Starting phenix.real_space_refine on Tue Sep 24 00:50:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xax_38206/09_2024/8xax_38206.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xax_38206/09_2024/8xax_38206.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.92 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xax_38206/09_2024/8xax_38206.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xax_38206/09_2024/8xax_38206.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xax_38206/09_2024/8xax_38206.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xax_38206/09_2024/8xax_38206.cif" } resolution = 2.92 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= 0.003 sd= 0.060 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: 6 Type Number sf(0) Gaussians P 39 5.49 5 Mg 4 5.21 5 S 84 5.16 5 C 31176 2.51 5 N 8165 2.21 5 O 9486 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 79 residue(s): 0.10s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 48954 Number of models: 1 Model: "" Number of chains: 25 Chain: "A" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "B" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "C" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "D" Number of atoms: 4513 Number of conformers: 1 Conformer: "" Number of residues, atoms: 563, 4513 Classifications: {'peptide': 563} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 541} Chain breaks: 1 Chain: "E" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "F" Number of atoms: 4539 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4539 Classifications: {'peptide': 567} Link IDs: {'PCIS': 1, 'PTRANS': 20, 'TRANS': 545} Chain: "G" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "H" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "I" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "J" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "K" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "L" Number of atoms: 2076 Number of conformers: 1 Conformer: "" Number of residues, atoms: 244, 2076 Classifications: {'peptide': 244} Link IDs: {'PTRANS': 7, 'TRANS': 236} Chain: "M" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "N" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "O" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "P" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "Q" Number of atoms: 1426 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1426 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 162} 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: "R" Number of atoms: 1436 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 1436 Classifications: {'peptide': 171} Link IDs: {'PTRANS': 7, 'TRANS': 163} Chain: "S" Number of atoms: 266 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 266 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "T" Number of atoms: 267 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 267 Classifications: {'DNA': 13} Link IDs: {'rna3p': 12} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ANP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ANP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 21.54, per 1000 atoms: 0.44 Number of scatterers: 48954 At special positions: 0 Unit cell: (186.2, 184.3, 202.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 84 16.00 P 39 15.00 Mg 4 11.99 O 9486 8.00 N 8165 7.00 C 31176 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 Number of custom bonds: simple=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 8.70 Conformation dependent library (CDL) restraints added in 4.7 seconds 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 11322 Finding SS restraints... Secondary structure from input PDB file: 254 helices and 33 sheets defined 43.6% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.61 Creating SS restraints... Processing helix chain 'A' and resid 30 through 35 removed outlier: 3.613A pdb=" N GLU A 34 " --> pdb=" O LYS A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 104 through 114 removed outlier: 3.935A pdb=" N TYR A 112 " --> pdb=" O ILE A 108 " (cutoff:3.500A) removed outlier: 3.772A pdb=" N ASP A 114 " --> pdb=" O SER A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 