001 PHE a 167 TYR 0.020 0.001 TYR A 181 ARG 0.013 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 94 poor density : 519 time to evaluate : 6.546 Fit side-chains REVERT: N 208 MET cc_start: 0.8571 (pmt) cc_final: 0.8344 (pmm) REVERT: N 223 ASP cc_start: 0.8672 (t70) cc_final: 0.8245 (t0) REVERT: N 228 GLN cc_start: 0.8942 (mp10) cc_final: 0.8603 (mp10) REVERT: N 259 CYS cc_start: 0.8568 (m) cc_final: 0.7987 (m) REVERT: A 203 ARG cc_start: 0.8700 (OUTLIER) cc_final: 0.7961 (mmm-85) REVERT: A 354 GLU cc_start: 0.8742 (tp30) cc_final: 0.8396 (tp30) REVERT: B 160 MET cc_start: 0.9237 (mmt) cc_final: 0.9004 (mmt) REVERT: D 429 GLU cc_start: 0.9142 (mp0) cc_final: 0.8818 (mp0) REVERT: E 29 MET cc_start: 0.8518 (mmm) cc_final: 0.8310 (mmm) REVERT: E 121 GLU cc_start: 0.8852 (tt0) cc_final: 0.8412 (tp30) REVERT: G 17 GLU cc_start: 0.8426 (OUTLIER) cc_final: 0.7719 (mp0) REVERT: G 47 MET cc_start: 0.9218 (OUTLIER) cc_final: 0.8855 (mtp) REVERT: H 160 MET cc_start: 0.9264 (mtp) cc_final: 0.9020 (mtp) REVERT: H 455 PHE cc_start: 0.7789 (m-10) cc_final: 0.7531 (m-10) REVERT: Q 357 ASP cc_start: 0.8599 (t70) cc_final: 0.8236 (t0) REVERT: b 195 ASN cc_start: 0.9302 (OUTLIER) cc_final: 0.9060 (p0) REVERT: d 307 ASP cc_start: 0.8727 (t0) cc_final: 0.8489 (t0) REVERT: e 21 ASP cc_start: 0.9157 (OUTLIER) cc_final: 0.8942 (t0) REVERT: e 474 MET cc_start: 0.9245 (tmm) cc_final: 0.8656 (ttm) REVERT: g 12 GLN cc_start: 0.8645 (mp10) cc_final: 0.8275 (mp10) REVERT: g 47 MET cc_start: 0.9103 (OUTLIER) cc_final: 0.8303 (mtp) REVERT: g 59 MET cc_start: 0.9249 (ttm) cc_final: 0.9009 (ttp) REVERT: g 152 MET cc_start: 0.9418 (mmm) cc_final: 0.9154 (mmm) REVERT: g 415 GLU cc_start: 0.8961 (mp0) cc_final: 0.8721 (mp0) REVERT: g 528 LYS cc_start: 0.9006 (tmtt) cc_final: 0.8769 (tmmt) REVERT: h 7 ILE cc_start: 0.8571 (OUTLIER) cc_final: 0.8203 (pp) REVERT: h 11 GLU cc_start: 0.9166 (mm-30) cc_final: 0.8785 (mp0) REVERT: h 81 ASP cc_start: 0.8721 (m-30) cc_final: 0.8087 (m-30) REVERT: h 185 MET cc_start: 0.8588 (mtm) cc_final: 0.8332 (mtm) REVERT: h 324 MET cc_start: 0.9480 (mmm) cc_final: 0.9183 (mmm) REVERT: q 41 GLN cc_start: 0.8863 (tp40) cc_final: 0.8308 (tp-100) REVERT: q 65 VAL cc_start: 0.9108 (OUTLIER) cc_final: 0.8888 (m) REVERT: z 244 VAL cc_start: 0.8519 (OUTLIER) cc_final: 0.8204 (t) REVERT: z 351 TYR cc_start: 0.9017 (p90) cc_final: 0.8627 (p90) REVERT: z 364 GLU cc_start: 0.8931 (mt-10) cc_final: 0.8599 (mt-10) REVERT: z 415 GLU cc_start: 0.9057 (mp0) cc_final: 0.8806 (mp0) REVERT: P 77 ARG cc_start: 0.5137 (ptt-90) cc_final: 0.4825 (ptt180) REVERT: P 86 ARG cc_start: 0.8270 (tpm170) cc_final: 0.7393 (tpm170) REVERT: P 145 MET cc_start: 0.8781 (ptp) cc_final: 0.8477 (mpp) outliers start: 94 outliers final: 34 residues processed: 574 average time/residue: 1.4494 time to fit residues: 1103.6239 Evaluate side-chains 540 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 497 time to evaluate : 6.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 195 ASN Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 65 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 801 optimal weight: 4.9990 chunk 697 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 435 optimal weight: 3.9990 chunk 77 optimal weight: 4.9990 chunk 355 optimal weight: 0.9990 chunk 57 optimal weight: 9.9990 chunk 727 optimal weight: 0.9990 chunk 361 optimal weight: 10.0000 chunk 527 optimal weight: 4.9990 chunk 347 optimal weight: 8.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 501 ASN z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.067638 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2695 r_free = 0.2695 target = 0.055480 restraints weight = 168429.394| |-----------------------------------------------------------------------------| r_work (start): 0.2689 rms_B_bonded: 2.77 r_work: 0.2554 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.2554 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2555 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2555 r_free = 0.2555 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2555 