Starting phenix.real_space_refine on Tue Jan 21 15:28:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sh9_40481/01_2025/8sh9_40481.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sh9_40481/01_2025/8sh9_40481.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sh9_40481/01_2025/8sh9_40481.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sh9_40481/01_2025/8sh9_40481.map" model { file = "/net/cci-nas-00/data/ceres_data/8sh9_40481/01_2025/8sh9_40481.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sh9_40481/01_2025/8sh9_40481.cif" } resolution = 2.7 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= 0.051 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 415 5.16 5 C 41982 2.51 5 N 11685 2.21 5 O 13003 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 48 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 67197 Number of models: 1 Model: "" Number of chains: 50 Chain: "N" Number of atoms: 322 Number of conformers: 1 Conformer: "" Number of residues, atoms: 43, 322 Classifications: {'peptide': 43} Link IDs: {'TRANS': 42} Chain breaks: 3 Chain: "A" Number of atoms: 4069 Number of conformers: 1 Conformer: "" Number of residues, atoms: 536, 4069 Classifications: {'peptide': 536} Link IDs: {'PTRANS': 14, 'TRANS': 521} Chain: "B" Number of atoms: 3952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 3952 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 10, 'TRANS': 515} Chain: "D" Number of atoms: 3923 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3923 Classifications: {'peptide': 520} Link IDs: {'PTRANS': 14, 'TRANS': 505} Chain: "E" Number of atoms: 4132 Number of conformers: 2 Conformer: "B" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} Conformer: "C" Number of residues, atoms: 535, 4121 Classifications: {'peptide': 535} Link IDs: {'PTRANS': 18, 'TRANS': 516} bond proxies already assigned to first conformer: 4158 Chain: "G" Number of atoms: 4089 Number of conformers: 1 Conformer: "" Number of residues, atoms: 526, 4089 Classifications: {'peptide': 526} Link IDs: {'PTRANS': 17, 'TRANS': 508} Chain: "H" Number of atoms: 4054 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4054 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 16, 'TRANS': 511} Chain: "Q" Number of atoms: 4086 Number of conformers: 1 Conformer: "" Number of residues, atoms: 538, 4086 Classifications: {'peptide': 538} Link IDs: {'PTRANS': 18, 'TRANS': 519} Chain: "Z" Number of atoms: 4022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4022 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 14, 'TRANS': 510} Chain: "a" Number of atoms: 4041 Number of conformers: 1 Conformer: "" Number of residues, atoms: 532, 4041 Classifications: {'peptide': 532} Link IDs: {'PTRANS': 13, 'TRANS': 518} Chain: "b" Number of atoms: 3943 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 3943 Classifications: {'peptide': 525} Link IDs: {'PTRANS': 10, 'TRANS': 514} Chain: "d" Number of atoms: 3917 Number of conformers: 1 Conformer: "" Number of residues, atoms: 520, 3917 Classifications: {'peptide': 520} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 505} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "e" Number of atoms: 4169 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} Conformer: "B" Number of residues, atoms: 540, 4158 Classifications: {'peptide': 540} Link IDs: {'PTRANS': 18, 'TRANS': 521} bond proxies already assigned to first conformer: 4195 Chain: "g" Number of atoms: 4102 Number of conformers: 1 Conformer: "" Number of residues, atoms: 528, 4102 Classifications: {'peptide': 528} Link IDs: {'PTRANS': 17, 'TRANS': 510} 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: 1727 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1727 Classifications: {'peptide': 218} Link IDs: {'PTRANS': 6, 'TRANS': 211} Chain breaks: 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: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "b" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "d" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "e" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "g" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "h" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "q" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "z" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 32 Unusual residues: {' MG': 1, 'ADP': 1, 'AF3': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "a" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "b" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "d" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "e" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "g" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "h" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "z" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 2 residue: pdb=" N BPHE E 9 " occ=0.38 ... (20 atoms not shown) pdb=" CZ CPHE E 9 " occ=0.62 residue: pdb=" N APHE e 9 " occ=0.50 ... (20 atoms not shown) pdb=" CZ BPHE e 9 " occ=0.50 Time building chain proxies: 35.02, per 1000 atoms: 0.52 Number of scatterers: 67197 At special positions: 0 Unit cell: (180.918, 176.686, 179.86, 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 415 16.00 P 32 15.00 Al 16 13.00 Mg 16 11.99 F 48 9.00 O 13003 8.00 N 11685 7.00 C 41982 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 "HETATM66848 O3A ADP H 601 .*. O " rejected from bonding due to valence issues. Number of custom bonds: simple=2, symmetry=0 Number of additional bonds: simple=2, symmetry=0 Coordination: Other bonds: Time building additional restraints: 13.11 Conformation dependent library (CDL) restraints added in 7.4 seconds 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 16252 Finding SS restraints... Secondary structure from input PDB file: 366 helices and 97 sheets defined 56.7% alpha, 13.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 7.39 Creating SS restraints... Processing helix chain 'A' and resid 14 through 33 removed outlier: 3.672A pdb=" N VAL A 32 " --> pdb=" O ILE A 28 " (cutoff:3.500A) Processing helix chain 'A' and resid 34 through 36 No H-bonds generated for 'chain 'A' and resid 34 through 36' Processing helix chain 'A' and resid 57 through 65 Processing helix chain 'A' and resid 69 through 86 Processing helix chain 'A' and resid 89 through 110 removed outlier: 3.710A pdb=" N VAL A 94 " --> pdb=" O THR A 90 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N GLN A 110 " --> pdb=" O GLU A 106 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 136 Processing helix chain 'A' and resid 141 through 143 No H-bonds generated for 'chain 'A' and resid 141 through 143' Processing helix chain 'A' and resid 144 through 157 removed outlier: 4.078A pdb=" N LEU A 148 " --> pdb=" O GLY A 144 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 179 removed outlier: 4.174A pdb=" N ASN A 170 " --> pdb=" O ASP A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 183 through 187 removed outlier: 3.863A pdb=" N GLN A 187 " --> pdb=" O ILE A 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 208 Processing helix chain 'A' and resid 258 through 281 removed outlier: 4.463A pdb=" N GLN A 262 " --> pdb=" O GLU A 258 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N SER A 268 " --> pdb=" O ARG A 264 " (cutoff:3.500A) removed outlier: 4.932A pdb=" N THR A 271 " --> pdb=" O GLU A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 304 Processing helix chain 'A' and resid 312 through 324 Processing helix chain 'A' and resid 341 through 345 Processing helix chain 'A' and resid 381 through 405 Processing helix chain 'A' and resid 413 through 427 Processing helix chain 'A' and resid 428 through 430 No H-bonds generated for 'chain 'A' and resid 428 through 430' Processing helix chain 'A' and resid 433 through 445 Processing helix chain 'A' and resid 446 through 456 Processing helix chain 'A' and resid 459 through 477 Processing helix chain 'A' and resid 478 through 484 removed outlier: 3.817A pdb=" N LYS A 481 " --> pdb=" O PRO A 478 " (cutoff:3.500A) removed outlier: 5.506A pdb=" N ASN A 482 " --> pdb=" O GLU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 498 through 502 Processing helix chain 'A' and resid 507 through 526 Processing helix chain 'B' and resid 20 through 40 Processing helix chain 'B' and resid 66 through 73 Processing helix chain 'B' and resid 78 through 95 Processing helix chain 'B' and resid 98 through 119 removed outlier: 3.565A pdb=" N THR B 103 " --> pdb=" O THR B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 144 Processing helix chain 'B' and resid 151 through 168 Processing helix chain 'B' and resid 169 through 174 removed outlier: 6.562A pdb=" N LEU B 172 " --> pdb=" O SER B 169 " (cutoff:3.500A) removed outlier: 3.623A 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: 3.556A 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 454 Proline residue: B 447 - end of helix removed outlier: 3.719A pdb=" N ALA B 454 " --> pdb=" O ILE B 450 " (cutoff:3.500A) Processing helix chain 'B' and resid 457 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing helix chain 'D' and resid 28 through 50 removed outlier: 4.461A pdb=" N THR D 50 " --> pdb=" O ASP D 46 " (cutoff:3.500A) Processing helix chain 'D' and resid 73 through 81 Processing helix chain 'D' and resid 85 through 102 Processing helix chain 'D' and resid 105 through 126 removed outlier: 4.213A pdb=" N VAL D 110 " --> pdb=" O THR D 106 " (cutoff:3.500A) removed outlier: 3.891A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 Processing helix chain 'D' and resid 159 through 173 removed outlier: 3.594A pdb=" N LEU D 163 " --> pdb=" O ASP D 159 " (cutoff:3.500A) removed outlier: 4.553A 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 293 removed outlier: 3.894A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 4.014A pdb=" N THR D 293 " --> pdb=" O GLN D 289 " (cutoff:3.500A) Processing helix chain 'D' and resid 310 through 320 Processing helix chain 'D' and resid 329 through 331 No H-bonds generated for 'chain 'D' and resid 329 through 331' Processing helix chain 'D' and resid 332 through 341 Processing helix chain 'D' and resid 347 through 351 Processing helix chain 'D' and resid 352 through 356 Processing helix chain 'D' and resid 394 through 418 Processing helix chain 'D' and resid 426 through 442 Processing helix chain 'D' and resid 446 through 459 removed outlier: 3.959A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) Processing helix chain 'D' and resid 459 through 470 removed outlier: 3.753A 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: 3.687A pdb=" N LYS E 25 " --> pdb=" O GLN E 22 " (cutoff:3.500A) Processing helix chain 'E' and resid 29 through 49 removed outlier: 3.678A pdb=" N ALA E 33 " --> pdb=" O MET E 29 " (cutoff:3.500A) removed outlier: 3.617A 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: 3.598A pdb=" N GLN E 122 " --> pdb=" O GLU E 118 " (cutoff:3.500A) removed outlier: 3.521A 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: 6.654A pdb=" N VAL E 178 " --> pdb=" O SER E 175 " (cutoff:3.500A) removed outlier: 3.955A 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: 3.890A pdb=" N THR E 295 " --> pdb=" O GLN E 291 " (cutoff:3.500A) Processing helix chain 'E' and resid 307 through 317 Processing helix chain 'E' and resid 326 through 338 Processing helix chain 'E' and resid 344 through 348 Processing helix chain 'E' and resid 349 through 353 Processing helix chain 'E' and resid 391 through 415 Processing helix chain 'E' and resid 423 through 438 Processing helix chain 'E' and resid 441 through 456 removed outlier: 3.543A pdb=" N GLN E 445 " --> pdb=" O PRO E 441 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N TYR E 446 " --> pdb=" O THR E 442 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA E 447 " --> pdb=" O LEU E 443 " (cutoff:3.500A) Processing helix chain 'E' and resid 456 through 466 removed outlier: 3.540A 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 37 removed outlier: 3.679A pdb=" N GLN G 23 " --> pdb=" O GLY G 19 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE G 37 " --> pdb=" O ILE G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 38 through 41 removed outlier: 4.030A pdb=" N LEU G 41 " --> pdb=" O ARG G 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 38 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: 3.647A pdb=" N ILE G 99 " --> pdb=" O THR G 95 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ILE G 100 " --> pdb=" O THR G 96 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N HIS G 111 " --> pdb=" O SER G 107 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N PHE G 112 " --> pdb=" O VAL G 108 " (cutoff:3.500A) Processing helix chain 'G' and resid 118 through 140 removed outlier: 3.557A 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: 4.185A pdb=" N ARG G 167 " --> pdb=" O ALA G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 168 through 184 Processing helix chain 'G' and resid 194 through 198 Processing helix chain 'G' and resid 208 through 212 Processing helix chain 'G' and resid 262 through 284 Processing helix chain 'G' and resid 297 through 307 removed outlier: 3.592A pdb=" N ALA G 307 " --> pdb=" O TYR G 303 " (cutoff:3.500A) Processing helix chain 'G' and resid 316 through 328 Processing helix chain 'G' and resid 334 through 338 Processing helix chain 'G' and resid 380 through 404 Processing helix chain 'G' and resid 412 through 427 Processing helix chain 'G' and resid 433 through 444 Processing helix chain 'G' and resid 445 through 456 Processing helix chain 'G' and resid 458 through 471 Processing helix chain 'G' and resid 490 through 494 Processing helix chain 'G' and resid 499 through 518 Processing helix chain 'H' and resid 18 through 35 removed outlier: 3.530A pdb=" N LEU H 22 " --> pdb=" O GLY H 18 " (cutoff:3.500A) Processing helix chain 'H' and resid 36 through 40 removed outlier: 3.771A pdb=" N LEU H 40 " --> pdb=" O ARG H 37 " (cutoff:3.500A) Processing helix chain 'H' and resid 61 through 69 Processing helix chain 'H' and resid 76 through 90 removed outlier: 3.780A pdb=" N VAL H 80 " --> pdb=" O ALA H 76 " (cutoff:3.500A) Processing helix chain 'H' and resid 93 through 114 removed outlier: 4.169A 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: 3.625A 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: 3.653A pdb=" N MET H 185 " --> pdb=" O ASP H 181 " (cutoff:3.500A) removed