139 through 145 removed outlier: 3.877A pdb=" N LYS A 145 " --> pdb=" O ARG A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 170 Processing helix chain 'A' and resid 211 through 215 removed outlier: 3.811A pdb=" N LEU A 214 " --> pdb=" O PRO A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 224 Processing helix chain 'A' and resid 231 through 249 removed outlier: 3.509A pdb=" N LEU A 244 " --> pdb=" O GLN A 240 " (cutoff:3.500A) removed outlier: 4.023A pdb=" N LYS A 247 " --> pdb=" O THR A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 253 through 259 removed outlier: 3.576A pdb=" N GLU A 258 " --> pdb=" O PRO A 254 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ILE A 259 " --> pdb=" O ALA A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 269 through 282 removed outlier: 3.585A pdb=" N ASN A 282 " --> pdb=" O ASN A 278 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 312 removed outlier: 3.604A pdb=" N PHE A 311 " --> pdb=" O HIS A 308 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LYS A 312 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 337 removed outlier: 3.665A pdb=" N ASP A 334 " --> pdb=" O LEU A 330 " (cutoff:3.500A) removed outlier: 4.186A pdb=" N ARG A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N LEU A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 342 through 344 No H-bonds generated for 'chain 'A' and resid 342 through 344' Processing helix chain 'A' and resid 345 through 350 Processing helix chain 'A' and resid 350 through 356 Processing helix chain 'A' and resid 357 through 366 Processing helix chain 'A' and resid 384 through 414 removed outlier: 4.205A pdb=" N SER A 389 " --> pdb=" O PHE A 385 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N ILE A 390 " --> pdb=" O GLU A 386 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N ILE A 409 " --> pdb=" O HIS A 405 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N LYS A 412 " --> pdb=" O LYS A 408 " (cutoff:3.500A) Processing helix chain 'A' and resid 427 through 432 removed outlier: 3.943A pdb=" N TYR A 431 " --> pdb=" O GLU A 427 " (cutoff:3.500A) Processing helix chain 'A' and resid 437 through 439 No H-bonds generated for 'chain 'A' and resid 437 through 439' Processing helix chain 'A' and resid 440 through 458 removed outlier: 5.547A pdb=" N ARG A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 6.148A pdb=" N LYS A 456 " --> pdb=" O LYS A 452 " (cutoff:3.500A) removed outlier: 3.954A pdb=" N TYR A 457 " --> pdb=" O GLU A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 467 through 471 removed outlier: 3.922A pdb=" N GLU A 470 " --> pdb=" O ARG A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 478 removed outlier: 3.524A pdb=" N GLN A 478 " --> pdb=" O THR A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 500 removed outlier: 3.542A pdb=" N LEU A 499 " --> pdb=" O TYR A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 548 through 554 Processing helix chain 'A' and resid 560 through 571 removed outlier: 3.622A pdb=" N ILE A 564 " --> pdb=" O GLU A 560 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 36 removed outlier: 4.282A pdb=" N ALA B 32 " --> pdb=" O GLU B 28 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N GLU B 33 " --> pdb=" O PHE B 29 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N GLU B 34 " --> pdb=" O LYS B 30 " (cutoff:3.500A) removed outlier: 3.679A pdb=" N LEU B 36 " --> pdb=" O ALA B 32 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 114 removed outlier: 4.134A pdb=" N TYR B 112 " --> pdb=" O ILE B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 117 through 119 No H-bonds generated for 'chain 'B' and resid 117 through 119' Processing helix chain 'B' and resid 139 through 145 removed outlier: 3.730A pdb=" N PHE B 143 " --> pdb=" O GLY B 139 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ASN B 144 " --> pdb=" O ASN B 140 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N LYS B 145 " --> pdb=" O ARG B 141 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 139 through 145' Processing helix chain 'B' and resid 156 through 170 Processing helix chain 'B' and resid 211 through 215 removed outlier: 