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 68506 Z= 0.280 Angle : 0.578 13.033 92496 Z= 0.283 Chirality : 0.042 0.168 11003 Planarity : 0.003 0.053 11814 Dihedral : 7.296 176.850 9513 Min Nonbonded Distance : 1.837 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.30 % Allowed : 11.56 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 1.58 (0.09), residues: 8760 helix: 2.39 (0.08), residues: 4526 sheet: 0.01 (0.16), residues: 1112 loop : -0.57 (0.11), residues: 3122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP N 266 HIS 0.014 0.001 HIS Z 161 PHE 0.015 0.001 PHE a 167 TYR 0.021 0.001 TYR B 456 ARG 0.011 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 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: 95 poor density : 502 time to evaluate : 6.476 Fit side-chains revert: symmetry clash REVERT: N 208 MET cc_start: 0.8623 (pmt) cc_final: 0.8364 (pmm) REVERT: N 223 ASP cc_start: 0.8734 (t70) cc_final: 0.8128 (t0) REVERT: N 228 GLN cc_start: 0.8982 (mp10) cc_final: 0.8627 (mp10) REVERT: N 259 CYS cc_start: 0.8580 (m) cc_final: 0.8012 (m) REVERT: A 156 MET cc_start: 0.8907 (OUTLIER) cc_final: 0.8566 (mtp) REVERT: A 164 ASN cc_start: 0.7273 (m110) cc_final: 0.6975 (m-40) REVERT: A 203 ARG cc_start: 0.8736 (OUTLIER) cc_final: 0.7986 (mmm-85) REVERT: A 344 MET cc_start: 0.9294 (mpp) cc_final: 0.8869 (mmm) REVERT: A 354 GLU cc_start: 0.8725 (tp30) cc_final: 0.8370 (tp30) REVERT: B 160 MET cc_start: 0.9213 (mmt) cc_final: 0.8947 (mmt) REVERT: D 429 GLU cc_start: 0.9130 (mp0) cc_final: 0.8811 (mp0) REVERT: E 121 GLU cc_start: 0.8875 (tt0) cc_final: 0.8405 (tp30) REVERT: G 17 GLU cc_start: 0.8413 (OUTLIER) cc_final: 0.7697 (mp0) REVERT: G 47 MET cc_start: 0.9219 (OUTLIER) cc_final: 0.8853 (mtp) REVERT: H 160 MET cc_start: 0.9270 (mtp) cc_final: 0.9012 (mtp) REVERT: H 455 PHE cc_start: 0.7867 (m-10) cc_final: 0.7563 (m-10) REVERT: Q 357 ASP cc_start: 0.8555 (t70) cc_final: 0.8213 (t0) REVERT: Z 86 ASP cc_start: 0.8778 (m-30) cc_final: 0.8513 (m-30) REVERT: d 307 ASP cc_start: 0.8742 (t0) cc_final: 0.8493 (t0) REVERT: e 21 ASP cc_start: 0.9173 (OUTLIER) cc_final: 0.8958 (t0) REVERT: e 67 ASP cc_start: 0.8877 (m-30) cc_final: 0.8566 (m-30) REVERT: e 474 MET cc_start: 0.9257 (tmm) cc_final: 0.8715 (ttm) REVERT: e 526 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8874 (ttm) REVERT: g 12 GLN cc_start: 0.8641 (mp10) cc_final: 0.8254 (mp10) REVERT: g 47 MET cc_start: 0.9108 (OUTLIER) cc_final: 0.8301 (mtp) REVERT: g 59 MET cc_start: 0.9248 (ttm) cc_final: 0.8962 (ttp) REVERT: g 152 MET cc_start: 0.9425 (mmm) cc_final: 0.9150 (mmm) REVERT: g 415 GLU cc_start: 0.9001 (mp0) cc_final: 0.8688 (mp0) REVERT: g 528 LYS cc_start: 0.9019 (tmtt) cc_final: 0.8779 (tmmt) REVERT: h 7 ILE cc_start: 0.8621 (OUTLIER) cc_final: 0.8274 (pp) REVERT: h 11 GLU cc_start: 0.9175 (mm-30) cc_final: 0.8821 (mp0) REVERT: h 81 ASP cc_start: 0.8693 (m-30) cc_final: 0.8042 (m-30) REVERT: h 185 MET cc_start: 0.8607 (mtm) cc_final: 0.8376 (mtm) REVERT: h 324 MET cc_start: 0.9472 (mmm) cc_final: 0.9182 (mmm) REVERT: q 41 GLN cc_start: 0.8860 (tp40) cc_final: 0.8297 (tp-100) REVERT: z 244 VAL cc_start: 0.8542 (OUTLIER) cc_final: 0.8225 (t) REVERT: z 351 TYR cc_start: 0.9024 (p90) cc_final: 0.8640 (p90) REVERT: z 364 GLU cc_start: 0.8940 (mt-10) cc_final: 0.8611 (mt-10) REVERT: P 86 ARG cc_start: 0.8281 (tpm170) cc_final: 0.7367 (tpm170) REVERT: P 145 MET cc_start: 0.8790 (ptp) cc_final: 0.8500 (mpp) REVERT: P 149 ARG cc_start: 0.8354 (ptt-90) cc_final: 0.8113 (ptt-90) outliers start: 95 outliers final: 43 residues processed: 560 average time/residue: 1.4963 time to fit residues: 1109.4048 Evaluate side-chains 546 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 494 time to evaluate : 6.