outlier: 3.904A 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 removed outlier: 3.509A pdb=" N SER H 284 " --> pdb=" O LYS H 280 " (cutoff:3.500A) Processing helix chain 'H' and resid 296 through 306 Processing helix chain 'H' and resid 315 through 327 Processing helix chain 'H' and resid 338 through 340 No H-bonds generated for 'chain 'H' and resid 338 through 340' Processing helix chain 'H' and resid 378 through 402 Processing helix chain 'H' and resid 410 through 425 Processing helix chain 'H' and resid 429 through 442 removed outlier: 3.584A pdb=" N LEU H 433 " --> pdb=" O GLY H 429 " (cutoff:3.500A) removed outlier: 4.003A 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 470 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: 4.317A pdb=" N TYR Q 30 " --> pdb=" O GLU Q 26 " (cutoff:3.500A) removed outlier: 4.829A pdb=" N ARG Q 31 " --> pdb=" O GLU Q 27 " (cutoff:3.500A) removed outlier: 4.525A pdb=" N THR Q 45 " --> pdb=" O GLN Q 41 " (cutoff:3.500A) Processing helix chain 'Q' and resid 68 through 76 Processing helix chain 'Q' and resid 80 through 97 Processing helix chain 'Q' and resid 100 through 122 Processing helix chain 'Q' and resid 124 through 143 Processing helix chain 'Q' and resid 144 through 147 removed outlier: 3.542A pdb=" N VAL Q 147 " --> pdb=" O PRO Q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'Q' and resid 144 through 147' Processing helix chain 'Q' and resid 156 through 168 removed outlier: 4.154A pdb=" N THR Q 166 " --> pdb=" O SER Q 162 " (cutoff:3.500A) removed outlier: 4.219A 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: 4.709A pdb=" N SER Q 269 " --> pdb=" O LEU Q 265 " (cutoff:3.500A) removed outlier: 4.883A pdb=" N LYS Q 270 " --> pdb=" O MET Q 266 " (cutoff:3.500A) Processing helix chain 'Q' and resid 298 through 308 Processing helix chain 'Q' and resid 317 through 329 Processing helix chain 'Q' and resid 340 through 344 removed outlier: 4.110A pdb=" N MET Q 344 " --> pdb=" O LEU Q 341 " (cutoff:3.500A) Processing helix chain 'Q' and resid 381 through 405 Processing helix chain 'Q' and resid 413 through 429 removed outlier: 3.519A pdb=" N GLU Q 428 " --> pdb=" O THR Q 424 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N THR Q 429 " --> pdb=" O SER Q 425 " (cutoff:3.500A) Processing helix chain 'Q' and resid 433 through 444 removed outlier: 4.281A pdb=" N ALA Q 437 " --> pdb=" O LEU Q 433 " (cutoff:3.500A) Processing helix chain 'Q' and resid 446 through 457 Processing helix chain 'Q' and resid 459 through 474 Processing helix chain 'Q' and resid 492 through 496 Processing helix chain 'Q' and resid 501 through 520 Processing helix chain 'Q' and resid 535 through 539 Processing helix chain 'Z' and resid 3 through 8 Processing helix chain 'Z' and resid 16 through 35 Processing helix chain 'Z' and resid 36 through 38 No H-bonds generated for 'chain 'Z' and resid 36 through 38' Processing helix chain 'Z' and resid 59 through 67 Processing helix chain 'Z' and resid 71 through 88 Processing helix chain 'Z' and resid 91 through 111 removed outlier: 3.614A pdb=" N TYR Z 109 " --> pdb=" O GLN Z 105 " (cutoff:3.500A) Processing helix chain 'Z' and resid 115 through 138 removed outlier: 3.786A pdb=" N ILE Z 119 " --> pdb=" O HIS Z 115 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 160 removed outlier: 3.662A pdb=" N THR Z 158 " --> pdb=" O THR Z 154 " (cutoff:3.500A) Processing helix chain 'Z' and resid 161 through 180 removed outlier: 3.571A 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 Processing helix chain 'Z' and resid 252 through 264 removed outlier: 4.087A pdb=" N ARG Z 264 " --> pdb=" O VAL Z 260 " (cutoff:3.500A) Processing helix chain 'Z' and resid 264 through 282 removed outlier: 3.624A pdb=" N ARG Z 270 " --> pdb=" O PHE Z 266 " (cutoff:3.500A) Processing helix chain 'Z' and resid 298 through 307 Processing helix chain 'Z' and resid 317 through 328 removed outlier: 3.706A pdb=" N MET Z 321 " --> pdb=" O LYS Z 317 " (cutoff:3.500A) removed outlier: 4.272A pdb=" N GLU Z 322 " --> pdb=" O ARG Z 318 " (cutoff:3.500A) Processing helix chain 'Z' and resid 340 through 344 Processing helix chain 'Z' and resid 380 through 404 Processing helix chain 'Z' and resid 412 through 426 Processing helix chain 'Z' and resid 427 through 429 No H-bonds generated for 'chain 'Z' and resid 427 through 429' Processing helix chain 'Z' and resid 430 through 431 No H-bonds generated for 'chain 'Z' and resid 430 through 431' Processing helix chain 'Z' and resid 432 through 445 removed outlier: 4.223A pdb=" N GLY Z 436 " --> pdb=" O ARG Z 432 " (cutoff:3.500A) Processing helix chain 'Z' and resid 445 through 456 removed outlier: 3.614A pdb=" N LYS Z 449 " --> pdb=" O LEU Z 445 " (cutoff:3.500A) Processing helix chain 'Z' and resid 458 through 474 Processing helix chain 'Z' and resid 489 through 493 Processing helix chain 'Z' and resid 497 through 517 Processing helix chain 'a' and resid 14 through 33 removed outlier: 3.719A pdb=" N VAL a 32 " --> pdb=" O ILE a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 34 through 36 No H-bonds generated for 'chain 'a' and resid 34 through 36' Processing helix chain 'a' and resid 57 through 65 Processing helix chain 'a' and resid 69 through 86 Processing helix chain 'a' and resid 89 through 110 removed outlier: 3.664A pdb=" N VAL a 94 " --> pdb=" O THR a 90 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLN a 110 " --> pdb=" O GLU a 106 " (cutoff:3.500A) Processing helix chain 'a' and resid 113 through 136 Processing helix chain 'a' and resid 141 through 143 No H-bonds generated for 'chain 'a' and resid 141 through 143' Processing helix chain 'a' and resid 144 through 157 removed outlier: 4.254A pdb=" N LEU a 148 " --> pdb=" O GLY a 144 " (cutoff:3.500A) Processing helix chain 'a' and resid 164 through 179 removed outlier: 4.103A pdb=" N ASN a 170 " --> pdb=" O ASP a 166 " (cutoff:3.500A) removed outlier: 3.660A 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: 3.920A pdb=" N SER a 268 " --> pdb=" O ARG a 264 " (cutoff:3.500A) removed outlier: 5.051A pdb=" N THR a 271 " --> pdb=" O GLU a 267 " (cutoff:3.500A) Processing helix chain 'a' and resid 293 through 304 Processing helix chain 'a' and resid 312 through 324 Processing helix chain 'a' and resid 341 through 345 Processing helix chain 'a' and resid 381 through 405 Processing helix chain 'a' and resid 413 through 428 removed outlier: 4.386A pdb=" N THR a 428 " --> pdb=" O GLU a 424 " (cutoff:3.500A) Processing helix chain 'a' and resid 433 through 445 Processing helix chain 'a' and resid 446 through 456 Processing helix chain 'a' and resid 459 through 477 Processing helix chain 'a' and resid 480 through 484 Processing helix chain 'a' and resid 498 through 502 Processing helix chain 'a' and resid 507 through 526 Processing helix chain 'b' and resid 20 through 40 Processing helix chain 'b' and resid 66 through 73 Processing helix chain 'b' and resid 78 through 95 Processing helix chain 'b' and resid 98 through 119 Processing helix chain 'b' and resid 122 through 145 Processing helix chain 'b' and resid 151 through 168 Processing helix chain 'b' and resid 169 through 174 removed outlier: 6.622A pdb=" N LEU b 172 " --> pdb=" O SER b 169 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N HIS b 174 " --> pdb=" O LEU b 171 " (cutoff:3.500A) Processing helix chain 'b' and resid 175 through 189 Processing helix chain 'b' and resid 208 through 212 Processing helix chain 'b' and resid 260 through 284 removed outlier: 3.614A pdb=" N VAL b 264 " --> pdb=" O SER b 260 " (cutoff:3.500A) Processing helix chain 'b' and resid 297 through 307 Processing helix chain 'b' and resid 316 through 328 Processing helix chain 'b' and resid 337 through 341 Processing helix chain 'b' and resid 379 through 403 Processing helix chain 'b' and resid 411 through 427 Processing helix chain 'b' and resid 430 through 454 removed outlier: 4.042A pdb=" N VAL b 434 " --> pdb=" O GLY b 430 " (cutoff:3.500A) Proline residue: b 447 - end of helix removed outlier: 3.660A pdb=" N ALA b 454 " --> pdb=" O ILE b 450 " (cutoff:3.500A) Processing helix chain 'b' and resid 457 through 471 Processing helix chain 'b' and resid 488 through 492 Processing helix chain 'b' and resid 497 through 516 Processing helix chain 'd' and resid 28 through 48 Processing helix chain 'd' and resid 73 through 81 Processing helix chain 'd' and resid 85 through 102 Processing helix chain 'd' and resid 105 through 126 removed outlier: 3.644A pdb=" N VAL d 110 " --> pdb=" O THR d 106 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N LYS d 122 " --> pdb=" O ASP d 118 " (cutoff:3.500A) Processing helix chain 'd' and resid 131 through 151 Processing helix chain 'd' and resid 159 through 172 removed outlier: 3.561A pdb=" N LEU d 163 " --> pdb=" O ASP d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 173 through 178 removed outlier: 6.748A pdb=" N VAL d 176 " --> pdb=" O SER d 173 " (cutoff:3.500A) removed outlier: 4.214A pdb=" N GLN d 178 " --> pdb=" O VAL d 175 " (cutoff:3.500A) Processing helix chain 'd' and resid 179 through 193 Proline residue: d 185 - end of helix Processing helix chain 'd' and resid 204 through 206 No H-bonds generated for 'chain 'd' and resid 204 through 206' Processing helix chain 'd' and resid 217 through 221 Processing helix chain 'd' and resid 268 through 293 removed outlier: 4.080A pdb=" N LEU d 276 " --> pdb=" O MET d 272 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N THR d 293 " --> pdb=" O GLN d 289 " (cutoff:3.500A) Processing helix chain 'd' and resid 310 through 320 Processing helix chain 'd' and resid 329 through 331 No H-bonds generated for 'chain 'd' and resid 329 through 331' Processing helix chain 'd' and resid 332 through 341 Processing helix chain 'd' and resid 347 through 351 Processing helix chain 'd' and resid 352 through 356 Processing helix chain 'd' and resid 394 through 417 Processing helix chain 'd' and resid 426 through 441 Processing helix chain 'd' and resid 445 through 459 removed outlier: 3.797A pdb=" N TYR d 449 " --> pdb=" O GLY d 445 " (cutoff:3.500A) Processing helix chain 'd' and resid 459 through 467 removed outlier: 3.599A pdb=" N SER d 463 " --> pdb=" O GLU d 459 " (cutoff:3.500A) Processing helix chain 'd' and resid 472 through 486 Processing helix chain 'd' and resid 504 through 507 Processing helix chain 'd' and resid 512 through 531 removed outlier: 4.923A pdb=" N SER d 517 " --> pdb=" O LEU d 513 " (cutoff:3.500A) Processing helix chain 'e' and resid 30 through 49 removed outlier: 3.525A 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: 3.598A pdb=" N GLN e 122 " --> pdb=" O GLU e 118 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N ARG e 126 " --> pdb=" O GLN e 122 " (cutoff:3.500A) Processing helix chain 'e' and resid 129 through 151 Processing helix chain 'e' and resid 162 through 174 Processing helix chain 'e' and resid 175 through 180 removed outlier: 6.556A pdb=" N VAL e 178 " --> pdb=" O SER e 175 " (cutoff:3.500A) removed outlier: 3.978A 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: 3.829A 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 439 removed outlier: 3.882A pdb=" N LYS e 439 " --> pdb=" O GLN e 435 " (cutoff:3.500A) Processing helix chain 'e' and resid 441 through 456 removed outlier: 3.509A pdb=" N GLN e 445 " --> pdb=" O PRO e 441 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR e 446 " --> pdb=" O THR e 442 " (cutoff:3.500A) removed outlier: 4.483A pdb=" N ALA e 447 " --> pdb=" O LEU e 443 " (cutoff:3.500A) Processing helix chain 'e' and resid 456 through 466 removed outlier: 3.571A pdb=" N MET e 460 " --> pdb=" O GLU e 456 " (cutoff:3.500A) Processing helix chain 'e' and resid 469 through 484 Processing helix chain 'e' and resid 510 through 529 Processing helix chain 'g' and resid 19 through 37 removed outlier: 3.614A pdb=" N GLN g 23 " --> pdb=" O GLY g 19 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N ILE g 37 " --> pdb=" O ILE g 33 " (cutoff:3.500A) Processing helix chain 'g' and resid 38 through 41 removed outlier: 4.017A pdb=" N LEU g 41 " --> pdb=" O ARG g 38 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 38 through 41' Processing helix chain 'g' and resid 62 through 69 Processing helix chain 'g' and resid 74 through 91 Processing helix chain 'g' and resid 94 through 115 removed outlier: 3.795A pdb=" N ILE g 99 " --> pdb=" O THR g 95 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N PHE g 112 " --> pdb=" O VAL g 108 " (cutoff:3.500A) removed outlier: 3.926A pdb=" N GLN g 115 " --> pdb=" O HIS g 111 " (cutoff:3.500A) Processing helix chain 'g' and resid 118 through 141 removed outlier: 3.542A 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: 3.943A pdb=" N ARG g 167 " --> pdb=" O ALA g 164 " (cutoff:3.500A) Processing helix chain 'g' and resid 168 through 184 Processing helix chain 'g' and resid 208 through 212 Processing helix chain 'g' and resid 262 through 284 Processing helix chain 'g' and resid 297 through 307 removed outlier: 3.718A pdb=" N ALA g 307 " --> pdb=" O TYR g 303 " (cutoff:3.500A) Processing helix chain 'g' and resid 316 through 328 Processing helix chain 'g' and resid 334 through 338 Processing helix chain 'g' and resid 339 through 343 Processing helix chain 'g' and resid 380 through 404 Processing helix chain 'g' and resid 412 through 427 removed outlier: 3.674A pdb=" N LYS g 427 " --> pdb=" O THR g 423 " (cutoff:3.500A) Processing helix chain 'g' and resid 433 through 443 Processing helix chain 'g' and resid 445 through 456 Processing helix chain 'g' and resid 458 through 471 Processing helix chain 'g' and resid 490 through 494 Processing helix chain 'g' and resid 499 through 518 Processing helix chain 'h' and resid 18 through 37 removed outlier: 3.553A pdb=" N LEU h 22 " --> pdb=" O GLY h 18 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL h 36 " --> pdb=" O ILE h 32 " (cutoff:3.500A) Processing helix chain 'h' and resid 61 through 69 Processing helix chain 'h' and resid 76 through 90 removed outlier: 3.697A pdb=" N VAL h 80 " --> pdb=" O ALA h 76 " (cutoff:3.500A) Processing helix chain 'h' and resid 93 through 114 removed outlier: 4.155A 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: 3.647A 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: 3.593A pdb=" N MET h 185 " --> pdb=" O ASP h 181 " (cutoff:3.500A) removed outlier: 3.981A 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 