3.709A pdb=" N LEU B 215 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 225 removed outlier: 3.536A pdb=" N GLU B 222 " --> pdb=" O ASP B 218 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N PHE B 224 " --> pdb=" O LEU B 220 " (cutoff:3.500A) Processing helix chain 'B' and resid 231 through 249 removed outlier: 3.568A pdb=" N HIS B 249 " --> pdb=" O ASN B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 269 through 281 Processing helix chain 'B' and resid 306 through 311 removed outlier: 3.560A pdb=" N LEU B 310 " --> pdb=" O ALA B 307 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N PHE B 311 " --> pdb=" O HIS B 308 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 341 removed outlier: 3.666A pdb=" N LYS B 339 " --> pdb=" O ARG B 335 " (cutoff:3.500A) Processing helix chain 'B' and resid 342 through 344 No H-bonds generated for 'chain 'B' and resid 342 through 344' Processing helix chain 'B' and resid 345 through 350 Processing helix chain 'B' and resid 351 through 354 Processing helix chain 'B' and resid 357 through 366 Processing helix chain 'B' and resid 384 through 405 Processing helix chain 'B' and resid 406 through 414 removed outlier: 3.815A pdb=" N LYS B 410 " --> pdb=" O SER B 406 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 431 Processing helix chain 'B' and resid 437 through 439 No H-bonds generated for 'chain 'B' and resid 437 through 439' Processing helix chain 'B' and resid 440 through 453 removed outlier: 3.943A pdb=" N ALA B 446 " --> pdb=" O THR B 442 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N ILE B 447 " --> pdb=" O SER B 443 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ILE B 450 " --> pdb=" O ALA B 446 " (cutoff:3.500A) Processing helix chain 'B' and resid 454 through 457 Processing helix chain 'B' and resid 467 through 471 removed outlier: 3.674A pdb=" N ILE B 471 " --> pdb=" O PRO B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 477 Processing helix chain 'B' and resid 489 through 500 removed outlier: 3.903A pdb=" N LEU B 499 " --> pdb=" O TYR B 495 " (cutoff:3.500A) Processing helix chain 'B' and resid 504 through 511 removed outlier: 3.626A pdb=" N ILE B 507 " --> pdb=" O VAL B 504 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N THR B 508 " --> pdb=" O GLY B 505 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N LEU B 510 " --> pdb=" O ILE B 507 " (cutoff:3.500A) Processing helix chain 'B' and resid 547 through 553 Processing helix chain 'B' and resid 560 through 571 removed outlier: 3.651A pdb=" N ILE B 564 " --> pdb=" O GLU B 560 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N GLN B 567 " --> pdb=" O LYS B 563 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N LYS B 570 " --> pdb=" O GLU B 566 " (cutoff:3.500A) Processing helix chain 'C' and resid 30 through 35 Processing helix chain 'C' and resid 104 through 112 removed outlier: 4.089A pdb=" N TYR C 112 " --> pdb=" O ILE C 108 " (cutoff:3.500A) Processing helix chain 'C' and resid 139 through 144 Processing helix chain 'C' and resid 156 through 171 Processing helix chain 'C' and resid 211 through 215 removed outlier: 3.786A pdb=" N LEU C 215 " --> pdb=" O TYR C 212 " (cutoff:3.500A) Processing helix chain 'C' and resid 216 through 225 removed outlier: 3.861A pdb=" N GLU C 221 " --> pdb=" O GLY C 217 " (cutoff:3.500A) Processing helix chain 'C' and resid 233 through 249 removed outlier: 3.654A pdb=" N PHE C 238 " --> pdb=" O GLN C 234 " (cutoff:3.500A) removed outlier: 4.863A pdb=" N ARG C 239 " --> pdb=" O ARG C 235 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA C 241 " --> pdb=" O VAL C 237 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N HIS C 249 " --> pdb=" O ASN C 245 " (cutoff:3.500A) Processing helix chain 'C' and resid 253 through 258 removed outlier: 3.577A pdb=" N LYS C 257 " --> pdb=" O ASP C 253 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU C 258 " --> pdb=" O PRO C 254 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 253 through 258' Processing helix chain 'C' and resid 269 through 281 Processing helix chain 'C' and resid 306 through 312 removed outlier: 3.636A pdb=" N PHE C 311 " --> pdb=" O HIS C 308 