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 21 ASP Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 435 optimal weight: 6.9990 chunk 469 optimal weight: 0.8980 chunk 43 optimal weight: 5.9990 chunk 299 optimal weight: 9.9990 chunk 551 optimal weight: 10.0000 chunk 119 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 174 optimal weight: 6.9990 chunk 518 optimal weight: 9.9990 chunk 240 optimal weight: 6.9990 chunk 18 optimal weight: 0.0020 overall best weight: 3.5794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS Z 218 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.067315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.054904 restraints weight = 185788.650| |-----------------------------------------------------------------------------| r_work (start): 0.2672 rms_B_bonded: 2.93 r_work: 0.2529 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2529 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2532 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2532 r_free = 0.2532 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2532 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8799 moved from start: 0.1276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 68506 Z= 0.307 Angle : 0.591 14.002 92496 Z= 0.289 Chirality : 0.043 0.167 11003 Planarity : 0.003 0.052 11814 Dihedral : 7.260 173.863 9513 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 1.35 % Allowed : 12.03 % Favored : 86.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % 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: 8760 helix: 2.37 (0.08), residues: 4523 sheet: 0.01 (0.16), residues: 1107 loop : -0.58 (0.11), residues: 3130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP e 304 HIS 0.014 0.001 HIS Z 161 PHE 0.016 0.001 PHE P 158 TYR 0.020 0.001 TYR B 456 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 502 time to evaluate : 6.386 Fit side-chains REVERT: N 208 MET cc_start: 0.8700 (pmt) cc_final: 0.8422 (pmm) REVERT: N 223 ASP cc_start: 0.8774 (t70) cc_final: 0.8163 (t0) REVERT: N 228 GLN cc_start: 0.8962 (mp10) cc_final: 0.8221 (mp10) REVERT: N 259 CYS cc_start: 0.8570 (m) cc_final: 0.8025 (m) REVERT: A 156 MET cc_start: 0.8944 (OUTLIER) cc_final: 0.8637 (mtp) REVERT: A 164 ASN cc_start: 0.7307 (m110) cc_final: 0.7023 (m-40) REVERT: A 203 ARG cc_start: 0.8775 (OUTLIER) cc_final: 0.8000 (mmm-85) REVERT: A 344 MET cc_start: 0.9321 (mpp) cc_final: 0.8883 (mmm) REVERT: A 354 GLU cc_start: 0.8762 (tp30) cc_final: 0.8415 (tp30) REVERT: A 384 MET cc_start: 0.9263 (OUTLIER) cc_final: 0.9028 (ptt) REVERT: D 399 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8002 (mp0) REVERT: D 429 GLU cc_start: 0.9161 (mp0) cc_final: 0.8845 (mp0) REVERT: E 121 GLU cc_start: 0.8901 (tt0) cc_final: 0.8408 (tp30) REVERT: G 17 GLU cc_start: 0.8404 (OUTLIER) cc_final: 0.7801 (mp0) REVERT: G 47 MET cc_start: 0.9266 (OUTLIER) cc_final: 0.8901 (mtp) REVERT: G 152 MET cc_start: 0.9512 (OUTLIER) cc_final: 0.9246 (mmm) REVERT: H 160 MET cc_start: 0.9291 (mtp) cc_final: 0.9029 (mtp) REVERT: H 455 PHE cc_start: 0.7842 (m-10) cc_final: 0.7552 (m-10) REVERT: Q 357 ASP cc_start: 0.8595 (t70) cc_final: 0.8243 (t0) REVERT: d 307 ASP cc_start: 0.8764 (t0) cc_final: 0.8517 (t0) REVERT: e 67 ASP cc_start: 0.8822 (m-30) cc_final: 0.8497 (m-30) REVERT: e 474 MET cc_start: 0.9268 (tmm) cc_final: 0.8707 (ttm) REVERT: e 526 MET cc_start: 0.9207 (OUTLIER) cc_final: 0.8880 (ttm) REVERT: g 12 GLN cc_start: 0.8605 (mp10) cc_final: 0.8228 (mp10) REVERT: g 47 MET cc_start: 0.9087 (OUTLIER) cc_final: 0.8341 (mtp) REVERT: g 59 MET cc_start: 0.9264 (ttm) cc_final: 0.9002 (ttp) REVERT: g 152 MET cc_start: 0.9429 (mmm) cc_final: 0.9155 (mmm) REVERT: g 415 GLU cc_start: 0.9032 (mp0) cc_final: 0.8753 (mp0) REVERT: g 528 LYS cc_start: 0.9013 (tmtt) cc_final: 0.8768 (tmmt) REVERT: h 7 ILE cc_start: 0.8578 (OUTLIER) cc_final: 0.8342 (pp) REVERT: h 11 GLU cc_start: 0.9145 (mm-30) cc_final: 0.8821 (mp0) REVERT: h 81 ASP cc_start: 0.8722 (m-30) cc_final: 0.8086 (m-30) REVERT: h 185 MET cc_start: 0.8615 (mtm) cc_final: 0.8295 (mtm) REVERT: h 324 MET cc_start: 0.9469 (mmm) cc_final: 0.9186 (mmm) REVERT: z 244 VAL cc_start: 0.8553 (OUTLIER) cc_final: 0.8232 (t) REVERT: z 351 TYR cc_start: 0.9051 (p90) cc_final: 0.8670 (p90) REVERT: z 364 GLU cc_start: 0.8980 (mt-10) cc_final: 0.8658 (mt-10) REVERT: P 77 ARG cc_start: 0.5001 (ptt-90) cc_final: 0.4694 (ptt180) REVERT: P 86 ARG cc_start: 0.8270 (tpm170) cc_final: 0.7366 (tpm170) REVERT: P 145 MET cc_start: 0.8829 (ptp) cc_final: 0.8612 (mpp) outliers start: 99 outliers final: 50 residues processed: 562 average time/residue: 1.5152 time to fit residues: 1125.2294 Evaluate side-chains 551 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 491 time to evaluate : 6.