removed outlier: 3.605A 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: 3.760A 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: 3.607A pdb=" N LEU h 433 " --> pdb=" O GLY h 429 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N LEU h 434 " --> pdb=" O LYS h 430 " (cutoff:3.500A) Processing helix chain 'h' and resid 443 through 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: 4.294A pdb=" N TYR q 30 " --> pdb=" O GLU q 26 " (cutoff:3.500A) removed outlier: 4.844A pdb=" N ARG q 31 " --> pdb=" O GLU q 27 " (cutoff:3.500A) removed outlier: 4.390A pdb=" N THR q 45 " --> pdb=" O GLN q 41 " (cutoff:3.500A) Processing helix chain 'q' and resid 68 through 76 Processing helix chain 'q' and resid 80 through 97 Processing helix chain 'q' and resid 100 through 122 Processing helix chain 'q' and resid 124 through 143 Processing helix chain 'q' and resid 144 through 147 removed outlier: 3.510A pdb=" N VAL q 147 " --> pdb=" O PRO q 144 " (cutoff:3.500A) No H-bonds generated for 'chain 'q' and resid 144 through 147' Processing helix chain 'q' and resid 156 through 168 removed outlier: 4.230A pdb=" N THR q 166 " --> pdb=" O SER q 162 " (cutoff:3.500A) removed outlier: 4.183A 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 211 through 215 Processing helix chain 'q' and resid 261 through 285 removed outlier: 4.851A pdb=" N SER q 269 " --> pdb=" O LEU q 265 " (cutoff:3.500A) removed outlier: 4.910A 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 428 Processing helix chain 'q' and resid 433 through 445 removed outlier: 4.335A pdb=" N ALA q 437 " --> pdb=" O LEU q 433 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N PHE q 445 " --> pdb=" O PHE q 441 " (cutoff:3.500A) Processing helix chain 'q' and resid 446 through 457 Processing helix chain 'q' and resid 459 through 474 Processing helix chain 'q' and resid 492 through 496 Processing helix chain 'q' and resid 501 through 520 Processing helix chain 'z' and resid 2 through 8 removed outlier: 3.561A pdb=" N LEU z 7 " --> pdb=" O ALA z 3 " (cutoff:3.500A) Processing helix chain 'z' and resid 16 through 35 Processing helix chain 'z' and resid 36 through 38 No H-bonds generated for 'chain 'z' and resid 36 through 38' Processing helix chain 'z' and resid 59 through 67 Processing helix chain 'z' and resid 71 through 88 Processing helix chain 'z' and resid 91 through 111 removed outlier: 3.681A pdb=" N TYR z 109 " --> pdb=" O GLN z 105 " (cutoff:3.500A) Processing helix chain 'z' and resid 115 through 138 removed outlier: 3.764A pdb=" N ILE z 119 " --> pdb=" O HIS z 115 " (cutoff:3.500A) Processing helix chain 'z' and resid 144 through 160 removed outlier: 4.139A pdb=" N THR z 158 " --> pdb=" O THR z 154 " (cutoff:3.500A) Processing helix chain 'z' and resid 161 through 180 removed outlier: 3.617A 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: 3.720A 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: 3.623A pdb=" N ARG z 270 " --> pdb=" O PHE z 266 " (cutoff:3.500A) Processing helix chain 'z' and resid 298 through 307 Processing helix chain 'z' and resid 317 through 328 removed outlier: 3.707A pdb=" N MET z 321 " --> pdb=" O LYS z 317 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N GLU z 322 " --> pdb=" O ARG z 318 " (cutoff:3.500A) Processing helix chain 'z' and resid 340 through 344 Processing helix chain 'z' and resid 380 through 404 Processing helix chain 'z' and resid 412 through 426 Processing helix chain 'z' and resid 427 through 429 No H-bonds generated for 'chain 'z' and resid 427 through 429' Processing helix chain 'z' and resid 432 through 445 removed outlier: 4.168A pdb=" N GLY z 436 " --> pdb=" O ARG z 432 " (cutoff:3.500A) Processing helix chain 'z' and resid 445 through 456 removed outlier: 3.584A pdb=" N LYS z 449 " --> pdb=" O LEU z 445 " (cutoff:3.500A) Processing helix chain 'z' and resid 458 through 474 Processing helix chain 'z' and resid 489 through 493 Processing helix chain 'z' and resid 497 through 517 Processing helix chain 'P' and resid 57 through 85 removed outlier: 4.892A pdb=" N ASN P 64 " --> pdb=" O LYS P 60 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ASP P 65 " --> pdb=" O GLY P 61 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N LEU P 72 " --> pdb=" O ARG P 68 " (cutoff:3.500A) Processing helix chain 'P' and resid 136 through 140 Processing helix chain 'P' and resid 141 through 152 removed outlier: 3.996A pdb=" N MET P 145 " --> pdb=" O ARG P 141 " (cutoff:3.500A) Processing helix chain 'P' and resid 166 through 176 Processing helix chain 'P' and resid 194 through 209 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: 4.306A pdb=" N GLN P 254 " --> pdb=" O ARG P 250 " (cutoff:3.500A) Processing helix chain 'P' and resid 260 through 270 Processing sheet with id=AA1, first strand: chain 'N' and resid 221 through 223 removed outlier: 7.340A pdb=" N LEU N 221 " --> pdb=" O LEU N 230 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N GLN N 228 " --> pdb=" O ASP N 223 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'N' and resid 242 through 244 removed outlier: 3.693A pdb=" N CYS N 242 " --> pdb=" O GLY N 257 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N VAL N 265 " --> pdb=" O VAL N 274 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N GLN N 272 " --> pdb=" O ASP N 267 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 9 through 13 removed outlier: 4.421A pdb=" N ILE A 527 " --> pdb=" O ASP D 58 " (cutoff:3.500A) removed outlier: 7.198A pdb=" N MET D 60 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 6.234A pdb=" N ASP A 529 " --> pdb=" O MET D 60 " (cutoff:3.500A) removed outlier: 7.702A pdb=" N GLN D 62 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 531 " --> pdb=" O GLN D 62 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 52 through 55 removed outlier: 5.960A pdb=" N MET A 44 " --> pdb=" O VAL G 523 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 138 through 139 Processing sheet with id=AA6, first strand: chain 'A' and resid 196 through 199 Processing sheet with id=AA7, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.545A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 213 through 216 removed outlier: 6.545A pdb=" N THR A 367 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ALA A 348 " --> pdb=" O THR A 367 " (cutoff:3.500A) removed outlier: 6.541A pdb=" N ILE A 286 " --> pdb=" O VAL A 308 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 254 through 256 removed outlier: 9.110A pdb=" N ASP G 255 " --> pdb=" O VAL A 250 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL A 252 " --> pdb=" O ASP G 255 " (cutoff:3.500A) removed outlier: 9.080A pdb=" N GLN D 263 " --> pdb=" O SER B 254 " (cutoff:3.500A) removed outlier: 6.299A pdb=" N VAL B 256 " --> pdb=" O GLN D 263 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N VAL D 265 " --> pdb=" O VAL B 256 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N VAL B 258 " --> pdb=" O VAL D 265 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N ARG B 255 " --> pdb=" O VAL E 268 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 486 through 489 Processing sheet with id=AB2, first strand: chain 'B' and resid 17 through 19 removed outlier: 4.401A pdb=" N VAL B 517 " --> pdb=" O ASP E 58 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N MET E 60 " --> pdb=" O VAL B 517 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N ASN B 519 " --> pdb=" O MET E 60 " (cutoff:3.500A) removed outlier: 7.791A pdb=" N VAL E 62 " --> pdb=" O ASN B 519 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N ILE B 521 " --> pdb=" O VAL E 62 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 61 through 64 removed outlier: 6.970A pdb=" N ASP B 49 " --> pdb=" O ASP D 534 " (cutoff:3.500A) removed outlier: 8.065A pdb=" N VAL D 536 " --> pdb=" O ASP B 49 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N ILE B 51 " --> pdb=" O VAL D 536 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N THR D 538 " --> pdb=" O ILE B 51 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU B 53 " --> pdb=" O THR D 538 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 146 through 147 Processing sheet with id=AB5, first strand: chain 'B' and resid 199 through 205 removed outlier: 3.765A pdb=" N GLY B 377 " --> pdb=" O LYS B 204 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 218 through 220 removed outlier: 6.390A pdb=" N VAL B 365 " --> pdb=" O CYS B 346 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N CYS B 346 " --> pdb=" O VAL B 365 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N CYS B 346 " --> pdb=" O ALA B 235 " (cutoff:3.500A) removed outlier: 6.604A pdb=" N LEU B 348 " --> pdb=" O GLU B 233 " (cutoff:3.500A) removed outlier: 6.903A pdb=" N GLU B 233 " --> pdb=" O LEU B 348 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N GLU B 350 " --> pdb=" O ARG B 231 " (cutoff:3.500A) removed outlier: 7.213A pdb=" N ARG B 231 " --> pdb=" O GLU B 350 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 476 through 479 Processing sheet with id=AB8, first strand: chain 'D' and resid 153 through 154 Processing sheet with id=AB9, first strand: chain 'D' and resid 208 through 214 removed outlier: 6.391A pdb=" N LYS D 209 " --> pdb=" O ILE D 388 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N VAL D 390 " --> pdb=" O LYS D 209 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N VAL D 211 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 8.208A pdb=" N GLY D 392 " --> pdb=" O VAL D 211 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LYS D 213 " --> pdb=" O GLY D 392 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 227 through 229 removed outlier: 6.534A pdb=" N CYS D 379 " --> pdb=" O ALA D 359 " (cutoff:3.500A) removed outlier: 6.836A pdb=" N ALA D 359 " --> pdb=" O CYS D 379 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU D 361 " --> pdb=" O GLU D 242 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLU D 242 " --> pdb=" O LEU D 361 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N GLU D 363 " --> pdb=" O ARG D 240 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N ARG D 240 " --> pdb=" O GLU D 363 " (cutoff:3.500A) removed outlier: 7.385A pdb=" N VAL D 297 " --> pdb=" O LYS D 243 " (cutoff:3.500A) removed outlier: 5.703A pdb=" N LYS D 245 " --> pdb=" O VAL D 297 " (cutoff:3.500A) removed outlier: 7.334A pdb=" N LEU D 299 " --> pdb=" O LYS D 245 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N GLY D 247 " --> pdb=" O LEU D 299 " (cutoff:3.500A) removed outlier: 7.493A pdb=" N GLN D 301 " --> pdb=" O GLY D 247 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE D 249 " --> pdb=" O GLN D 301 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'D' and resid 491 through 494 removed outlier: 3.616A pdb=" N SER D 501 " --> pdb=" O GLY D 492 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'E' and resid 153 through 154 Processing sheet with id=AC4, first strand: chain 'E' and resid 209 through 215 removed outlier: 3.926A pdb=" N GLY E 389 " --> pdb=" O LYS E 214 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'E' and resid 228 through 230 removed outlier: 6.687A pdb=" N PHE E 355 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.952A 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: 7.109A pdb=" N LEU E 299 " --> pdb=" O ASP E 245 " (cutoff:3.500A) removed outlier: 5.890A pdb=" N LYS E 247 " --> pdb=" O LEU E 299 " (cutoff:3.500A) removed outlier: 7.554A pdb=" N ILE E 301 " --> pdb=" O LYS E 247 " (cutoff:3.500A) removed outlier: 6.174A pdb=" N ALA E 249 " --> pdb=" O ILE E 301 " (cutoff:3.500A) removed outlier: 6.654A pdb=" N ALA E 300 " --> pdb=" O VAL E 322 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'E' and resid 530 through 534 removed outlier: 7.292A pdb=" N LEU H 48 " --> pdb=" O ASP E 531 " (cutoff:3.500A) removed outlier: 4.168A pdb=" N ILE E 533 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 7.321A pdb=" N VAL H 50 " --> pdb=" O ILE E 533 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 57 through 60 removed outlier: 6.486A pdb=" N MET G 47 " --> pdb=" O VAL Z 518 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N GLU Z 520 " --> pdb=" O MET G 47 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 142 through 143 Processing sheet with id=AC9, first strand: chain 'G' and resid 185 through 187 Processing sheet with id=AD1, first strand: chain 'G' and resid 199 through 205 removed outlier: 6.846A pdb=" N ARG G 200 " --> pdb=" O ILE G 374 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N LEU G 376 " --> pdb=" O ARG G 200 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N GLU G 202 " --> pdb=" O LEU G 376 " (cutoff:3.500A) removed outlier: 8.216A pdb=" N GLY G 378 " --> pdb=" O GLU G 202 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N ILE G 204 " --> pdb=" O GLY G 378 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'G' and resid 219 through 220 Processing sheet with id=AD3, first strand: chain 'G' and resid 238 through 241 Processing sheet with id=AD4, first strand: chain 'G' and resid 478 through 481 removed outlier: 3.718A pdb=" N THR G 486 " --> pdb=" O ASN G 481 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'H' and resid 14 through 17 removed outlier: 6.432A pdb=" N ASN Q 53 " --> pdb=" O VAL H 516 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU H 518 " --> pdb=" O ASN Q 53 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'H' and resid 141 through 142 Processing sheet with id=AD7, first strand: chain 'H' and resid 195 through 201 removed outlier: 3.715A pdb=" N GLY H 376 " --> pdb=" O VAL H 200 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N THR H 371 " --> pdb=" O VAL H 211 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'H' and resid 214 through 217 Processing sheet with id=AD9, first strand: chain 'H' and resid 309 through 311 Processing sheet with id=AE1, first strand: chain 'H' and resid 475 through 478 Processing sheet with id=AE2, first strand: chain 'Q' and resid 20 through 23 removed outlier: 7.183A pdb=" N MET Z 46 " --> pdb=" O ASP Q 522 " (cutoff:3.500A) removed outlier: 4.396A pdb=" N ILE Q 524 " --> pdb=" O MET Z 46 " (cutoff:3.500A) removed outlier: 7.397A pdb=" N VAL Z 48 " --> pdb=" O ILE Q 524 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N MET Q 526 " --> pdb=" O VAL Z 48 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 'Q' and resid 149 through 150 