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N LYS C 312 " --> pdb=" O ARG C 309 " (cutoff:3.500A) Processing helix chain 'C' and resid 329 through 341 removed outlier: 3.799A pdb=" N LYS C 339 " --> pdb=" O ARG C 335 " (cutoff:3.500A) Processing helix chain 'C' and resid 342 through 344 No H-bonds generated for 'chain 'C' and resid 342 through 344' Processing helix chain 'C' and resid 345 through 350 Processing helix chain 'C' and resid 351 through 355 removed outlier: 3.635A pdb=" N SER C 355 " --> pdb=" O GLY C 352 " (cutoff:3.500A) Processing helix chain 'C' and resid 357 through 366 Processing helix chain 'C' and resid 384 through 413 removed outlier: 4.391A pdb=" N ILE C 390 " --> pdb=" O GLU C 386 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER C 413 " --> pdb=" O ILE C 409 " (cutoff:3.500A) Processing helix chain 'C' and resid 428 through 431 Processing helix chain 'C' and resid 437 through 439 No H-bonds generated for 'chain 'C' and resid 437 through 439' Processing helix chain 'C' and resid 440 through 454 removed outlier: 3.829A pdb=" N ALA C 446 " --> pdb=" O THR C 442 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ILE C 447 " --> pdb=" O SER C 443 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ILE C 450 " --> pdb=" O ALA C 446 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 479 removed outlier: 3.733A pdb=" N GLN C 478 " --> pdb=" O THR C 474 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N CYS C 479 " --> pdb=" O ILE C 475 " (cutoff:3.500A) Processing helix chain 'C' and resid 489 through 500 Processing helix chain 'C' and resid 501 through 511 removed outlier: 3.688A pdb=" N GLY C 505 " --> pdb=" O ASP C 502 " (cutoff:3.500A) removed outlier: 5.099A pdb=" N ASP C 506 " --> pdb=" O THR C 503 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE C 507 " --> pdb=" O VAL C 504 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N THR C 508 " --> pdb=" O GLY C 505 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N ASN C 509 " --> pdb=" O ASP C 506 " (cutoff:3.500A) Processing helix chain 'C' and resid 547 through 554 removed outlier: 3.755A pdb=" N LYS C 554 " --> pdb=" O ASP C 550 " (cutoff:3.500A) Processing helix chain 'C' and resid 560 through 571 removed outlier: 3.779A pdb=" N ILE C 564 " --> pdb=" O GLU C 560 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ILE C 565 " --> pdb=" O PHE C 561 " (cutoff:3.500A) Processing helix chain 'D' and resid 28 through 35 removed outlier: 4.276A pdb=" N ALA D 32 " --> pdb=" O GLU D 28 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N GLU D 33 " --> pdb=" O PHE D 29 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N GLU D 34 " --> pdb=" O LYS D 30 " (cutoff:3.500A) Processing helix chain 'D' and resid 104 through 116 removed outlier: 4.153A pdb=" N TYR D 112 " --> pdb=" O ILE D 108 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N SER D 115 " --> pdb=" O ILE D 111 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE D 116 " --> pdb=" O TYR D 112 " (cutoff:3.500A) Processing helix chain 'D' and resid 139 through 145 removed outlier: 3.558A pdb=" N LYS D 145 " --> pdb=" O ARG D 141 " (cutoff:3.500A) Processing helix chain 'D' and resid 156 through 171 Processing helix chain 'D' and resid 211 through 215 Processing helix chain 'D' and resid 216 through 224 removed outlier: 3.624A pdb=" N GLU D 221 " --> pdb=" O GLY D 217 " (cutoff:3.500A) Processing helix chain 'D' and resid 231 through 249 Processing helix chain 'D' and resid 253 through 260 removed outlier: 3.573A pdb=" N LYS D 257 " --> pdb=" O ASP D 253 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N GLU D 258 " --> pdb=" O PRO D 254 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 259 " --> pdb=" O ALA D 255 " (cutoff:3.500A) Processing helix chain 'D' and resid 269 through 282 Processing helix chain 'D' and resid 307 through 311 removed outlier: 3.626A pdb=" N PHE D 311 " --> pdb=" O HIS D 308 " (cutoff:3.500A) Processing helix chain 'D' and resid 329 through 342 removed outlier: 3.750A pdb=" N ASP D 334 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N ARG D 335 " --> pdb=" O ASN D 331 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS D 339 " --> pdb=" O ARG D 335 " (cutoff:3.500A) Processing helix chain 'D' and resid 345 through 350 Processing helix chain 'D' and resid 351 through 354 Processing helix chain 'D' and resid 357 through 366 Processing helix chain 'D' and resid 384 through 413 removed outlier: 3.616A pdb=" N ILE D 390 " --> pdb=" O GLU D 386 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ILE D 395 " --> pdb=" O CYS D 391 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N SER D 413 " --> pdb=" O ILE D 409 " (cutoff:3.500A) Processing helix chain 'D' and resid 440 through 454 removed outlier: 3.975A pdb=" N ALA D 446 " --> pdb=" O THR D 442 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ILE D 447 " --> pdb=" O SER D 443 " (cutoff:3.500A) Processing helix chain 'D' and resid 467 through 471 removed outlier: 4.111A pdb=" N GLU D 470 " --> pdb=" O ARG D 467 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 479 removed outlier: 3.769A pdb=" N GLN D 478 " --> pdb=" O THR D 474 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N CYS D 479 " --> pdb=" O ILE D 475 " (cutoff:3.500A) Processing helix chain 'D' and resid 489 through 500 removed outlier: 3.574A pdb=" N GLN D 493 " --> pdb=" O ASN D 489 " (cutoff:3.500A) Processing helix chain 'D' and resid 507 through 511 Processing helix chain 'D' and resid 547 through 553 Processing helix chain 'D' and resid 561 through 571 removed outlier: 3.903A pdb=" N GLN D 567 " --> pdb=" O LYS D 563 " (cutoff:3.500A) Processing helix chain 'E' and resid 28 through 35 removed outlier: 4.288A pdb=" N ALA E 32 " --> pdb=" O GLU E 28 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N GLU E 33 " --> pdb=" O PHE E 29 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N GLU E 34 " --> pdb=" O LYS E 30 " (cutoff:3.500A) Processing helix chain 'E' and resid 104 through 113 removed outlier: 3.551A pdb=" N ILE E 108 " --> pdb=" O LYS E 104 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N TYR E 112 " --> pdb=" O ILE E 108 " (cutoff:3.500A) Processing helix chain 'E' and resid 139 through 144 removed outlier: 3.674A pdb=" N PHE E 143 " --> pdb=" O GLY E 139 " (cutoff:3.500A) Processing helix chain 'E' and resid 156 through 171 Processing helix chain 'E' and resid 211 through 215 removed outlier: 3.540A pdb=" N LEU E 214 " --> pdb=" O PRO E 211 " (cutoff:3.500A) Processing helix chain 'E' and resid 216 through 225 removed outlier: 3.783A pdb=" N GLU E 221 " --> pdb=" O GLY E 217 " (cutoff:3.500A) removed outlier: 3.767A pdb=" N GLU E 222 " --> pdb=" O ASP E 218 " (cutoff:3.500A) Processing helix chain 'E' and resid 231 through 249 removed outlier: 3.714A pdb=" N ALA E 241 " --> pdb=" O VAL E 237 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ILE E 242 " --> pdb=" O PHE E 238 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N LEU E 244 " --> pdb=" O GLN E 240 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LYS E 247 " --> pdb=" O THR E 243 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N ILE E 248 " --> pdb=" O LEU E 244 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N HIS E 249 " --> pdb=" O ASN E 245 " (cutoff:3.500A) Processing helix chain 'E' and resid 254 through 259 removed outlier: 3.667A pdb=" N GLU E 258 " --> pdb=" O PRO E 254 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ILE E 259 " --> pdb=" O ALA E 255 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 254 through 259' Processing helix chain 'E' and resid 269 through 281 Processing helix chain 'E' and resid 307 through 311 Processing helix chain 'E' and resid 329 through 338 Processing helix chain 'E' and resid 342 through 344 No H-bonds generated for 'chain 'E' and resid 342 through 344' Processing helix chain 'E' and resid 345 through 350 Processing helix chain 'E' and resid 351 through 354 Processing helix chain 'E' and resid 357 through 366 removed outlier: 3.501A pdb=" N ILE E 366 " --> pdb=" O LEU E 362 " (cutoff:3.500A) Processing helix chain 'E' and resid 381 through 383 No H-bonds generated for 'chain 'E' and resid 381 through 383' Processing helix chain 'E' and resid 384 through 414 removed outlier: 4.247A pdb=" N SER E 389 " --> pdb=" O PHE E 385 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N