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 253 THR Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 384 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 574 optimal weight: 7.9990 chunk 447 optimal weight: 7.9990 chunk 640 optimal weight: 3.9990 chunk 170 optimal weight: 0.9990 chunk 89 optimal weight: 5.9990 chunk 609 optimal weight: 3.9990 chunk 453 optimal weight: 6.9990 chunk 1 optimal weight: 7.9990 chunk 752 optimal weight: 2.9990 chunk 799 optimal weight: 1.9990 chunk 532 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS Z 161 HIS Z 218 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2954 r_free = 0.2954 target = 0.067818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2692 r_free = 0.2692 target = 0.055401 restraints weight = 185730.672| |-----------------------------------------------------------------------------| r_work (start): 0.2686 rms_B_bonded: 2.93 r_work: 0.2545 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.2545 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2545 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2545 r_free = 0.2545 target_work(ls_wunit_k1) = 0.049 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2545 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 68506 Z= 0.253 Angle : 0.577 14.737 92496 Z= 0.281 Chirality : 0.042 0.168 11003 Planarity : 0.003 0.053 11814 Dihedral : 7.145 172.382 9513 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 6.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.19 % Allowed : 12.61 % Favored : 86.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.09), residues: 8760 helix: 2.39 (0.08), residues: 4519 sheet: 0.02 (0.16), residues: 1104 loop : -0.56 (0.11), residues: 3137 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 0.014 0.001 PHE a 167 TYR 0.019 0.001 TYR Z 498 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 591 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 504 time to evaluate : 6.572 Fit side-chains REVERT: N 208 MET cc_start: 0.8714 (pmt) cc_final: 0.8396 (pmm) REVERT: N 228 GLN cc_start: 0.8956 (mp10) cc_final: 0.8561 (mp10) REVERT: N 259 CYS cc_start: 0.8637 (m) cc_final: 0.8018 (m) REVERT: A 156 MET cc_start: 0.8935 (OUTLIER) cc_final: 0.8648 (mtp) REVERT: A 164 ASN cc_start: 0.7262 (m110) cc_final: 0.6968 (m-40) REVERT: A 203 ARG cc_start: 0.8751 (OUTLIER) cc_final: 0.7997 (mmm-85) REVERT: A 344 MET cc_start: 0.9325 (mpp) cc_final: 0.8885 (mmm) REVERT: A 354 GLU cc_start: 0.8732 (tp30) cc_final: 0.8370 (tp30) REVERT: D 429 GLU cc_start: 0.9153 (mp0) cc_final: 0.8835 (mp0) REVERT: E 121 GLU cc_start: 0.8878 (tt0) cc_final: 0.8355 (tp30) REVERT: G 17 GLU cc_start: 0.8574 (OUTLIER) cc_final: 0.7731 (mp0) REVERT: G 47 MET cc_start: 0.9242 (OUTLIER) cc_final: 0.8756 (mtp) REVERT: G 152 MET cc_start: 0.9493 (OUTLIER) cc_final: 0.9253 (mmm) REVERT: H 160 MET cc_start: 0.9285 (mtp) cc_final: 0.9010 (mtp) REVERT: H 455 PHE cc_start: 0.7819 (m-10) cc_final: 0.7325 (m-10) REVERT: H 482 GLU cc_start: 0.9025 (OUTLIER) cc_final: 0.8478 (tp30) REVERT: Q 357 ASP cc_start: 0.8582 (t70) cc_final: 0.8247 (t0) REVERT: d 307 ASP cc_start: 0.8762 (t0) cc_final: 0.8502 (t0) REVERT: e 67 ASP cc_start: 0.8860 (m-30) cc_final: 0.8525 (m-30) REVERT: e 474 MET cc_start: 0.9230 (tmm) cc_final: 0.8682 (ttm) REVERT: e 526 MET cc_start: 0.9199 (OUTLIER) cc_final: 0.8868 (ttm) REVERT: g 12 GLN cc_start: 0.8632 (mp10) cc_final: 0.8248 (mp10) REVERT: g 47 MET cc_start: 0.9066 (OUTLIER) cc_final: 0.8275 (mtp) REVERT: g 59 MET cc_start: 0.9241 (ttm) cc_final: 0.8946 (ttp) REVERT: g 152 MET cc_start: 0.9416 (mmm) cc_final: 0.9152 (mmm) REVERT: g 415 GLU cc_start: 0.9017 (mp0) cc_final: 0.8741 (mp0) REVERT: g 528 LYS cc_start: 0.9004 (tmtt) cc_final: 0.8769 (tmmt) REVERT: h 7 ILE cc_start: 