removed outlier: 3.935A pdb=" N CYS Q 149 " --> pdb=" O LEU Q 408 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'Q' and resid 202 through 208 removed outlier: 6.512A pdb=" N ARG Q 203 " --> pdb=" O ILE Q 375 " (cutoff:3.500A) removed outlier: 7.301A pdb=" N LEU Q 377 " --> pdb=" O ARG Q 203 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N CYS Q 205 " --> pdb=" O LEU Q 377 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N GLY Q 379 " --> pdb=" O CYS Q 205 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N ILE Q 207 " --> pdb=" O GLY Q 379 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'Q' and resid 220 through 223 Processing sheet with id=AE6, first strand: chain 'Q' and resid 240 through 242 Processing sheet with id=AE7, first strand: chain 'Q' and resid 478 through 480 Processing sheet with id=AE8, first strand: chain 'Z' and resid 139 through 140 Processing sheet with id=AE9, first strand: chain 'Z' and resid 191 through 196 removed outlier: 6.660A pdb=" N GLU Z 192 " --> pdb=" O LEU Z 374 " (cutoff:3.500A) removed outlier: 7.186A pdb=" N ILE Z 376 " --> pdb=" O GLU Z 192 " (cutoff:3.500A) removed outlier: 6.391A pdb=" N MET Z 194 " --> pdb=" O ILE Z 376 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N SER Z 205 " --> pdb=" O LEU Z 375 " (cutoff:3.500A) Processing sheet with id=AF1, first strand: chain 'Z' and resid 210 through 212 Processing sheet with id=AF2, first strand: chain 'Z' and resid 310 through 313 removed outlier: 6.337A pdb=" N ASP Z 227 " --> pdb=" O GLY Z 288 " (cutoff:3.500A) removed outlier: 7.264A pdb=" N VAL Z 290 " --> pdb=" O ASP Z 227 " (cutoff:3.500A) removed outlier: 6.071A pdb=" N TYR Z 229 " --> pdb=" O VAL Z 290 " (cutoff:3.500A) removed outlier: 7.242A pdb=" N ILE Z 292 " --> pdb=" O TYR Z 229 " (cutoff:3.500A) removed outlier: 6.210A pdb=" N LEU Z 231 " --> pdb=" O ILE Z 292 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'Z' and resid 477 through 479 Processing sheet with id=AF4, first strand: chain 'a' and resid 9 through 13 removed outlier: 6.214A pdb=" N ASP d 58 " --> pdb=" O ILE a 527 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ASP a 529 " --> pdb=" O ASP d 58 " (cutoff:3.500A) Processing sheet with id=AF5, first strand: chain 'a' and resid 52 through 55 removed outlier: 6.416A pdb=" N ASP a 42 " --> pdb=" O ILE g 519 " (cutoff:3.500A) removed outlier: 4.068A pdb=" N ASP g 521 " --> pdb=" O ASP a 42 " (cutoff:3.500A) Processing sheet with id=AF6, first strand: chain 'a' and resid 138 through 139 Processing sheet with id=AF7, first strand: chain 'a' and resid 181 through 182 Processing sheet with id=AF8, first strand: chain 'a' and resid 196 through 201 removed outlier: 6.350A pdb=" N ASN a 196 " --> pdb=" O ILE a 375 " (cutoff:3.500A) removed outlier: 7.471A pdb=" N LEU a 377 " --> pdb=" O ASN a 196 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N LEU a 198 " --> pdb=" O LEU a 377 " (cutoff:3.500A) removed outlier: 7.978A pdb=" N GLY a 379 " --> pdb=" O LEU a 198 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ALA a 200 " --> pdb=" O GLY a 379 " (cutoff:3.500A) Processing sheet with id=AF9, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.491A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG1, first strand: chain 'a' and resid 213 through 216 removed outlier: 6.491A pdb=" N THR a 367 " --> pdb=" O ALA a 348 " (cutoff:3.500A) removed outlier: 6.658A pdb=" N ALA a 348 " --> pdb=" O THR a 367 " (cutoff:3.500A) Processing sheet with id=AG2, first strand: chain 'g' and resid 254 through 256 removed outlier: 9.312A pdb=" N GLN d 263 " --> pdb=" O SER b 254 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N VAL b 256 " --> pdb=" O GLN d 263 " (cutoff:3.500A) removed outlier: 7.030A pdb=" N VAL d 265 " --> pdb=" O VAL b 256 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL b 258 " --> pdb=" O VAL d 265 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N ARG b 255 " --> pdb=" O VAL e 268 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'a' and resid 486 through 489 Processing sheet with id=AG4, first strand: chain 'b' and resid 17 through 19 removed outlier: 4.207A pdb=" N VAL b 517 " --> pdb=" O ASP e 58 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N MET e 60 " --> pdb=" O VAL b 517 " (cutoff:3.500A) removed outlier: 6.579A pdb=" N ASN b 519 " --> pdb=" O MET e 60 " (cutoff:3.500A) removed outlier: 7.711A pdb=" N VAL e 62 " --> pdb=" O ASN b 519 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE b 521 " --> pdb=" O VAL e 62 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'b' and resid 61 through 64 removed outlier: 6.948A pdb=" N ASP b 49 " --> pdb=" O ASP d 534 " (cutoff:3.500A) removed outlier: 8.122A pdb=" N VAL d 536 " --> pdb=" O ASP b 49 " (cutoff:3.500A) removed outlier: 6.050A pdb=" N ILE b 51 " --> pdb=" O VAL d 536 " (cutoff:3.500A) Processing sheet with id=AG6, first strand: chain 'b' and resid 146 through 147 Processing sheet with id=AG7, first strand: chain 'b' and resid 199 through 205 removed outlier: 3.760A pdb=" N GLY b 377 " --> pdb=" O LYS b 204 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'b' and resid 218 through 220 removed outlier: 6.428A pdb=" N VAL b 365 " --> pdb=" O CYS b 346 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N CYS b 346 " --> pdb=" O VAL b 365 " (cutoff:3.500A) removed outlier: 6.752A pdb=" N SER b 345 " --> pdb=" O LYS b 236 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LYS b 236 " --> pdb=" O SER b 345 " (cutoff:3.500A) removed outlier: 6.830A pdb=" N LYS b 347 " --> pdb=" O ASN b 234 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'b' and resid 476 through 479 Processing sheet with id=AH1, first strand: chain 'd' and resid 208 through 214 removed outlier: 4.002A pdb=" N GLY d 392 " --> pdb=" O LYS d 213 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.613A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) Processing sheet with id=AH3, first strand: chain 'd' and resid 227 through 229 removed outlier: 6.613A pdb=" N LYS d 372 " --> pdb=" O ASN d 366 " (cutoff:3.500A) removed outlier: 6.638A pdb=" N ASN d 366 " --> pdb=" O LYS d 372 " (cutoff:3.500A) removed outlier: 6.556A pdb=" N LEU d 374 " --> pdb=" O GLU d 364 " (cutoff:3.500A) removed outlier: 6.605A pdb=" N GLU d 364 " --> pdb=" O LEU d 374 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE d 376 " --> pdb=" O ALA d 362 " (cutoff:3.500A) removed outlier: 6.639A pdb=" N ALA d 362 " --> pdb=" O ILE d 376 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N GLY d 378 " --> pdb=" O GLU d 360 " (cutoff:3.500A) removed outlier: 5.792A pdb=" N LYS d 245 " --> pdb=" O VAL d 297 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU d 299 " --> pdb=" O LYS d 245 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLY d 247 " --> pdb=" O LEU d 299 " (cutoff:3.500A) removed outlier: 7.595A pdb=" N GLN d 301 " --> pdb=" O GLY d 247 " (cutoff:3.500A) removed outlier: 7.705A pdb=" N ILE d 249 " --> pdb=" O GLN d 301 " (cutoff:3.500A) Processing sheet with id=AH4, first strand: chain 'd' and resid 421 through 423 Processing sheet with id=AH5, first strand: chain 'd' and resid 491 through 494 Processing sheet with id=AH6, first strand: chain 'e' and resid 26 through 29 removed outlier: 4.601A pdb=" N ILE e 530 " --> pdb=" O ASP h 46 " (cutoff:3.500A) removed outlier: 7.391A pdb=" N LEU h 48 " --> pdb=" O ILE e 530 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N ASP e 532 " --> pdb=" O LEU h 48 " (cutoff:3.500A) removed outlier: 7.931A pdb=" N VAL h 50 " --> pdb=" O ASP e 532 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N ARG e 534 " --> pdb=" O VAL h 50 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'e' and resid 153 through 154 Processing sheet with id=AH8, first strand: chain 'e' and resid 209 through 215 removed outlier: 4.008A pdb=" N GLY e 389 " --> pdb=" O LYS e 214 " (cutoff:3.500A) Processing sheet with id=AH9, first strand: chain 'e' and resid 228 through 230 removed outlier: 6.383A pdb=" N CYS e 377 " --> pdb=" O ALA e 356 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N ALA e 356 " --> pdb=" O CYS e 377 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N PHE e 355 " --> pdb=" O LYS e 247 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LYS e 247 " --> pdb=" O PHE e 355 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N GLY e 357 " --> pdb=" O ASP e 245 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'g' and resid 57 through 60 removed outlier: 7.212A pdb=" N MET g 47 " --> pdb=" O GLU z 520 " (cutoff:3.500A) removed outlier: 8.678A pdb=" N MET z 522 " --> pdb=" O MET g 47 " (cutoff:3.500A) removed outlier: 6.484A pdb=" N MET g 49 " --> pdb=" O MET z 522 " (cutoff:3.500A) Processing sheet with id=AI2, first strand: chain 'g' and resid 142 through 143 Processing sheet with id=AI3, first strand: chain 'g' and resid 185 through 187 Processing sheet with id=AI4, first strand: chain 'g' and resid 200 through 205 removed outlier: 6.901A pdb=" N ARG g 200 " --> pdb=" O ILE g 374 " (cutoff:3.500A) removed outlier: 7.477A pdb=" N LEU g 376 " --> pdb=" O ARG g 200 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N GLU g 202 " --> pdb=" O LEU g 376 " (cutoff:3.500A) removed outlier: 8.199A pdb=" N GLY g 378 " --> pdb=" O GLU g 202 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ILE g 204 " --> pdb=" O GLY g 378 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'g' and resid 218 through 220 Processing sheet with id=AI6, first strand: chain 'g' and resid 238 through 241 removed outlier: 6.306A pdb=" N VAL g 239 " --> pdb=" O ILE g 291 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'g' and resid 478 through 481 removed outlier: 3.713A pdb=" N THR g 486 " --> pdb=" O ASN g 481 " (cutoff:3.500A) Processing sheet with id=AI8, first strand: chain 'h' and resid 14 through 17 removed outlier: 6.220A pdb=" N ASN q 53 " --> pdb=" O VAL h 516 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N GLU h 518 " --> pdb=" O ASN q 53 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'h' and resid 141 through 142 Processing sheet with id=AJ1, first strand: chain 'h' and resid 195 through 201 removed outlier: 6.325A pdb=" N GLY h 196 " --> pdb=" O PHE h 372 " (cutoff:3.500A) removed outlier: 7.586A pdb=" N LEU h 374 " --> pdb=" O GLY h 196 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS h 198 " --> pdb=" O LEU h 374 " (cutoff:3.500A) removed outlier: 7.976A pdb=" N GLY h 376 " --> pdb=" O LYS h 198 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N VAL h 200 " --> pdb=" O GLY h 376 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'h' and resid 214 through 217 Processing sheet with id=AJ3, first strand: chain 'h' and resid 309 through 311 Processing sheet with id=AJ4, first strand: chain 'h' and resid 475 through 478 Processing sheet with id=AJ5, first strand: chain 'q' and resid 20 through 23 removed outlier: 6.742A pdb=" N MET z 44 " --> pdb=" O VAL q 521 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N GLN q 523 " --> pdb=" O MET z 44 " (cutoff:3.500A) Processing sheet with id=AJ6, first strand: chain 'q' and resid 149 through 150 removed outlier: 3.812A pdb=" N CYS q 149 " --> pdb=" O LEU q 408 " (cutoff:3.500A) Processing sheet with id=AJ7, first strand: chain 'q' and resid 202 through 208 removed outlier: 6.564A pdb=" N ARG q 203 " --> pdb=" O ILE q 375 " (cutoff:3.500A) removed outlier: 7.284A pdb=" N LEU q 377 " --> pdb=" O ARG q 203 " (cutoff:3.500A) removed outlier: 6.303A pdb=" N CYS q 205 " --> pdb=" O LEU q 377 " (cutoff:3.500A) removed outlier: 8.041A pdb=" N GLY q 379 " --> pdb=" O CYS q 205 " (cutoff:3.500A) removed outlier: 6.782A pdb=" N ILE q 207 " --> pdb=" O GLY q 379 " (cutoff:3.500A) Processing sheet with id=AJ8, first strand: chain 'q' and resid 220 through 223 Processing sheet with id=AJ9, first strand: chain 'q' and resid 240 through 242 Processing sheet with id=AK1, first strand: chain 'q' and resid 478 through 480 Processing sheet with id=AK2, first strand: chain 'z' and resid 139 through 140 Processing sheet with id=AK3, first strand: chain 'z' and resid 191 through 196 removed outlier: 6.458A pdb=" N GLU z 192 " --> pdb=" O LEU z 374 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N ILE z 376 " --> pdb=" O GLU z 192 " (cutoff:3.500A) removed outlier: 6.349A pdb=" N MET z 194 " --> pdb=" O ILE z 376 " (cutoff:3.500A) Processing sheet with id=AK4, first strand: chain 'z' and resid 210 through 212 Processing sheet with id=AK5, first strand: chain 'z' and resid 310 through 313 removed outlier: 8.936A pdb=" N VAL z 311 " --> pdb=" O LYS z 287 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N PHE z 289 " --> pdb=" O VAL z 311 " (cutoff:3.500A) removed outlier: 7.941A pdb=" N LEU z 313 " --> pdb=" O PHE z 289 " (cutoff:3.500A) removed outlier: 6.237A pdb=" N VAL z 291 " --> pdb=" O LEU z 313 " (cutoff:3.500A) removed outlier: 6.202A pdb=" N ASP z 227 " --> pdb=" O GLY z 288 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N VAL z 290 " --> pdb=" O ASP z 227 " (cutoff:3.500A) removed outlier: 6.013A pdb=" N TYR z 229 " --> pdb=" O VAL z 290 " (cutoff:3.500A) removed outlier: 7.286A pdb=" N ILE z 292 " --> pdb=" O TYR z 229 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N LEU z 231 " --> pdb=" O ILE z 292 " (cutoff:3.500A) Processing sheet with id=AK6, first strand: chain 'z' and resid 477 through 479 Processing sheet with id=AK7, first strand: chain 'P' and resid 162 through 164 removed outlier: 6.122A pdb=" N PHE P 162 " --> pdb=" O LYS P 216 " (cutoff:3.500A) removed outlier: 8.085A pdb=" N LYS P 218 " --> pdb=" O PHE P 162 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N ILE P 164 " --> pdb=" O LYS P 218 " (cutoff:3.500A) removed outlier: 7.935A pdb=" N CYS P 215 " --> pdb=" O VAL P 182 " (cutoff:3.500A) removed outlier: 6.062A pdb=" N MET P 184 " --> pdb=" O CYS P 215 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL P 217 " --> pdb=" O MET P 184 " (cutoff:3.500A) removed outlier: 5.725A pdb=" N HIS P 186 " --> pdb=" O VAL P 217 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA P 235 " --> pdb=" O ILE P 187 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LEU P 236 " --> pdb=" O ASN P 247 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N ASN P 247 " --> pdb=" O LEU P 236 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N ILE P 238 " --> pdb=" O ILE P 245 " (cutoff:3.500A) 4102 hydrogen bonds defined for protein. 