ILE E 390 " --> pdb=" O GLU E 386 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N PHE E 402 " --> pdb=" O LEU E 398 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N LYS E 407 " --> pdb=" O GLY E 403 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N LYS E 408 " --> pdb=" O TYR E 404 " (cutoff:3.500A) removed outlier: 4.033A pdb=" N LYS E 412 " --> pdb=" O LYS E 408 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N SER E 413 " --> pdb=" O ILE E 409 " (cutoff:3.500A) Processing helix chain 'E' and resid 427 through 432 removed outlier: 4.020A pdb=" N TYR E 431 " --> pdb=" O GLU E 427 " (cutoff:3.500A) Processing helix chain 'E' and resid 437 through 439 No H-bonds generated for 'chain 'E' and resid 437 through 439' Processing helix chain 'E' and resid 440 through 452 removed outlier: 3.679A pdb=" N ILE E 450 " --> pdb=" O ALA E 446 " (cutoff:3.500A) Processing helix chain 'E' and resid 467 through 471 Processing helix chain 'E' and resid 472 through 477 Processing helix chain 'E' and resid 489 through 498 Processing helix chain 'E' and resid 510 through 514 removed outlier: 3.930A pdb=" N LEU E 514 " --> pdb=" O LEU E 511 " (cutoff:3.500A) Processing helix chain 'E' and resid 547 through 553 Processing helix chain 'E' and resid 560 through 571 removed outlier: 3.566A pdb=" N ILE E 564 " --> pdb=" O GLU E 560 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N ILE E 565 " --> pdb=" O PHE E 561 " (cutoff:3.500A) removed outlier: 5.067A pdb=" N GLU E 566 " --> pdb=" O ASP E 562 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N GLN E 567 " --> pdb=" O LYS E 563 " (cutoff:3.500A) Processing helix chain 'F' and resid 29 through 35 removed outlier: 3.595A pdb=" N GLU F 33 " --> pdb=" O PHE F 29 " (cutoff:3.500A) Processing helix chain 'F' and resid 104 through 113 removed outlier: 3.732A pdb=" N ILE F 108 " --> pdb=" O LYS F 104 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N TYR F 112 " --> pdb=" O ILE F 108 " (cutoff:3.500A) Processing helix chain 'F' and resid 117 through 119 No H-bonds generated for 'chain 'F' and resid 117 through 119' Processing helix chain 'F' and resid 139 through 145 removed outlier: 3.756A pdb=" N PHE F 143 " --> pdb=" O GLY F 139 " (cutoff:3.500A) removed outlier: 3.824A pdb=" N LYS F 145 " --> pdb=" O ARG F 141 " (cutoff:3.500A) Processing helix chain 'F' and resid 156 through 171 removed outlier: 3.668A pdb=" N GLU F 171 " --> pdb=" O LYS F 167 " (cutoff:3.500A) Processing helix chain 'F' and resid 211 through 215 removed outlier: 3.523A pdb=" N LEU F 214 " --> pdb=" O PRO F 211 " (cutoff:3.500A) Processing helix chain 'F' and resid 216 through 225 Processing helix chain 'F' and resid 231 through 249 removed outlier: 3.902A pdb=" N ARG F 235 " --> pdb=" O ASP F 231 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN F 236 " --> pdb=" O HIS F 232 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N VAL F 237 " --> pdb=" O ASN F 233 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N PHE F 238 " --> pdb=" O GLN F 234 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU F 244 " --> pdb=" O GLN F 240 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 281 Processing helix chain 'F' and resid 305 through 312 removed outlier: 4.060A pdb=" N HIS F 308 " --> pdb=" O GLU F 305 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N ARG F 309 " --> pdb=" O ASN F 306 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N PHE F 311 " --> pdb=" O HIS F 308 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N LYS F 312 " --> pdb=" O ARG F 309 " (cutoff:3.500A) Processing helix chain 'F' and resid 330 through 341 removed outlier: 3.653A pdb=" N LYS F 339 " --> pdb=" O ARG F 335 " (cutoff:3.500A) Processing helix chain 'F' and resid 345 through 350 Processing helix chain 'F' and resid 350 through 356 removed outlier: 3.621A pdb=" N LYS F 354 " --> pdb=" O GLY F 350 " (cutoff:3.500A) Processing helix chain 'F' and resid 357 through 366 removed outlier: 3.660A pdb=" N LEU F 362 " --> pdb=" O PHE F 358 " (cutoff:3.500A) Processing helix chain 'F' and resid 384 through 411 removed outlier: 4.400A pdb=" N SER F 389 " --> pdb=" O PHE F 385 " (cutoff:3.500A) removed