0.8538 (OUTLIER) cc_final: 0.8286 (pp) REVERT: h 11 GLU cc_start: 0.9161 (mm-30) cc_final: 0.8815 (mp0) REVERT: h 81 ASP cc_start: 0.8751 (m-30) cc_final: 0.8102 (m-30) REVERT: h 185 MET cc_start: 0.8576 (mtm) cc_final: 0.8266 (mtm) REVERT: h 324 MET cc_start: 0.9460 (mmm) cc_final: 0.9180 (mmm) REVERT: z 137 VAL cc_start: 0.9288 (OUTLIER) cc_final: 0.9063 (p) REVERT: z 244 VAL cc_start: 0.8529 (OUTLIER) cc_final: 0.8214 (t) REVERT: z 351 TYR cc_start: 0.9046 (p90) cc_final: 0.8655 (p90) REVERT: z 364 GLU cc_start: 0.8945 (mt-10) cc_final: 0.8620 (mt-10) REVERT: P 77 ARG cc_start: 0.4954 (ptt-90) cc_final: 0.4638 (ptt180) REVERT: P 86 ARG cc_start: 0.8204 (tpm170) cc_final: 0.7285 (tpm170) REVERT: P 145 MET cc_start: 0.8808 (ptp) cc_final: 0.8540 (mpp) outliers start: 87 outliers final: 50 residues processed: 561 average time/residue: 1.5348 time to fit residues: 1150.0970 Evaluate side-chains 552 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 61 poor density : 491 time to evaluate : 6.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain N residue 283 ASP Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain B residue 415 MET Chi-restraints excluded: chain D residue 95 SER Chi-restraints excluded: chain D residue 121 THR Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain E residue 533 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain G residue 480 VAL Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 482 GLU Chi-restraints excluded: chain H residue 497 MET Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 179 ILE Chi-restraints excluded: chain Z residue 331 VAL Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain e residue 81 MET Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 1 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 312 LEU Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 7 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 84 MET Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 529 optimal weight: 10.0000 chunk 418 optimal weight: 0.9980 chunk 402 optimal weight: 5.9990 chunk 326 optimal weight: 0.0370 chunk 404 optimal weight: 0.8980 chunk 524 optimal weight: 9.9990 chunk 265 optimal weight: 1.9990 chunk 756 optimal weight: 4.9990 chunk 612 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 259 optimal weight: 7.9990 overall best weight: 1.1862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 195 ASN ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 ASN z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.069741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2724 r_free = 0.2724 target = 0.056983 restraints weight = 205878.008| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 3.15 r_work: 0.2569 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2569 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2575 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2575 r_free = 0.2575 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2575 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8748 moved from start: 0.1412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.042 68506 Z= 0.155 Angle : 0.557 13.528 92496 Z= 0.270 Chirality : 0.041 0.169 11003 Planarity : 0.003 0.052 11814 Dihedral : 6.935 168.510 9513 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 0.91 % Allowed : 13.05 % Favored : 86.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 8760 helix: 2.47 (0.08), residues: 4517 sheet: 0.04 (0.16), residues: 1105 loop : -0.51 (0.11), residues: 3138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.017 0.001 PHE P 158 TYR 0.029 0.001 TYR D 24 ARG 0.008 0.000 ARG H 524 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 598 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 531 time to evaluate : 6.680 Fit side-chains REVERT: N 208 MET cc_start: 0.8678 (pmt) cc_final: 0.8413 (pmm) REVERT: N 223 ASP cc_start: 0.8705 (t70) cc_final: 0.8122 (t0) REVERT: N 228 GLN cc_start: 0.8991 (mp10) cc_final: 0.8640 (mp10) REVERT: N 259 CYS cc_start: 0.8629 (m) cc_final: 0.8008 (m) REVERT: A 156 MET cc_start: 0.8911 (OUTLIER) cc_final: 0.8634 (mtp) REVERT: A 164 ASN cc_start: 0.7061 (m110) cc_final: 0.6783 (m-40) REVERT: A 203 ARG cc_start: 0.8727 (OUTLIER) cc_final: 0.8038 (mmm-85) REVERT: A 344 MET cc_start: 0.9355 (mpp) cc_final: 0.8906 (mmm) REVERT: A 354 GLU cc_start: 0.8704 (tp30) cc_final: 0.8434 (tp30) REVERT: D 399 GLU cc_start: 0.8654 (mt-10) cc_final: 0.8284 (mp0) REVERT: D 429 GLU cc_start: 0.9133 (mp0) cc_final: 0.8820 (mp0) REVERT: E 121 GLU cc_start: 0.8858 (tt0) cc_final: 0.8327 (tp30) REVERT: G 17 GLU cc_start: 0.8425 (OUTLIER) cc_final: 0.7785 (mp0) REVERT: G 47 MET cc_start: 0.9236 (OUTLIER) cc_final: 0.8906 (mtp) REVERT: G 152 MET cc_start: 0.9469 (OUTLIER) cc_final: 0.9256 (mmm) REVERT: H 45 MET cc_start: 0.9306 (mmm) cc_final: 0.9105 (mmm) REVERT: H 160 MET cc_start: 0.9277 (mtp) cc_final: 0.8993 (mtp) REVERT: H 455 PHE cc_start: 0.7678 (m-10) cc_final: 0.7268 (m-10) REVERT: H 482 GLU cc_start: 0.9015 (OUTLIER) cc_final: 0.8506 (tp30) REVERT: H 524 ARG cc_start: 0.7383 (tpm170) cc_final: 0.7141 (tpm170) REVERT: Q 357 ASP cc_start: 0.8534 (t70) cc_final: 0.8285 (t0) REVERT: Z 66 GLU cc_start: 0.8667 (mm-30) cc_final: 0.8244 (mm-30) REVERT: d 307 ASP cc_start: 0.8765 (t0) cc_final: 0.8503 (t0) REVERT: e 67 ASP cc_start: 0.8859 (m-30) cc_final: 0.8520 (m-30) REVERT: e 474 MET cc_start: 0.9198 (tmm) cc_final: 0.8667 (ttm) REVERT: e 526 MET cc_start: 0.9220 (OUTLIER) cc_final: 0.8870 (ttm) REVERT: g 12 GLN cc_start: 0.8667 (mp10) cc_final: 0.8282 (mp10) REVERT: g 47 MET cc_start: 0.9026 (OUTLIER) cc_final: 0.8251 (mtp) REVERT: g 59 MET cc_start: 0.9235 (ttm) cc_final: 0.8996 (ttp) REVERT: g 415 GLU cc_start: 0.9060 (mp0) cc_final: 0.8761 (mp0) REVERT: g 437 TYR cc_start: 0.8969 (t80) cc_final: 0.8549 (t80) REVERT: g 528 LYS cc_start: 0.9009 (tmtt) cc_final: 0.8761 (tmmt) REVERT: h 7 ILE cc_start: 0.8591 (OUTLIER) cc_final: 0.8321 (pp) REVERT: h 11 GLU cc_start: 0.9207 (mm-30) cc_final: 0.8827 (mp0) REVERT: h 185 MET cc_start: 0.8552 (mtm) cc_final: 0.8341 (mtm) REVERT: h 187 ASP cc_start: 0.8249 (p0) cc_final: 0.7983 (p0) REVERT: h 324 MET cc_start: 0.9465 (mmm) cc_final: 0.9180 (mmm) REVERT: q 41 GLN cc_start: 0.8895 (tp40) cc_final: 0.8335 (tp-100) REVERT: z 137 VAL cc_start: 0.9252 (OUTLIER) cc_final: 0.9050 (p) REVERT: z 244 VAL cc_start: 0.8436 (OUTLIER) cc_final: 0.8120 (t) REVERT: P 77 ARG cc_start: 0.4588 (ptt-90) cc_final: 0.4269 (ptt180) REVERT: P 86 ARG cc_start: 0.8159 (tpm170) cc_final: 0.7249 (tpm170) outliers start: 67 outliers final: 38 residues processed: 578 average time/residue: 1.5146 time to fit residues: 1154.5897 Evaluate side-chains 558 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 509 time to evaluate : 6.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 216 ASP Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain E residue 23 ASP Chi-restraints excluded: chain E residue 91 MET Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 482 GLU Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 187 VAL Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain b residue 422 THR Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 635 optimal weight: 3.9990 chunk 604 optimal weight: 5.9990 chunk 90 optimal weight: 0.9980 chunk 239 optimal weight: 9.9990 chunk 266 optimal weight: 0.8980 chunk 406 optimal weight: 4.9990 chunk 59 optimal weight: 9.9990 chunk 251 optimal weight: 3.9990 chunk 659 optimal weight: 0.6980 chunk 731 optimal weight: 10.0000 chunk 80 optimal weight: 2.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** N 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 111 HIS H 501 ASN Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 8 ASN z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2981 r_free = 0.2981 target = 0.069202 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2718 r_free = 0.2718 target = 0.056659 restraints weight = 189217.285| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 3.02 r_work: 0.2566 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2566 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2570 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2570 r_free = 0.2570 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2570 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8754 moved from start: 0.1437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68506 Z= 0.199 Angle : 0.569 13.868 92496 Z= 0.275 Chirality : 0.041 0.174 11003 Planarity : 0.003 0.052 11814 Dihedral : 6.897 165.577 9513 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % Rotamer: Outliers : 0.82 % Allowed : 13.51 % Favored : 85.