11712 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 34.49 Time building geometry restraints manager: 15.49 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: 22621 1.34 - 1.46: 11837 1.46 - 1.58: 32719 1.58 - 1.70: 48 1.70 - 1.81: 735 Bond restraints: 67960 Sorted by residual: bond pdb=" F2 AF3 z 603 " pdb="AL AF3 z 603 " ideal model delta sigma weight residual 1.637 1.799 -0.162 2.00e-02 2.50e+03 6.54e+01 bond pdb=" F2 AF3 Z 603 " pdb="AL AF3 Z 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" F2 AF3 D 603 " pdb="AL AF3 D 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 d 603 " pdb="AL AF3 d 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.39e+01 bond pdb=" F2 AF3 g 603 " pdb="AL AF3 g 603 " ideal model delta sigma weight residual 1.637 1.797 -0.160 2.00e-02 2.50e+03 6.38e+01 ... (remaining 67955 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 90646 1.93 - 3.86: 836 3.86 - 5.79: 218 5.79 - 7.73: 52 7.73 - 9.66: 3 Bond angle restraints: 91755 Sorted by residual: angle pdb=" CA ARG P 149 " pdb=" CB ARG P 149 " pdb=" CG ARG P 149 " ideal model delta sigma weight residual 114.10 123.76 -9.66 2.00e+00 2.50e-01 2.33e+01 angle pdb=" C MET P 148 " pdb=" N ARG P 149 " pdb=" CA ARG P 149 " ideal model delta sigma weight residual 121.14 115.09 6.05 1.75e+00 3.27e-01 1.20e+01 angle pdb=" N GLY Q 209 " pdb=" CA GLY Q 209 " pdb=" C GLY Q 209 " ideal model delta sigma weight residual 113.18 120.95 -7.77 2.37e+00 1.78e-01 1.07e+01 angle pdb=" N GLY q 209 " pdb=" CA GLY q 209 " pdb=" C GLY q 209 " ideal model delta sigma weight residual 113.18 120.80 -7.62 2.37e+00 1.78e-01 1.03e+01 angle pdb=" C CYS E 181 " pdb=" N HIS E 182 " pdb=" CA HIS E 182 " ideal model delta sigma weight residual 121.54 127.28 -5.74 1.91e+00 2.74e-01 9.02e+00 ... (remaining 91750 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.66: 41312 35.66 - 71.32: 624 71.32 - 106.98: 63 106.98 - 142.63: 11 142.63 - 178.29: 8 Dihedral angle restraints: 42018 sinusoidal: 16924 harmonic: 25094 Sorted by residual: 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 -60.00 118.29 -178.29 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP Q 601 " pdb=" O3A ADP Q 601 " pdb=" PA ADP Q 601 " pdb=" PB ADP Q 601 " ideal model delta sinusoidal sigma weight residual 300.00 123.46 176.54 1 2.00e+01 2.50e-03 4.80e+01 dihedral pdb=" O2A ADP Z 601 " pdb=" O3A ADP Z 601 " pdb=" PA ADP Z 601 " pdb=" PB ADP Z 601 " ideal model delta sinusoidal sigma weight residual 300.00 127.50 172.50 1 2.00e+01 2.50e-03 4.78e+01 ... (remaining 42015 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 8475 0.045 - 0.090: 1758 0.090 - 0.135: 679 0.135 - 0.179: 10 0.179 - 0.224: 1 Chirality restraints: 10923 Sorted by residual: chirality pdb=" CA ARG P 149 " pdb=" N ARG P 149 " pdb=" C ARG P 149 " pdb=" CB ARG P 149 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CA ILE g 363 " pdb=" N ILE g 363 " pdb=" C ILE g 363 " pdb=" CB ILE g 363 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.75e-01 chirality pdb=" CB ILE G 460 " pdb=" CA ILE G 460 " pdb=" CG1 ILE G 460 " pdb=" CG2 ILE G 460 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 10920 not shown) Planarity restraints: 11716 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS e 440 " 0.033 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO e 441 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO e 441 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO e 441 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET H 2 " 0.027 5.00e-02 4.00e+02 4.06e-02 2.64e+00 pdb=" N PRO H 3 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO H 3 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO H 3 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU P 274 " 0.024 5.00e-02 4.00e+02 3.74e-02 2.24e+00 pdb=" N PRO P 275 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO P 275 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO P 275 " 0.021 5.00e-02 4.00e+02 ... (remaining 11713 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 566 2.54 - 3.13: 51628 3.13 - 3.72: 106521 3.72 - 4.31: 150008 4.31 - 4.90: 255885 Nonbonded interactions: 564608 Sorted by model distance: nonbonded pdb="MG MG D 602 " pdb=" F2 AF3 D 603 " model vdw 1.955 2.120 nonbonded pdb="MG MG H 602 " pdb=" F2 AF3 H 603 " model vdw 1.957 2.120 nonbonded pdb="MG MG E 602 " pdb=" F1 AF3 E 603 " model vdw 1.971 2.120 nonbonded pdb="MG MG d 602 " pdb=" F1 AF3 d 603 " model vdw 1.971 2.120 nonbonded pdb="MG MG e 602 " pdb=" F1 AF3 e 603 " model vdw 1.987 2.120 ... (remaining 564603 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' selection = (chain 'g' and (resid 3 through 528 or resid 601 through 603)) } ncs_group { reference = (chain 'H' and (resid 1 through 525 or resid 601 through 603)) selection = chain 'h' } ncs_group { reference = (chain 'Q' and (resid 2 through 534 or resid 601 through 603)) selection = chain 'q' } ncs_group { reference = chain 'Z' selection = (chain 'z' and (resid 2 through 526 or resid 601 through 603)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.800 Set stop_for_unknowns flag: 0.010 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.070 Extract box with map and model: 2.140 Check model and map are aligned: 0.390 Set scattering table: 0.470 Process input model: 132.990 Find NCS groups from input model: 5.940 Set up NCS constraints: 0.510 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:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 155.680 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.162 67960 Z= 0.272 Angle : 0.521 9.658 91755 Z= 0.254 Chirality : 0.041 0.224 10923 Planarity : 0.003 0.051 11716 Dihedral : 14.495 178.292 25766 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8685 helix: 2.33 (0.08), residues: 4481 sheet: 0.55 (0.16), residues: 1109 loop : -0.28 (0.11), residues: 3095 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP g 168 HIS 0.007 0.001 HIS z 161 PHE 0.019 0.001 PHE e 386 TYR 0.015 0.001 TYR b 297 ARG 0.007 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 606 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 606 time to evaluate : 5.961 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 187 GLN cc_start: 0.8734 (mm110) cc_final: 0.8301 (pm20) REVERT: G 15 LYS cc_start: 0.8634 (mmtm) cc_final: 0.8393 (mmtt) REVERT: G 52 ASP cc_start: 0.8311 (t70) cc_final: 0.7583 (t0) REVERT: G 54 MET cc_start: 0.8158 (mpp) cc_final: 0.7777 (mpt) REVERT: G 497 GLU cc_start: 0.8370 (pt0) cc_final: 0.8128 (pt0) REVERT: H 14 ASP cc_start: 0.8445 (t0) cc_final: 0.8200 (t0) REVERT: H 81 ASP cc_start: 0.8430 (m-30) cc_final: 0.8065 (m-30) REVERT: H 185 MET cc_start: 0.8635 (mtp) cc_final: 0.8417 (mtp) REVERT: H 316 GLU cc_start: 0.8142 (tt0) cc_final: 0.7831 (tp30) REVERT: H 324 MET cc_start: 0.9172 (mmm) cc_final: 0.8905 (mmm) REVERT: Q 34 GLN cc_start: 0.7921 (tp-100) cc_final: 0.7506 (tp-100) REVERT: Z 10 LYS cc_start: 0.8899 (mtmm) cc_final: 0.8688 (mtmm) REVERT: Z 108 LEU cc_start: 0.9113 (tp) cc_final: 0.8907 (tp) REVERT: e 20 LYS cc_start: 0.8769 (ttmt) cc_final: 0.8567 (ttmm) REVERT: h 401 LYS cc_start: 0.8088 (mmtt) cc_final: 0.7723 (tmmt) REVERT: h 440 LYS cc_start: 0.9049 (ttmt) cc_final: 0.8849 (ttmm) REVERT: z 53 ASP cc_start: 0.8614 (m-30) cc_final: 0.8338 (m-30) REVERT: z 472 GLU cc_start: 0.8334 (tm-30) cc_final: 0.8127 (tp30) REVERT: P 80 GLN cc_start: 0.8651 (mm-40) cc_final: 0.8336 (mm-40) REVERT: P 231 ASN cc_start: 0.8140 (p0) cc_final: 0.7475 (p0) outliers start: 0 outliers final: 0 residues processed: 606 average time/residue: 1.6949 time to fit residues: 1303.7797 Evaluate side-chains 499 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 499 time to evaluate : 5.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 729 optimal weight: 10.0000 chunk 654 optimal weight: 0.0870 chunk 363 optimal weight: 6.9990 chunk 223 optimal weight: 1.9990 chunk 441 optimal weight: 9.9990 chunk 349 optimal weight: 9.9990 chunk 677 optimal weight: 1.9990 chunk 262 optimal weight: 0.7980 chunk 411 optimal weight: 2.9990 chunk 504 optimal weight: 5.9990 chunk 784 optimal weight: 1.9990 overall best weight: 1.3764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 84 GLN ** a 534 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 394 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 84 GLN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.073156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2705 r_free = 0.2705 target = 0.059314 restraints weight = 164917.559| |-----------------------------------------------------------------------------| r_work (start): 0.2705 rms_B_bonded: 2.91 r_work: 0.2566 rms_B_bonded: 3.27 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) = 0.053 | | 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) = 0.053 | | 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: 0.8535 moved from start: 0.0757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 67960 Z= 0.183 Angle : 0.548 9.152 91755 Z= 0.273 Chirality : 0.042 0.170 10923 Planarity : 0.003 0.052 11716 Dihedral : 7.832 178.265 9433 Min Nonbonded Distance : 1.950 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.59 % Allowed : 5.83 % Favored : 93.58 % 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: 1.78 (0.09), residues: 8685 helix: 2.37 (0.08), residues: 4510 sheet: 0.39 (0.16), residues: 1098 loop : -0.31 (0.11), residues: 3077 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP P 66 HIS 0.010 0.001 HIS z 161 PHE 0.018 0.001 PHE A 167 TYR 0.023 0.001 TYR A 181 ARG 0.012 0.000 ARG P 230 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 588 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 545 time to evaluate : 5.933 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8626 (tp30) cc_final: 0.8390 (tp30) REVERT: A 187 GLN cc_start: 0.8944 (mm110) cc_final: 0.8112 (pm20) REVERT: E 393 MET cc_start: 0.8828 (mpt) cc_final: 0.8571 (mpt) REVERT: G 52 ASP cc_start: 0.8459 (t70) cc_final: 0.7702 (t0) REVERT: G 54 MET cc_start: 0.8632 (mpp) cc_final: 0.8257 (mpt) REVERT: G 497 GLU cc_start: 0.8641 (pt0) cc_final: 0.8385 (pt0) REVERT: H 14 ASP cc_start: 0.8481 (t0) cc_final: 0.8161 (t0) REVERT: H 81 ASP cc_start: 0.8824 (m-30) cc_final: 0.8487 (m-30) REVERT: H 185 MET cc_start: 0.8916 (mtp) cc_final: 0.8601 (mtp) REVERT: H 316 GLU cc_start: 0.8613 (tt0) cc_final: 0.7798 (tp30) REVERT: H 324 MET cc_start: 0.9269 (mmm) cc_final: 0.8993 (mmm) REVERT: Q 27 GLU cc_start: 0.8787 (mt-10) cc_final: 0.8530 (mt-10) REVERT: Q 34 GLN cc_start: 0.8073 (tp-100) cc_final: 0.7628 (tp-100) REVERT: Z 353 TYR cc_start: 0.8940 (t80) cc_final: 0.8641 (t80) REVERT: a 66 GLU cc_start: 0.9127 (tt0) cc_final: 0.8821 (pt0) REVERT: a 246 MET cc_start: 0.9191 (mmm) cc_final: 0.8933 (mmt) REVERT: a 306 MET cc_start: 0.9058 (mtp) cc_final: 0.8789 (mtm) REVERT: e 20 LYS cc_start: 0.8828 (ttmt) cc_final: 0.8584 (ttmm) REVERT: e 160 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.9012 (mtmm) REVERT: g 306 ARG cc_start: 0.8428 (OUTLIER) cc_final: 0.8028 (mtm-85) REVERT: g 415 GLU cc_start: 0.8986 (mp0) cc_final: 0.8736 (mp0) REVERT: g 521 ASP cc_start: 0.8914 (t0) cc_final: 0.8693 (t0) REVERT: g 528 LYS cc_start: 0.8925 (OUTLIER) cc_final: 0.8484 (tmmt) REVERT: h 221 SER cc_start: 0.9201 (m) cc_final: 0.8860 (p) REVERT: h 401 LYS cc_start: 0.8087 (mmtt) cc_final: 0.7610 (tmmt) REVERT: h 440 LYS cc_start: 0.9140 (ttmt) cc_final: 0.8873 (ttmm) REVERT: q 61 GLU cc_start: 0.9038 (mp0) cc_final: 0.8246 (mp0) REVERT: z 53 ASP cc_start: 0.8798 (m-30) cc_final: 0.8520 (m-30) REVERT: z 352 GLU cc_start: 0.9098 (OUTLIER) cc_final: 0.8661 (tt0) REVERT: P 80 GLN cc_start: 0.8662 (mm-40) cc_final: 0.8249 (tp40) REVERT: P 231 ASN cc_start: 0.8327 (p0) cc_final: 0.8097 (p0) outliers start: 43 outliers final: 9 residues processed: 562 average time/residue: 1.6617 time to fit residues: 1190.3101 Evaluate side-chains 523 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 510 time to evaluate : 5.916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 29 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 161 HIS Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 352 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 187 optimal weight: 4.9990 chunk 145 optimal weight: 10.0000 chunk 558 optimal weight: 4.9990 chunk 701 optimal weight: 10.0000 chunk 543 optimal weight: 9.9990 chunk 852 optimal weight: 4.9990 chunk 378 optimal weight: 0.9990 chunk 440 optimal weight: 3.9990 chunk 490 optimal weight: 10.0000 chunk 350 optimal weight: 3.9990 chunk 293 optimal weight: 1.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS D 366 ASN D 502 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 501 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2918 r_free = 0.2918 target = 0.070727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2652 r_free = 0.2652 target = 0.056789 restraints weight = 170965.108| |-----------------------------------------------------------------------------| r_work (start): 0.2654 rms_B_bonded: 2.94 r_work: 0.2513 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.2513 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2527 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2527 r_free = 0.2527 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 = 0.2527 r_free = 0.2527 target_work(ls_wunit_k1) = 0.051 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2527 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8557 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 67960 Z= 0.313 Angle : 0.581 9.633 91755 Z= 0.288 Chirality : 0.043 0.170 10923 Planarity : 0.003 0.052 11716 Dihedral : 7.755 176.876 9433 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 0.85 % Allowed : 7.64 % Favored : 91.