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.09), residues: 8760 helix: 2.49 (0.08), residues: 4516 sheet: 0.08 (0.16), residues: 1100 loop : -0.51 (0.11), residues: 3144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP N 222 HIS 0.016 0.001 HIS Z 161 PHE 0.014 0.001 PHE H 381 TYR 0.020 0.001 TYR z 498 ARG 0.009 0.000 ARG P 149 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17520 Ramachandran restraints generated. 8760 Oldfield, 0 Emsley, 8760 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 511 time to evaluate : 6.583 Fit side-chains REVERT: N 208 MET cc_start: 0.8676 (pmt) cc_final: 0.8389 (pmm) REVERT: N 223 ASP cc_start: 0.8696 (t70) cc_final: 0.8111 (t0) REVERT: N 228 GLN cc_start: 0.9008 (mp10) cc_final: 0.8665 (mp10) REVERT: N 259 CYS cc_start: 0.8643 (m) cc_final: 0.8018 (m) REVERT: A 156 MET cc_start: 0.8923 (OUTLIER) cc_final: 0.8600 (mtp) REVERT: A 164 ASN cc_start: 0.7010 (m110) cc_final: 0.6735 (m-40) REVERT: A 203 ARG cc_start: 0.8742 (OUTLIER) cc_final: 0.8012 (mmm-85) REVERT: A 344 MET cc_start: 0.9340 (mpp) cc_final: 0.8897 (mmm) REVERT: A 354 GLU cc_start: 0.8694 (tp30) cc_final: 0.8295 (tp30) REVERT: B 415 MET cc_start: 0.9362 (mmm) cc_final: 0.9159 (mmp) REVERT: D 399 GLU cc_start: 0.8657 (mt-10) cc_final: 0.8284 (mp0) REVERT: D 429 GLU cc_start: 0.9161 (mp0) cc_final: 0.8846 (mp0) REVERT: G 17 GLU cc_start: 0.8553 (OUTLIER) cc_final: 0.7794 (mp0) REVERT: G 47 MET cc_start: 0.9230 (OUTLIER) cc_final: 0.8892 (mtp) REVERT: G 152 MET cc_start: 0.9467 (OUTLIER) cc_final: 0.9256 (mmm) REVERT: H 160 MET cc_start: 0.9270 (mtp) cc_final: 0.8976 (mtp) REVERT: H 455 PHE cc_start: 0.7721 (m-10) cc_final: 0.7259 (m-10) REVERT: H 482 GLU cc_start: 0.9034 (OUTLIER) cc_final: 0.8498 (tp30) REVERT: H 524 ARG cc_start: 0.7291 (tpm170) cc_final: 0.7076 (tpm170) REVERT: Q 357 ASP cc_start: 0.8648 (t70) cc_final: 0.8297 (t0) REVERT: Z 66 GLU cc_start: 0.8661 (mm-30) cc_final: 0.8240 (mm-30) REVERT: d 307 ASP cc_start: 0.8762 (t0) cc_final: 0.8506 (t0) REVERT: e 67 ASP cc_start: 0.8839 (m-30) cc_final: 0.8493 (m-30) REVERT: e 474 MET cc_start: 0.9204 (tmm) cc_final: 0.8659 (ttm) REVERT: e 526 MET cc_start: 0.9237 (OUTLIER) cc_final: 0.8898 (ttm) REVERT: g 12 GLN cc_start: 0.8651 (mp10) cc_final: 0.8269 (mp10) REVERT: g 47 MET cc_start: 0.9011 (OUTLIER) cc_final: 0.8233 (mtp) REVERT: g 59 MET cc_start: 0.9246 (ttm) cc_final: 0.8997 (ttp) REVERT: g 82 GLU cc_start: 0.9158 (mm-30) cc_final: 0.8923 (tp30) REVERT: g 415 GLU cc_start: 0.9061 (mp0) cc_final: 0.8757 (mp0) REVERT: g 528 LYS cc_start: 0.8997 (tmtt) cc_final: 0.8742 (tmmt) REVERT: h 7 ILE cc_start: 0.8596 (OUTLIER) cc_final: 0.8342 (pp) REVERT: h 11 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8827 (mp0) REVERT: h 187 ASP cc_start: 0.8271 (p0) cc_final: 0.8028 (p0) REVERT: h 324 MET cc_start: 0.9469 (mmm) cc_final: 0.9185 (mmm) REVERT: q 41 GLN cc_start: 0.8882 (tp40) cc_final: 0.8319 (tp-100) REVERT: z 244 VAL cc_start: 0.8476 (OUTLIER) cc_final: 0.8162 (t) REVERT: z 357 GLU cc_start: 0.8524 (pt0) cc_final: 0.8279 (pm20) REVERT: P 77 ARG cc_start: 0.4592 (ptt-90) cc_final: 0.4269 (ptt180) REVERT: P 86 ARG cc_start: 0.8172 (tpm170) cc_final: 0.7266 (tpm170) REVERT: P 144 ARG cc_start: 0.8853 (mpp-170) cc_final: 0.8194 (mpp-170) REVERT: P 145 MET cc_start: 0.8312 (mpp) cc_final: 0.8030 (pmm) REVERT: P 148 MET cc_start: 0.8537 (tpt) cc_final: 0.8060 (mpp) outliers start: 60 outliers final: 36 residues processed: 549 average time/residue: 1.5178 time to fit residues: 1106.9615 Evaluate side-chains 550 residues out of total 7334 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 504 time to evaluate : 6.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 236 HIS Chi-restraints excluded: chain N residue 280 HIS Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 203 ARG Chi-restraints excluded: chain A residue 225 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 153 VAL Chi-restraints excluded: chain E residue 229 ILE Chi-restraints excluded: chain G residue 17 GLU Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 152 MET Chi-restraints excluded: chain H residue 143 VAL Chi-restraints excluded: chain H residue 482 GLU Chi-restraints excluded: chain Q residue 43 THR Chi-restraints excluded: chain Q residue 45 THR Chi-restraints excluded: chain Q residue 65 VAL Chi-restraints excluded: chain Q residue 212 ILE Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 232 THR Chi-restraints excluded: chain a residue 80 ASP Chi-restraints excluded: chain a residue 194 SER Chi-restraints excluded: chain a residue 230 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain b residue 353 MET Chi-restraints excluded: chain d residue 224 VAL Chi-restraints excluded: chain d residue 227 LEU Chi-restraints excluded: chain d residue 397 VAL Chi-restraints excluded: chain d residue 503 ILE Chi-restraints excluded: chain e residue 526 MET Chi-restraints excluded: chain g residue 7 VAL Chi-restraints excluded: chain g residue 8 LEU Chi-restraints excluded: chain g residue 47 MET Chi-restraints excluded: chain h residue 7 ILE Chi-restraints excluded: chain h residue 57 THR Chi-restraints excluded: chain h residue 143 VAL Chi-restraints excluded: chain q residue 253 THR Chi-restraints excluded: chain q residue 336 LEU Chi-restraints excluded: chain z residue 4 VAL Chi-restraints excluded: chain z residue 244 VAL Chi-restraints excluded: chain z residue 289 PHE Chi-restraints excluded: chain P residue 87 LEU Chi-restraints excluded: chain P residue 204 CYS Chi-restraints excluded: chain P residue 212 VAL Chi-restraints excluded: chain P residue 251 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 872 random chunks: chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 7.9990 chunk 265 optimal weight: 0.7980 chunk 595 optimal weight: 7.9990 chunk 676 optimal weight: 0.9990 chunk 248 optimal weight: 6.9990 chunk 273 optimal weight: 8.9990 chunk 354 optimal weight: 0.9990 chunk 613 optimal weight: 0.0670 chunk 528 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 overall best weight: 1.3724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 236 HIS A 475 GLN D 502 ASN G 111 HIS Z 161 HIS ** a 217 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 65 HIS z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.069878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2729 r_free = 0.2729 target = 0.057180 restraints weight = 205960.664| |-----------------------------------------------------------------------------| r_work (start): 0.2719 rms_B_bonded: 3.15 r_work: 0.2572 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2572 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2579 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2579 r_free = 0.2579 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2579 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8749 moved from start: 0.1507 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 68506 Z= 0.166 Angle : 0.558 14.522 92496 Z= 0.269 Chirality : 0.041 0.211 11003 Planarity : 0.003 0.052 11814 Dihedral : 6.817 161.963 9513 Min Nonbonded Distance : 1.940 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 0.87 % Allowed : 13.53 % Favored : 85.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.09), residues: 8760 helix: 2.50 (0.08), residues: 4522 sheet: 0.06 (0.16), residues: 1109 loop : -0.49 (0.11), residues: 3129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP N 222 HIS 0.017 0.001 HIS z 161 PHE 0.016 0.001 PHE P 158 TYR 0.030 0.001 TYR D 24 ARG 0.008 0.000 ARG e 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 31039.78 seconds wall clock time: 535 minutes 59.00 seconds (32159.00 seconds total)