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.09), residues: 8685 helix: 2.30 (0.08), residues: 4530 sheet: 0.28 (0.16), residues: 1103 loop : -0.34 (0.11), residues: 3052 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.011 0.001 HIS Z 161 PHE 0.020 0.002 PHE A 167 TYR 0.015 0.001 TYR Q 304 ARG 0.010 0.000 ARG P 250 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 586 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 62 poor density : 524 time to evaluate : 6.067 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8567 (tp30) cc_final: 0.8311 (tp30) REVERT: A 187 GLN cc_start: 0.8943 (mm110) cc_final: 0.8080 (pm20) REVERT: A 358 ASP cc_start: 0.8893 (OUTLIER) cc_final: 0.8607 (t0) REVERT: G 52 ASP cc_start: 0.8462 (t70) cc_final: 0.7710 (t0) REVERT: G 54 MET cc_start: 0.8629 (mpp) cc_final: 0.8261 (mpt) REVERT: G 497 GLU cc_start: 0.8710 (pt0) cc_final: 0.8410 (pt0) REVERT: H 14 ASP cc_start: 0.8469 (t0) cc_final: 0.8067 (t0) REVERT: H 81 ASP cc_start: 0.8812 (m-30) cc_final: 0.8506 (m-30) REVERT: H 185 MET cc_start: 0.8941 (mtp) cc_final: 0.8694 (mtp) REVERT: H 316 GLU cc_start: 0.8613 (tt0) cc_final: 0.7995 (tp30) REVERT: H 317 GLU cc_start: 0.8560 (mt-10) cc_final: 0.8300 (mp0) REVERT: H 324 MET cc_start: 0.9258 (mmm) cc_final: 0.8980 (mmm) REVERT: Q 27 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8612 (mt-10) REVERT: Q 34 GLN cc_start: 0.8139 (tp-100) cc_final: 0.7724 (tp-100) REVERT: a 246 MET cc_start: 0.9281 (mmm) cc_final: 0.8992 (mmt) REVERT: a 306 MET cc_start: 0.9022 (mtp) cc_final: 0.8807 (mtm) REVERT: a 344 MET cc_start: 0.9307 (mmt) cc_final: 0.9092 (mmt) REVERT: b 495 GLU cc_start: 0.8793 (mt-10) cc_final: 0.8568 (mt-10) REVERT: e 20 LYS cc_start: 0.8768 (ttmt) cc_final: 0.8538 (ttmm) REVERT: e 160 LYS cc_start: 0.9285 (OUTLIER) cc_final: 0.9039 (mtmm) REVERT: e 185 MET cc_start: 0.9031 (mmt) cc_final: 0.8747 (mmm) REVERT: g 306 ARG cc_start: 0.8522 (OUTLIER) cc_final: 0.8103 (mtm-85) REVERT: g 415 GLU cc_start: 0.9032 (mp0) cc_final: 0.8771 (mp0) REVERT: g 521 ASP cc_start: 0.8914 (t0) cc_final: 0.8701 (t0) REVERT: g 528 LYS cc_start: 0.8843 (OUTLIER) cc_final: 0.8428 (tmmt) REVERT: h 401 LYS cc_start: 0.8184 (mmtt) cc_final: 0.7690 (tmmt) REVERT: h 440 LYS cc_start: 0.9138 (ttmt) cc_final: 0.8867 (ttmm) REVERT: q 61 GLU cc_start: 0.8989 (mp0) cc_final: 0.8294 (mp0) REVERT: z 53 ASP cc_start: 0.8779 (m-30) cc_final: 0.8514 (m-30) REVERT: P 145 MET cc_start: 0.8859 (ppp) cc_final: 0.8638 (ppp) REVERT: P 149 ARG cc_start: 0.8583 (OUTLIER) cc_final: 0.8377 (ptt90) REVERT: P 230 ARG cc_start: 0.8376 (ptm-80) cc_final: 0.8063 (ptm-80) REVERT: P 231 ASN cc_start: 0.8325 (p0) cc_final: 0.7981 (p0) outliers start: 62 outliers final: 22 residues processed: 555 average time/residue: 1.6621 time to fit residues: 1180.2124 Evaluate side-chains 525 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 498 time to evaluate : 5.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain N residue 268 MET Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain P residue 149 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 364 optimal weight: 2.9990 chunk 467 optimal weight: 4.9990 chunk 780 optimal weight: 0.0020 chunk 430 optimal weight: 2.9990 chunk 238 optimal weight: 0.9990 chunk 262 optimal weight: 7.9990 chunk 18 optimal weight: 0.9990 chunk 742 optimal weight: 0.8980 chunk 426 optimal weight: 2.9990 chunk 655 optimal weight: 10.0000 chunk 400 optimal weight: 6.9990 overall best weight: 1.1794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 366 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 390 ASN Q 53 ASN ** a 534 HIS ** 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 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2964 r_free = 0.2964 target = 0.073224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2708 r_free = 0.2708 target = 0.059452 restraints weight = 155734.124| |-----------------------------------------------------------------------------| r_work (start): 0.2709 rms_B_bonded: 2.82 r_work: 0.2571 rms_B_bonded: 3.18 restraints_weight: 0.5000 r_work (final): 0.2571 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2588 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2588 r_free = 0.2588 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2588 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8510 moved from start: 0.1001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 67960 Z= 0.162 Angle : 0.528 10.184 91755 Z= 0.260 Chirality : 0.041 0.173 10923 Planarity : 0.003 0.052 11716 Dihedral : 7.485 172.483 9433 Min Nonbonded Distance : 1.945 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.02 % Favored : 96.98 % Rotamer: Outliers : 0.80 % Allowed : 8.62 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8685 helix: 2.42 (0.08), residues: 4520 sheet: 0.23 (0.16), residues: 1075 loop : -0.35 (0.11), residues: 3090 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.009 0.001 HIS z 161 PHE 0.025 0.001 PHE P 69 TYR 0.027 0.001 TYR A 181 ARG 0.009 0.000 ARG P 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 600 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 542 time to evaluate : 6.085 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8592 (tp30) cc_final: 0.8292 (tp30) REVERT: A 187 GLN cc_start: 0.8969 (mm110) cc_final: 0.8089 (pm20) REVERT: A 306 MET cc_start: 0.8550 (mtt) cc_final: 0.8335 (mtt) REVERT: D 25 GLN cc_start: 0.8620 (tp-100) cc_final: 0.8381 (tp-100) REVERT: D 65 LYS cc_start: 0.9066 (OUTLIER) cc_final: 0.8506 (mtmm) REVERT: D 331 GLU cc_start: 0.8868 (mp0) cc_final: 0.8578 (pm20) REVERT: D 486 GLN cc_start: 0.8841 (OUTLIER) cc_final: 0.8501 (mt0) REVERT: G 52 ASP cc_start: 0.8453 (t70) cc_final: 0.7674 (t0) REVERT: G 54 MET cc_start: 0.8659 (mpp) cc_final: 0.8252 (mpt) REVERT: G 497 GLU cc_start: 0.8650 (pt0) cc_final: 0.8368 (pt0) REVERT: H 14 ASP cc_start: 0.8446 (t0) cc_final: 0.8103 (t0) REVERT: H 81 ASP cc_start: 0.8790 (m-30) cc_final: 0.8454 (m-30) REVERT: H 316 GLU cc_start: 0.8577 (tt0) cc_final: 0.7835 (tp30) REVERT: H 324 MET cc_start: 0.9244 (mmm) cc_final: 0.8953 (mmm) REVERT: Q 34 GLN cc_start: 0.8053 (tp-100) cc_final: 0.7626 (tp-100) REVERT: Z 353 TYR cc_start: 0.8926 (t80) cc_final: 0.8603 (t80) REVERT: a 66 GLU cc_start: 0.9113 (tt0) cc_final: 0.8706 (pt0) REVERT: a 306 MET cc_start: 0.8990 (mtp) cc_final: 0.8788 (mtm) REVERT: b 495 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8587 (mt-10) REVERT: e 20 LYS cc_start: 0.8832 (ttmt) cc_final: 0.8611 (ttmm) REVERT: e 160 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.9076 (mtmm) REVERT: e 185 MET cc_start: 0.8990 (mmt) cc_final: 0.8709 (mmm) REVERT: g 306 ARG cc_start: 0.8412 (OUTLIER) cc_final: 0.8053 (mtm-85) REVERT: g 415 GLU cc_start: 0.9044 (mp0) cc_final: 0.8747 (mp0) REVERT: g 521 ASP cc_start: 0.8910 (t0) cc_final: 0.8697 (t0) REVERT: g 528 LYS cc_start: 0.8867 (OUTLIER) cc_final: 0.8454 (tmmt) REVERT: h 221 SER cc_start: 0.9228 (m) cc_final: 0.8850 (p) REVERT: h 401 LYS cc_start: 0.8156 (mmtt) cc_final: 0.7661 (tmmt) REVERT: h 440 LYS cc_start: 0.9107 (ttmt) cc_final: 0.8842 (ttmm) REVERT: q 61 GLU cc_start: 0.8997 (OUTLIER) cc_final: 0.8361 (mp0) REVERT: q 318 LYS cc_start: 0.8720 (pptt) cc_final: 0.8487 (pptt) REVERT: z 53 ASP cc_start: 0.8714 (m-30) cc_final: 0.8459 (m-30) REVERT: P 80 GLN cc_start: 0.8610 (mm-40) cc_final: 0.8227 (mm-40) REVERT: P 230 ARG cc_start: 0.8321 (ptm-80) cc_final: 0.8062 (ptm-80) REVERT: P 231 ASN cc_start: 0.8141 (p0) cc_final: 0.7767 (p0) REVERT: P 271 PHE cc_start: 0.8577 (m-10) cc_final: 0.8373 (m-10) outliers start: 58 outliers final: 21 residues processed: 565 average time/residue: 1.6230 time to fit residues: 1175.6350 Evaluate side-chains 535 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 508 time to evaluate : 5.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 486 GLN Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 430 CYS Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 161 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 298 optimal weight: 10.0000 chunk 329 optimal weight: 0.8980 chunk 157 optimal weight: 9.9990 chunk 723 optimal weight: 8.9990 chunk 615 optimal weight: 5.9990 chunk 224 optimal weight: 6.9990 chunk 361 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 537 optimal weight: 0.5980 chunk 12 optimal weight: 7.9990 chunk 572 optimal weight: 7.9990 overall best weight: 2.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** z 95 ASN z 161 HIS ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.071943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.058143 restraints weight = 161279.198| |-----------------------------------------------------------------------------| r_work (start): 0.2681 rms_B_bonded: 2.84 r_work: 0.2544 rms_B_bonded: 3.17 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2561 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2561 r_free = 0.2561 target_work(ls_wunit_k1) = 0.053 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2561 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 67960 Z= 0.236 Angle : 0.547 10.660 91755 Z= 0.268 Chirality : 0.042 0.169 10923 Planarity : 0.003 0.052 11716 Dihedral : 7.378 171.335 9433 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 5.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.98 % Allowed : 9.37 % Favored : 89.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.74 (0.09), residues: 8685 helix: 2.40 (0.08), residues: 4526 sheet: 0.17 (0.16), residues: 1093 loop : -0.35 (0.11), residues: 3066 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.010 0.001 HIS z 161 PHE 0.018 0.001 PHE A 167 TYR 0.012 0.001 TYR Q 304 ARG 0.008 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 71 poor density : 519 time to evaluate : 6.048 Fit side-chains revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8597 (tp30) cc_final: 0.8281 (tp30) REVERT: A 142 GLU cc_start: 0.8514 (OUTLIER) cc_final: 0.8271 (pm20) REVERT: A 187 GLN cc_start: 0.9002 (mm110) cc_final: 0.8160 (pm20) REVERT: A 358 ASP cc_start: 0.8908 (OUTLIER) cc_final: 0.8706 (t0) REVERT: D 25 GLN cc_start: 0.8669 (tp-100) cc_final: 0.8430 (tp-100) REVERT: D 65 LYS cc_start: 0.9047 (OUTLIER) cc_final: 0.8536 (mtmm) REVERT: D 331 GLU cc_start: 0.8917 (mp0) cc_final: 0.8536 (pm20) REVERT: G 52 ASP cc_start: 0.8467 (t70) cc_final: 0.7680 (t0) REVERT: G 54 MET cc_start: 0.8663 (mpp) cc_final: 0.8254 (mpt) REVERT: G 497 GLU cc_start: 0.8676 (pt0) cc_final: 0.8407 (pt0) REVERT: H 14 ASP cc_start: 0.8467 (t0) cc_final: 0.8121 (t0) REVERT: H 81 ASP cc_start: 0.8794 (m-30) cc_final: 0.8480 (m-30) REVERT: H 316 GLU cc_start: 0.8623 (tt0) cc_final: 0.7884 (tp30) REVERT: H 324 MET cc_start: 0.9247 (mmm) cc_final: 0.8983 (mmm) REVERT: Q 34 GLN cc_start: 0.8093 (tp-100) cc_final: 0.7685 (tp-100) REVERT: a 66 GLU cc_start: 0.9107 (tt0) cc_final: 0.8832 (pt0) REVERT: b 495 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8566 (mt-10) REVERT: e 20 LYS cc_start: 0.8808 (ttmt) cc_final: 0.8587 (ttmm) REVERT: e 160 LYS cc_start: 0.9301 (OUTLIER) cc_final: 0.9080 (mtmm) REVERT: e 185 MET cc_start: 0.8976 (mmt) cc_final: 0.8692 (mmm) REVERT: g 59 MET cc_start: 0.9398 (ttp) cc_final: 0.9185 (ttp) REVERT: g 306 ARG cc_start: 0.8491 (OUTLIER) cc_final: 0.8112 (mtm-85) REVERT: g 415 GLU cc_start: 0.9013 (mp0) cc_final: 0.8706 (mp0) REVERT: g 521 ASP cc_start: 0.8904 (t0) cc_final: 0.8665 (t0) REVERT: g 528 LYS cc_start: 0.8853 (OUTLIER) cc_final: 0.8420 (tmmt) REVERT: h 221 SER cc_start: 0.9204 (m) cc_final: 0.8882 (p) REVERT: h 356 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: h 401 LYS cc_start: 0.8179 (mmtt) cc_final: 0.7670 (tmmt) REVERT: h 440 LYS cc_start: 0.9124 (ttmt) cc_final: 0.8855 (ttmm) REVERT: h 524 ARG cc_start: 0.8532 (mmm-85) cc_final: 0.8163 (mmm-85) REVERT: q 61 GLU cc_start: 0.8984 (OUTLIER) cc_final: 0.8255 (mp0) REVERT: q 152 LYS cc_start: 0.9363 (OUTLIER) cc_final: 0.9143 (ptmm) REVERT: z 53 ASP cc_start: 0.8711 (m-30) cc_final: 0.8456 (m-30) REVERT: P 80 GLN cc_start: 0.8519 (mm-40) cc_final: 0.8131 (mm-40) REVERT: P 202 MET cc_start: 0.9145 (mtp) cc_final: 0.8904 (mtm) REVERT: P 230 ARG cc_start: 0.8252 (ptm-80) cc_final: 0.8006 (ptm-80) REVERT: P 231 ASN cc_start: 0.8090 (p0) cc_final: 0.7793 (p0) REVERT: P 271 PHE cc_start: 0.8543 (m-10) cc_final: 0.8310 (m-10) outliers start: 71 outliers final: 30 residues processed: 559 average time/residue: 1.6592 time to fit residues: 1195.6586 Evaluate side-chains 541 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 502 time to evaluate : 5.928 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain A residue 358 ASP Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 55 MET Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 191 optimal weight: 8.9990 chunk 287 optimal weight: 7.9990 chunk 209 optimal weight: 0.4980 chunk 763 optimal weight: 6.9990 chunk 26 optimal weight: 6.9990 chunk 147 optimal weight: 5.9990 chunk 169 optimal weight: 0.0060 chunk 676 optimal weight: 9.9990 chunk 440 optimal weight: 2.9990 chunk 439 optimal weight: 0.9990 chunk 585 optimal weight: 9.9990 overall best weight: 2.1002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 515 GLN ** 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 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.072157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2681 r_free = 0.2681 target = 0.058140 restraints weight = 170173.107| |-----------------------------------------------------------------------------| r_work (start): 0.2680 rms_B_bonded: 2.96 r_work: 0.2537 rms_B_bonded: 3.30 restraints_weight: 0.5000 r_work (final): 0.2537 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2554 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2554 r_free = 0.2554 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2554 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8531 moved from start: 0.1076 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 67960 Z= 0.223 Angle : 0.548 11.172 91755 Z= 0.269 Chirality : 0.042 0.169 10923 Planarity : 0.003 0.052 11716 Dihedral : 7.240 168.508 9433 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.95 % Allowed : 10.02 % Favored : 89.04 % 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: 1.74 (0.09), residues: 8685 helix: 2.41 (0.08), residues: 4525 sheet: 0.15 (0.16), residues: 1097 loop : -0.36 (0.11), residues: 3063 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.009 0.001 HIS z 161 PHE 0.017 0.001 PHE P 69 TYR 0.027 0.001 TYR A 181 ARG 0.008 0.000 ARG P 149 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 585 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 516 time to evaluate : 6.051 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7310 (m-30) cc_final: 0.7100 (p0) REVERT: A 106 GLU cc_start: 0.8621 (tp30) cc_final: 0.8304 (tp30) REVERT: A 142 GLU cc_start: 0.8563 (OUTLIER) cc_final: 0.8297 (pm20) REVERT: A 187 GLN cc_start: 0.9019 (mm110) cc_final: 0.8156 (pm20) REVERT: A 306 MET cc_start: 0.8627 (mtt) cc_final: 0.8321 (mtt) REVERT: B 302 GLN cc_start: 0.9411 (OUTLIER) cc_final: 0.9164 (tt0) REVERT: D 25 GLN cc_start: 0.8657 (tp-100) cc_final: 0.8404 (tp-100) REVERT: D 65 LYS cc_start: 0.9027 (OUTLIER) cc_final: 0.8495 (mtmm) REVERT: D 331 GLU cc_start: 0.8901 (mp0) cc_final: 0.8511 (pm20) REVERT: G 52 ASP cc_start: 0.8439 (t70) cc_final: 0.7539 (t0) REVERT: G 54 MET cc_start: 0.8682 (mpp) cc_final: 0.8258 (mpt) REVERT: G 497 GLU cc_start: 0.8671 (pt0) cc_final: 0.8399 (pt0) REVERT: H 14 ASP cc_start: 0.8460 (t0) cc_final: 0.8112 (t0) REVERT: H 81 ASP cc_start: 0.8803 (m-30) cc_final: 0.8476 (m-30) REVERT: H 316 GLU cc_start: 0.8636 (tt0) cc_final: 0.7889 (tp30) REVERT: H 324 MET cc_start: 0.9247 (mmm) cc_final: 0.8984 (mmm) REVERT: Q 34 GLN cc_start: 0.8090 (tp-100) cc_final: 0.7693 (tp-100) REVERT: Z 353 TYR cc_start: 0.8915 (t80) cc_final: 0.8629 (t80) REVERT: a 66 GLU cc_start: 0.9144 (tt0) cc_final: 0.8844 (pt0) REVERT: a 344 MET cc_start: 0.9301 (mmt) cc_final: 0.9095 (mmt) REVERT: b 495 GLU cc_start: 0.8834 (mt-10) cc_final: 0.8609 (mt-10) REVERT: e 20 LYS cc_start: 0.8814 (ttmt) cc_final: 0.8592 (ttmm) REVERT: e 160 LYS cc_start: 0.9302 (OUTLIER) cc_final: 0.9085 (mtmm) REVERT: e 185 MET cc_start: 0.8969 (mmt) cc_final: 0.8687 (mmm) REVERT: e 212 GLU cc_start: 0.8435 (OUTLIER) cc_final: 0.8201 (tp30) REVERT: g 306 ARG cc_start: 0.8478 (OUTLIER) cc_final: 0.8127 (mtm-85) REVERT: g 415 GLU cc_start: 0.9027 (mp0) cc_final: 0.8708 (mp0) REVERT: g 521 ASP cc_start: 0.8915 (t0) cc_final: 0.8684 (t0) REVERT: g 528 LYS cc_start: 0.8857 (OUTLIER) cc_final: 0.8423 (tmmt) REVERT: h 221 SER cc_start: 0.9201 (m) cc_final: 0.8884 (p) REVERT: h 356 GLU cc_start: 0.8603 (OUTLIER) cc_final: 0.8139 (mt-10) REVERT: h 401 LYS cc_start: 0.8147 (mmtt) cc_final: 0.7661 (tmmt) REVERT: h 440 LYS cc_start: 0.9126 (ttmt) cc_final: 0.8857 (ttmm) REVERT: h 524 ARG cc_start: 0.8533 (mmm-85) cc_final: 0.8139 (mmm-85) REVERT: q 61 GLU cc_start: 0.9009 (OUTLIER) cc_final: 0.8320 (mp0) REVERT: q 152 LYS cc_start: 0.9355 (OUTLIER) cc_final: 0.9133 (ptmm) REVERT: q 318 LYS cc_start: 0.8775 (pptt) cc_final: 0.8496 (pptt) REVERT: z 53 ASP cc_start: 0.8695 (m-30) cc_final: 0.8464 (m-30) REVERT: P 80 GLN cc_start: 0.8556 (mm-40) cc_final: 0.8197 (mm-40) REVERT: P 86 ARG cc_start: 0.8797 (tmm160) cc_final: 0.8495 (tmm160) REVERT: P 145 MET cc_start: 0.8762 (ppp) cc_final: 0.8225 (ppp) REVERT: P 202 MET cc_start: 0.9146 (mtp) cc_final: 0.8919 (mtm) REVERT: P 230 ARG cc_start: 0.8247 (ptm-80) cc_final: 0.7980 (ptm-80) REVERT: P 231 ASN cc_start: 0.8111 (p0) cc_final: 0.7799 (p0) REVERT: P 271 PHE cc_start: 0.8547 (m-10) cc_final: 0.8309 (m-10) outliers start: 69 outliers final: 29 residues processed: 554 average time/residue: 1.6298 time to fit residues: 1167.2109 Evaluate side-chains 548 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 509 time to evaluate : 6.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 302 GLN Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain H residue 160 MET Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain e residue 212 GLU Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 356 GLU Chi-restraints excluded: chain h residue 366 LYS Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 423 optimal weight: 9.9990 chunk 42 optimal weight: 4.9990 chunk 578 optimal weight: 9.9990 chunk 181 optimal weight: 0.0970 chunk 782 optimal weight: 8.9990 chunk 841 optimal weight: 6.9990 chunk 465 optimal weight: 9.9990 chunk 652 optimal weight: 2.9990 chunk 111 optimal weight: 8.9990 chunk 566 optimal weight: 2.9990 chunk 121 optimal weight: 1.9990 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** 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 153 HIS P 199 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2932 r_free = 0.2932 target = 0.071418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2676 r_free = 0.2676 target = 0.057922 restraints weight = 143418.559| |-----------------------------------------------------------------------------| r_work (start): 0.2687 rms_B_bonded: 2.68 r_work: 0.2557 rms_B_bonded: 3.00 restraints_weight: 0.5000 r_work: 0.2434 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.2434 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2438 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2438 r_free = 0.2438 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2438 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 67960 Z= 0.264 Angle : 0.558 11.265 91755 Z= 0.275 Chirality : 0.042 0.169 10923 Planarity : 0.003 0.079 11716 Dihedral : 7.188 167.099 9433 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.34 % Favored : 96.66 % Rotamer: Outliers : 0.92 % Allowed : 10.48 % Favored : 88.60 % 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: 1.71 (0.09), residues: 8685 helix: 2.37 (0.08), residues: 4537 sheet: 0.14 (0.16), residues: 1099 loop : -0.36 (0.11), residues: 3049 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.010 0.001 HIS z 161 PHE 0.017 0.001 PHE A 167 TYR 0.013 0.001 TYR Q 304 ARG 0.009 0.000 ARG P 141 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 575 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 67 poor density : 508 time to evaluate : 6.176 Fit side-chains REVERT: A 47 ASP cc_start: 0.7500 (m-30) cc_final: 0.7197 (p0) REVERT: A 106 GLU cc_start: 0.8739 (tp30) cc_final: 0.8443 (tp30) REVERT: A 142 GLU cc_start: 0.8674 (OUTLIER) cc_final: 0.8398 (pm20) REVERT: A 187 GLN cc_start: 0.9029 (mm110) cc_final: 0.8180 (pm20) REVERT: A 306 MET cc_start: 0.8819 (mtt) cc_final: 0.8567 (mtt) REVERT: D 25 GLN cc_start: 0.8730 (tp-100) cc_final: 0.8475 (tp-100) REVERT: D 65 LYS cc_start: 0.9051 (OUTLIER) cc_final: 0.8568 (mtmm) REVERT: D 331 GLU cc_start: 0.9015 (mp0) cc_final: 0.8620 (pm20) REVERT: D 458 MET cc_start: 0.9017 (OUTLIER) cc_final: 0.8718 (mmm) REVERT: D 493 ILE cc_start: 0.9432 (OUTLIER) cc_final: 0.9226 (mt) REVERT: G 52 ASP cc_start: 0.8607 (t70) cc_final: 0.7753 (t0) REVERT: G 54 MET cc_start: 0.8779 (mpp) cc_final: 0.8368 (mpt) REVERT: G 497 GLU cc_start: 0.8828 (pt0) cc_final: 0.8556 (pt0) REVERT: H 14 ASP cc_start: 0.8545 (t0) cc_final: 0.8212 (t0) REVERT: H 81 ASP cc_start: 0.8952 (m-30) cc_final: 0.8669 (m-30) REVERT: H 316 GLU cc_start: 0.8790 (tt0) cc_final: 0.7995 (tp30) REVERT: H 324 MET cc_start: 0.9293 (mmm) cc_final: 0.9045 (mmm) REVERT: Q 34 GLN cc_start: 0.8294 (tp-100) cc_final: 0.7924 (tp-100) REVERT: Z 353 TYR cc_start: 0.8964 (t80) cc_final: 0.8678 (t80) REVERT: a 66 GLU cc_start: 0.9233 (tt0) cc_final: 0.8968 (pt0) REVERT: a 430 MET cc_start: 0.8064 (mtt) cc_final: 0.7737 (mtt) REVERT: b 495 GLU cc_start: 0.9020 (mt-10) cc_final: 0.8786 (mt-10) REVERT: e 20 LYS cc_start: 0.8890 (ttmt) cc_final: 0.8670 (ttmm) REVERT: e 160 LYS cc_start: 0.9307 (OUTLIER) cc_final: 0.9089 (mtmm) REVERT: e 185 MET cc_start: 0.9042 (mmt) cc_final: 0.8763 (mmm) REVERT: g 59 MET cc_start: 0.9463 (ttp) cc_final: 0.9156 (ttp) REVERT: g 144 VAL cc_start: 0.9258 (OUTLIER) cc_final: 0.9052 (m) REVERT: g 306 ARG cc_start: 0.8594 (OUTLIER) cc_final: 0.8261 (mtm-85) REVERT: g 415 GLU cc_start: 0.9191 (mp0) cc_final: 0.8882 (mp0) REVERT: g 521 ASP cc_start: 0.9109 (t0) cc_final: 0.8903 (t0) REVERT: g 528 LYS cc_start: 0.8878 (OUTLIER) cc_final: 0.8438 (tmmt) REVERT: h 221 SER cc_start: 0.9246 (m) cc_final: 0.8931 (p) REVERT: h 401 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7707 (tmmt) REVERT: h 440 LYS cc_start: 0.9184 (ttmt) cc_final: 0.8908 (ttmm) REVERT: h 524 ARG cc_start: 0.8626 (mmm-85) cc_final: 0.8240 (mmm-85) REVERT: q 61 GLU cc_start: 0.9069 (OUTLIER) cc_final: 0.8317 (mp0) REVERT: q 152 LYS cc_start: 0.9403 (OUTLIER) cc_final: 0.9183 (ptmm) REVERT: q 319 TRP cc_start: 0.8689 (m100) cc_final: 0.8310 (m100) REVERT: z 53 ASP cc_start: 0.8765 (m-30) cc_final: 0.8552 (m-30) REVERT: P 80 GLN cc_start: 0.8554 (mm-40) cc_final: 0.8222 (mm-40) REVERT: P 171 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8819 (mp) REVERT: P 202 MET cc_start: 0.9163 (mtp) cc_final: 0.8943 (mtm) REVERT: P 230 ARG cc_start: 0.8319 (ptm-80) cc_final: 0.8114 (ptm-80) REVERT: P 231 ASN cc_start: 0.8226 (p0) cc_final: 0.8014 (p0) REVERT: P 271 PHE cc_start: 0.8572 (m-10) cc_final: 0.8311 (m-10) outliers start: 67 outliers final: 34 residues processed: 547 average time/residue: 1.6796 time to fit residues: 1180.3357 Evaluate side-chains 544 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 499 time to evaluate : 5.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 264 MET Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 156 MET Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 295 MET Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 65 LYS Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 47 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Q residue 526 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 113 LEU Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 366 LYS Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 430 LYS Chi-restraints excluded: chain P residue 171 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 138 optimal weight: 0.5980 chunk 559 optimal weight: 2.9990 chunk 135 optimal weight: 1.9990 chunk 650 optimal weight: 5.9990 chunk 511 optimal weight: 4.9990 chunk 78 optimal weight: 0.8980 chunk 263 optimal weight: 3.9990 chunk 313 optimal weight: 9.9990 chunk 353 optimal weight: 4.9990 chunk 804 optimal weight: 0.9980 chunk 434 optimal weight: 3.9990 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2956 r_free = 0.2956 target = 0.072775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2701 r_free = 0.2701 target = 0.059163 restraints weight = 147424.491| |-----------------------------------------------------------------------------| r_work (start): 0.2702 rms_B_bonded: 2.74 r_work: 0.2568 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work: 0.2447 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2447 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2461 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2461 r_free = 0.2461 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 = 0.2461 r_free = 0.2461 target_work(ls_wunit_k1) = 0.048 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2461 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 67960 Z= 0.181 Angle : 0.544 11.579 91755 Z= 0.266 Chirality : 0.041 0.175 10923 Planarity : 0.003 0.055 11716 Dihedral : 7.043 163.277 9433 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 0.77 % Allowed : 10.87 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.77 (0.09), residues: 8685 helix: 2.44 (0.08), residues: 4527 sheet: 0.10 (0.16), residues: 1119 loop : -0.34 (0.11), residues: 3039 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.003 0.001 HIS P 186 PHE 0.019 0.001 PHE H 455 TYR 0.028 0.001 TYR A 181 ARG 0.011 0.000 ARG P 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 578 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 522 time to evaluate : 7.300 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7558 (m-30) cc_final: 0.7259 (p0) REVERT: A 106 GLU cc_start: 0.8750 (tp30) cc_final: 0.8450 (tp30) REVERT: A 142 GLU cc_start: 0.8655 (OUTLIER) cc_final: 0.8403 (pm20) REVERT: A 187 GLN cc_start: 0.9024 (mm110) cc_final: 0.8147 (pm20) REVERT: A 306 MET cc_start: 0.8728 (mtt) cc_final: 0.8504 (mtt) REVERT: D 25 GLN cc_start: 0.8640 (tp-100) cc_final: 0.8360 (tp-100) REVERT: D 179 TYR cc_start: 0.9239 (m-80) cc_final: 0.8994 (m-80) REVERT: D 331 GLU cc_start: 0.9080 (mp0) cc_final: 0.8670 (pm20) REVERT: D 458 MET cc_start: 0.8999 (OUTLIER) cc_final: 0.8675 (mmm) REVERT: D 493 ILE cc_start: 0.9414 (OUTLIER) cc_final: 0.9197 (mt) REVERT: G 52 ASP cc_start: 0.8591 (t70) cc_final: 0.7790 (t0) REVERT: G 54 MET cc_start: 0.8798 (mpp) cc_final: 0.8474 (mpp) REVERT: G 497 GLU cc_start: 0.8778 (pt0) cc_final: 0.8521 (pt0) REVERT: H 14 ASP cc_start: 0.8529 (t0) cc_final: 0.8191 (t0) REVERT: H 81 ASP cc_start: 0.8942 (m-30) cc_final: 0.8643 (m-30) REVERT: H 316 GLU cc_start: 0.8753 (tt0) cc_final: 0.7998 (tp30) REVERT: H 324 MET cc_start: 0.9271 (mmm) cc_final: 0.9019 (mmm) REVERT: Q 34 GLN cc_start: 0.8231 (tp-100) cc_final: 0.7860 (tp-100) REVERT: Q 55 MET cc_start: 0.9171 (mtt) cc_final: 0.8889 (ttm) REVERT: Z 353 TYR cc_start: 0.8947 (t80) cc_final: 0.8689 (t80) REVERT: a 66 GLU cc_start: 0.9234 (tt0) cc_final: 0.8946 (pt0) REVERT: b 495 GLU cc_start: 0.8987 (mt-10) cc_final: 0.8738 (mt-10) REVERT: e 20 LYS cc_start: 0.8875 (ttmt) cc_final: 0.8662 (ttmm) REVERT: e 160 LYS cc_start: 0.9304 (OUTLIER) cc_final: 0.9100 (mtmm) REVERT: e 185 MET cc_start: 0.9001 (mmt) cc_final: 0.8727 (mmm) REVERT: g 144 VAL cc_start: 0.9248 (OUTLIER) cc_final: 0.9038 (m) REVERT: g 306 ARG cc_start: 0.8489 (OUTLIER) cc_final: 0.8188 (mtm-85) REVERT: g 415 GLU cc_start: 0.9190 (mp0) cc_final: 0.8881 (mp0) REVERT: g 528 LYS cc_start: 0.8879 (OUTLIER) cc_final: 0.8432 (tmmt) REVERT: h 221 SER cc_start: 0.9221 (m) cc_final: 0.8890 (p) REVERT: h 401 LYS cc_start: 0.8172 (mmtt) cc_final: 0.7670 (tmmt) REVERT: h 440 LYS cc_start: 0.9169 (ttmt) cc_final: 0.8897 (ttmm) REVERT: h 524 ARG cc_start: 0.8616 (mmm-85) cc_final: 0.8228 (mmm-85) REVERT: q 61 GLU cc_start: 0.9088 (OUTLIER) cc_final: 0.8397 (mp0) REVERT: q 152 LYS cc_start: 0.9384 (OUTLIER) cc_final: 0.9169 (ptmm) REVERT: q 319 TRP cc_start: 0.8642 (m100) cc_final: 0.8319 (m100) REVERT: P 80 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8201 (mm-40) REVERT: P 86 ARG cc_start: 0.8877 (tmm160) cc_final: 0.8505 (tmm160) REVERT: P 202 MET cc_start: 0.9148 (mtp) cc_final: 0.8941 (mtm) REVERT: P 230 ARG cc_start: 0.8307 (ptm-80) cc_final: 0.8074 (ptm-80) REVERT: P 231 ASN cc_start: 0.8200 (p0) cc_final: 0.7949 (p0) outliers start: 56 outliers final: 25 residues processed: 557 average time/residue: 1.6324 time to fit residues: 1173.2902 Evaluate side-chains 542 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 508 time to evaluate : 5.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 4 LEU Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 366 LYS Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 311 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 702 optimal weight: 2.9990 chunk 814 optimal weight: 6.9990 chunk 362 optimal weight: 7.9990 chunk 482 optimal weight: 7.9990 chunk 820 optimal weight: 1.9990 chunk 211 optimal weight: 3.9990 chunk 170 optimal weight: 7.9990 chunk 605 optimal weight: 0.0470 chunk 555 optimal weight: 0.8980 chunk 810 optimal weight: 8.9990 chunk 338 optimal weight: 9.9990 overall best weight: 1.9884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS B 302 GLN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2947 r_free = 0.2947 target = 0.072217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2684 r_free = 0.2684 target = 0.058231 restraints weight = 173593.392| |-----------------------------------------------------------------------------| r_work (start): 0.2685 rms_B_bonded: 2.97 r_work: 0.2544 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.2544 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2558 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2558 r_free = 0.2558 target_work(ls_wunit_k1) = 0.052 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2558 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 67960 Z= 0.217 Angle : 0.551 11.463 91755 Z= 0.270 Chirality : 0.042 0.176 10923 Planarity : 0.003 0.060 11716 Dihedral : 7.000 162.614 9433 Min Nonbonded Distance : 1.888 Molprobity Statistics. All-atom Clashscore : 5.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.70 % Allowed : 11.12 % Favored : 88.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.09), residues: 8685 helix: 2.43 (0.08), residues: 4526 sheet: 0.08 (0.16), residues: 1125 loop : -0.33 (0.11), residues: 3034 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP g 168 HIS 0.004 0.001 HIS P 186 PHE 0.019 0.001 PHE H 455 TYR 0.014 0.001 TYR e 420 ARG 0.009 0.000 ARG e 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 555 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 504 time to evaluate : 6.210 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 47 ASP cc_start: 0.7513 (m-30) cc_final: 0.7262 (p0) REVERT: A 106 GLU cc_start: 0.8633 (tp30) cc_final: 0.8317 (tp30) REVERT: A 142 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8390 (pm20) REVERT: A 187 GLN cc_start: 0.9021 (mm110) cc_final: 0.8143 (pm20) REVERT: A 306 MET cc_start: 0.8688 (mtt) cc_final: 0.8423 (mtt) REVERT: B 415 MET cc_start: 0.9122 (mmm) cc_final: 0.8791 (mmp) REVERT: D 25 GLN cc_start: 0.8735 (tp-100) cc_final: 0.8435 (tp-100) REVERT: D 179 TYR cc_start: 0.9233 (m-80) cc_final: 0.8987 (m-80) REVERT: D 331 GLU cc_start: 0.8979 (mp0) cc_final: 0.8558 (pm20) REVERT: D 458 MET cc_start: 0.8969 (OUTLIER) cc_final: 0.8656 (mmm) REVERT: D 493 ILE cc_start: 0.9356 (OUTLIER) cc_final: 0.9136 (mt) REVERT: G 52 ASP cc_start: 0.8490 (t70) cc_final: 0.7563 (t0) REVERT: G 54 MET cc_start: 0.8692 (mpp) cc_final: 0.8260 (mpt) REVERT: G 497 GLU cc_start: 0.8637 (pt0) cc_final: 0.8369 (pt0) REVERT: H 14 ASP cc_start: 0.8461 (t0) cc_final: 0.8118 (t0) REVERT: H 81 ASP cc_start: 0.8799 (m-30) cc_final: 0.8470 (m-30) REVERT: H 316 GLU cc_start: 0.8636 (tt0) cc_final: 0.7920 (tp30) REVERT: H 324 MET cc_start: 0.9230 (mmm) cc_final: 0.8962 (mmm) REVERT: Q 34 GLN cc_start: 0.8111 (tp-100) cc_final: 0.7728 (tp-100) REVERT: Q 55 MET cc_start: 0.9057 (mtt) cc_final: 0.8753 (ttm) REVERT: Z 353 TYR cc_start: 0.8910 (t80) cc_final: 0.8624 (t80) REVERT: a 66 GLU cc_start: 0.9128 (tt0) cc_final: 0.8865 (pt0) REVERT: b 495 GLU cc_start: 0.8799 (mt-10) cc_final: 0.8536 (mt-10) REVERT: d 90 MET cc_start: 0.8934 (OUTLIER) cc_final: 0.8709 (mtt) REVERT: e 20 LYS cc_start: 0.8804 (ttmt) cc_final: 0.8588 (ttmm) REVERT: e 160 LYS cc_start: 0.9290 (OUTLIER) cc_final: 0.9085 (mtmm) REVERT: e 185 MET cc_start: 0.8950 (mmt) cc_final: 0.8671 (mmm) REVERT: g 144 VAL cc_start: 0.9233 (OUTLIER) cc_final: 0.9029 (m) REVERT: g 306 ARG cc_start: 0.8422 (OUTLIER) cc_final: 0.8105 (mtm-85) REVERT: g 415 GLU cc_start: 0.9032 (mp0) cc_final: 0.8701 (mp0) REVERT: g 528 LYS cc_start: 0.8861 (OUTLIER) cc_final: 0.8487 (tptp) REVERT: h 221 SER cc_start: 0.9196 (m) cc_final: 0.8887 (p) REVERT: h 401 LYS cc_start: 0.8143 (mmtt) cc_final: 0.7674 (tmmt) REVERT: h 440 LYS cc_start: 0.9119 (ttmt) cc_final: 0.8846 (ttmm) REVERT: h 524 ARG cc_start: 0.8556 (mmm-85) cc_final: 0.8153 (mmm-85) REVERT: q 61 GLU cc_start: 0.8996 (OUTLIER) cc_final: 0.8227 (mp0) REVERT: q 152 LYS cc_start: 0.9382 (OUTLIER) cc_final: 0.9167 (ptmm) REVERT: q 319 TRP cc_start: 0.8620 (m100) cc_final: 0.8268 (m100) REVERT: P 77 ARG cc_start: 0.7130 (ptp-170) cc_final: 0.6808 (ptt180) REVERT: P 80 GLN cc_start: 0.8540 (mm-40) cc_final: 0.8049 (mm-40) REVERT: P 84 MET cc_start: 0.8428 (mmt) cc_final: 0.8149 (mpm) REVERT: P 86 ARG cc_start: 0.8824 (tmm160) cc_final: 0.8554 (tmm160) REVERT: P 202 MET cc_start: 0.9150 (mtp) cc_final: 0.8942 (mtm) REVERT: P 230 ARG cc_start: 0.8300 (ptm-80) cc_final: 0.8096 (ptm-80) REVERT: P 231 ASN cc_start: 0.8136 (p0) cc_final: 0.7899 (p0) outliers start: 51 outliers final: 31 residues processed: 536 average time/residue: 1.6495 time to fit residues: 1141.6746 Evaluate side-chains 540 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 499 time to evaluate : 6.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain D residue 493 ILE Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain G residue 71 GLN Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Z residue 4 VAL Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 113 LEU Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain h residue 366 LYS Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 430 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 598 optimal weight: 3.9990 chunk 480 optimal weight: 3.9990 chunk 182 optimal weight: 8.9990 chunk 361 optimal weight: 0.9990 chunk 767 optimal weight: 10.0000 chunk 107 optimal weight: 6.9990 chunk 640 optimal weight: 6.9990 chunk 34 optimal weight: 9.9990 chunk 836 optimal weight: 7.9990 chunk 573 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 534 HIS B 288 ASN ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN ** d 263 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** 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 = 0.2895 r_free = 0.2895 target = 0.069397 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2626 r_free = 0.2626 target = 0.055537 restraints weight = 168686.481| |-----------------------------------------------------------------------------| r_work (start): 0.2629 rms_B_bonded: 2.90 r_work: 0.2486 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2486 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2490 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2490 r_free = 0.2490 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 = 0.2490 r_free = 0.2490 target_work(ls_wunit_k1) = 0.050 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2490 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 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 : 0.006 0.063 67960 Z= 0.409 Angle : 0.629 12.299 91755 Z= 0.311 Chirality : 0.045 0.179 10923 Planarity : 0.004 0.057 11716 Dihedral : 7.218 166.591 9433 Min Nonbonded Distance : 1.865 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.70 % Allowed : 11.17 % Favored : 88.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.58 (0.09), residues: 8685 helix: 2.27 (0.08), residues: 4533 sheet: 0.02 (0.16), residues: 1095 loop : -0.41 (0.11), residues: 3057 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.005 0.001 HIS a 201 PHE 0.023 0.002 PHE h 455 TYR 0.030 0.002 TYR A 181 ARG 0.013 0.000 ARG P 144 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 17370 Ramachandran restraints generated. 8685 Oldfield, 0 Emsley, 8685 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 494 time to evaluate : 6.050 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 106 GLU cc_start: 0.8636 (tp30) cc_final: 0.8291 (tp30) REVERT: A 142 GLU cc_start: 0.8627 (OUTLIER) cc_final: 0.8386 (pm20) REVERT: A 187 GLN cc_start: 0.9032 (mm110) cc_final: 0.8102 (pm20) REVERT: B 415 MET cc_start: 0.9228 (mmm) cc_final: 0.8853 (mmp) REVERT: D 25 GLN cc_start: 0.8786 (tp-100) cc_final: 0.8546 (tp-100) REVERT: D 458 MET cc_start: 0.9012 (OUTLIER) cc_final: 0.8738 (mmm) REVERT: G 52 ASP cc_start: 0.8497 (t70) cc_final: 0.7673 (t0) REVERT: G 54 MET cc_start: 0.8660 (mpp) cc_final: 0.8282 (mpt) REVERT: G 497 GLU cc_start: 0.8752 (pt0) cc_final: 0.8451 (pt0) REVERT: H 14 ASP cc_start: 0.8511 (t0) cc_final: 0.8120 (t0) REVERT: H 81 ASP cc_start: 0.8816 (m-30) cc_final: 0.8552 (m-30) REVERT: H 316 GLU cc_start: 0.8723 (tt0) cc_final: 0.7947 (tp30) REVERT: H 324 MET cc_start: 0.9245 (mmm) cc_final: 0.8978 (mmm) REVERT: Q 34 GLN cc_start: 0.8219 (tp-100) cc_final: 0.7829 (tp-100) REVERT: Q 55 MET cc_start: 0.9130 (mtt) cc_final: 0.8872 (mtt) REVERT: a 66 GLU cc_start: 0.9156 (tt0) cc_final: 0.8850 (pt0) REVERT: b 495 GLU cc_start: 0.8810 (mt-10) cc_final: 0.8550 (mt-10) REVERT: d 90 MET cc_start: 0.9028 (OUTLIER) cc_final: 0.8471 (mpp) REVERT: e 20 LYS cc_start: 0.8815 (ttmt) cc_final: 0.8551 (ttmm) REVERT: e 160 LYS cc_start: 0.9283 (OUTLIER) cc_final: 0.9050 (mtmm) REVERT: e 185 MET cc_start: 0.9047 (mmt) cc_final: 0.8764 (mmm) REVERT: g 144 VAL cc_start: 0.9264 (OUTLIER) cc_final: 0.9049 (m) REVERT: g 306 ARG cc_start: 0.8566 (OUTLIER) cc_final: 0.8165 (mtm-85) REVERT: g 415 GLU cc_start: 0.9025 (mp0) cc_final: 0.8696 (mp0) REVERT: g 528 LYS cc_start: 0.8852 (OUTLIER) cc_final: 0.8449 (tptp) REVERT: h 221 SER cc_start: 0.9230 (m) cc_final: 0.8931 (p) REVERT: h 401 LYS cc_start: 0.8292 (mmtt) cc_final: 0.7817 (tmmt) REVERT: h 440 LYS cc_start: 0.9163 (ttmt) cc_final: 0.8905 (ttmm) REVERT: h 524 ARG cc_start: 0.8552 (mmm-85) cc_final: 0.8204 (mmm-85) REVERT: q 61 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8135 (mp0) REVERT: q 152 LYS cc_start: 0.9442 (OUTLIER) cc_final: 0.9237 (ptmm) REVERT: q 319 TRP cc_start: 0.8631 (m100) cc_final: 0.8307 (m100) REVERT: z 46 MET cc_start: 0.8918 (ttt) cc_final: 0.8642 (ttt) REVERT: P 77 ARG cc_start: 0.7170 (ptp-170) cc_final: 0.6713 (ptt180) REVERT: P 80 GLN cc_start: 0.8535 (mm-40) cc_final: 0.8284 (mm-40) REVERT: P 84 MET cc_start: 0.8451 (mmt) cc_final: 0.8071 (mpm) REVERT: P 86 ARG cc_start: 0.8884 (tmm160) cc_final: 0.8521 (tmm160) REVERT: P 202 MET cc_start: 0.9149 (mtp) cc_final: 0.8945 (mtm) outliers start: 51 outliers final: 32 residues processed: 527 average time/residue: 1.6566 time to fit residues: 1127.1598 Evaluate side-chains 525 residues out of total 7276 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 484 time to evaluate : 6.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 142 GLU Chi-restraints excluded: chain A residue 171 MET Chi-restraints excluded: chain A residue 352 VAL Chi-restraints excluded: chain B residue 6 LEU Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 353 MET Chi-restraints excluded: chain D residue 69 THR Chi-restraints excluded: chain D residue 458 MET Chi-restraints excluded: chain E residue 288 MET Chi-restraints excluded: chain H residue 17 GLN Chi-restraints excluded: chain Q residue 42 THR Chi-restraints excluded: chain Q residue 253 THR Chi-restraints excluded: chain Q residue 266 MET Chi-restraints excluded: chain Z residue 59 ASP Chi-restraints excluded: chain Z residue 137 VAL Chi-restraints excluded: chain Z residue 241 LYS Chi-restraints excluded: chain Z residue 354 THR Chi-restraints excluded: chain a residue 5 LEU Chi-restraints excluded: chain a residue 248 LEU Chi-restraints excluded: chain a residue 281 THR Chi-restraints excluded: chain b residue 39 VAL Chi-restraints excluded: chain b residue 485 ILE Chi-restraints excluded: chain d residue 90 MET Chi-restraints excluded: chain e residue 23 ASP Chi-restraints excluded: chain e residue 160 LYS Chi-restraints excluded: chain g residue 144 VAL Chi-restraints excluded: chain g residue 306 ARG Chi-restraints excluded: chain g residue 408 VAL Chi-restraints excluded: chain g residue 528 LYS Chi-restraints excluded: chain h residue 21 GLN Chi-restraints excluded: chain h residue 211 VAL Chi-restraints excluded: chain q residue 61 GLU Chi-restraints excluded: chain q residue 152 LYS Chi-restraints excluded: chain q residue 480 LEU Chi-restraints excluded: chain q residue 499 ASP Chi-restraints excluded: chain q residue 526 MET Chi-restraints excluded: chain z residue 137 VAL Chi-restraints excluded: chain z residue 161 HIS Chi-restraints excluded: chain z residue 311 VAL Chi-restraints excluded: chain z residue 430 LYS Chi-restraints excluded: chain P residue 285 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 864 random chunks: chunk 687 optimal weight: 9.9990 chunk 718 optimal weight: 6.9990 chunk 318 optimal weight: 0.7980 chunk 321 optimal weight: 4.9990 chunk 513 optimal weight: 8.9990 chunk 267 optimal weight: 9.9990 chunk 756 optimal weight: 5.9990 chunk 628 optimal weight: 0.9980 chunk 500 optimal weight: 0.0060 chunk 685 optimal weight: 0.9990 chunk 691 optimal weight: 6.9990 overall best weight: 1.5600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 353 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 164 ASN ** e 515 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 56 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 199 ASN P 227 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.072174 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2720 r_free = 0.2720 target = 0.058813 restraints weight = 166446.018| |-----------------------------------------------------------------------------| r_work (start): 0.2708 rms_B_bonded: 2.73 r_work: 0.2573 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2454 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2454 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2439 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2439 r_free = 0.2439 target_work(ls_wunit_k1) = 0.047 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.2439 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8717 moved from start: 0.1186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 67960 Z= 0.197 Angle : 0.558 10.841 91755 Z= 0.274 Chirality : 0.042 0.182 10923 Planarity : 0.003 0.058 11716 Dihedral : 7.031 161.965 9433 Min Nonbonded Distance : 1.902 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.55 % Allowed : 11.47 % Favored : 87.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.09), residues: 8685 helix: 2.36 (0.08), residues: 4537 sheet: 0.09 (0.16), residues: 1084 loop : -0.38 (0.11), residues: 3064 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP g 168 HIS 0.004 0.001 HIS P 186 PHE 0.022 0.001 PHE H 455 TYR 0.012 0.001 TYR e 420 ARG 0.009 0.000 ARG e 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 34981.27 seconds wall clock time: 601 minutes 32.28 seconds (36092.28 seconds total)