outlier: 4.842A pdb=" N ILE F 390 " --> pdb=" O GLU F 386 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LYS F 407 " --> pdb=" O GLY F 403 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS F 408 " --> pdb=" O TYR F 404 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N ILE F 409 " --> pdb=" O HIS F 405 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N LYS F 410 " --> pdb=" O SER F 406 " (cutoff:3.500A) Processing helix chain 'F' and resid 427 through 432 removed outlier: 4.030A pdb=" N TYR F 431 " --> pdb=" O GLU F 427 " (cutoff:3.500A) Processing helix chain 'F' and resid 437 through 439 No H-bonds generated for 'chain 'F' and resid 437 through 439' Processing helix chain 'F' and resid 440 through 458 removed outlier: 3.520A pdb=" N ILE F 447 " --> pdb=" O SER F 443 " (cutoff:3.500A) removed outlier: 5.901A pdb=" N ARG F 455 " --> pdb=" O ALA F 451 " (cutoff:3.500A) removed outlier: 6.524A pdb=" N LYS F 456 " --> pdb=" O LYS F 452 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N TYR F 457 " --> pdb=" O GLU F 453 " (cutoff:3.500A) Processing helix chain 'F' and resid 467 through 471 removed outlier: 3.630A pdb=" N GLU F 470 " --> pdb=" O ARG F 467 " (cutoff:3.500A) Processing helix chain 'F' and resid 472 through 477 Processing helix chain 'F' and resid 489 through 500 removed outlier: 3.521A pdb=" N LEU F 499 " --> pdb=" O TYR F 495 " (cutoff:3.500A) Processing helix chain 'F' and resid 506 through 511 Processing helix chain 'F' and resid 547 through 553 Processing helix chain 'F' and resid 558 through 571 removed outlier: 4.227A pdb=" N ASP F 562 " --> pdb=" O ASP F 558 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N LYS F 563 " --> pdb=" O SER F 559 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ILE F 565 " --> pdb=" O PHE F 561 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLU F 566 " --> pdb=" O ASP F 562 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLN F 567 " --> pdb=" O LYS F 563 " (cutoff:3.500A) Processing helix chain 'G' and resid 152 through 169 removed outlier: 3.652A pdb=" N GLN G 156 " --> pdb=" O SER G 152 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LYS G 158 " --> pdb=" O ASP G 154 " (cutoff:3.500A) removed outlier: 4.001A pdb=" N GLU G 159 " --> pdb=" O ASP G 155 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR G 160 " --> pdb=" O GLN G 156 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ILE G 164 " --> pdb=" O THR G 160 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ASN G 166 " --> pdb=" O GLN G 162 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N HIS G 167 " --> pdb=" O ILE G 163 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE G 168 " --> pdb=" O ILE G 164 " (cutoff:3.500A) Processing helix chain 'G' and resid 173 through 178 removed outlier: 4.038A pdb=" N HIS G 177 " --> pdb=" O TYR G 173 " (cutoff:3.500A) Processing helix chain 'G' and resid 179 through 192 removed outlier: 3.590A pdb=" N ARG G 185 " --> pdb=" O SER G 181 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N LYS G 186 " --> pdb=" O ASN G 182 " (cutoff:3.500A) Processing helix chain 'G' and resid 201 through 209 removed outlier: 3.591A pdb=" N VAL G 205 " --> pdb=" O LYS G 201 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N GLU G 206 " --> pdb=" O SER G 202 " (cutoff:3.500A) Processing helix chain 'G' and resid 216 through 223 removed outlier: 3.833A pdb=" N TYR G 220 " --> pdb=" O ASN G 216 " (cutoff:3.500A) Processing helix chain 'G' and resid 224 through 237 removed outlier: 3.848A pdb=" N LEU G 229 " --> pdb=" O ARG G 225 " (cutoff:3.500A) removed outlier: 3.854A pdb=" N ARG G 230 " --> pdb=" O LYS G 226 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N LEU G 232 " --> pdb=" O TYR G 228 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N GLU G 234 " --> pdb=" O ARG G 230 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N PHE G 236 " --> pdb=" O LEU G 232 " (cutoff:3.500A) Processing helix chain 'G' and resid 260 through 274 removed outlier: 3.974A pdb=" N ASP G 265 " --> pdb=" O LYS G 261 " (cutoff:3.500A) removed outlier: 4.695A pdb=" N CYS G 266 " --> pdb=" O THR G 262 " (cutoff:3.500A) Processing helix chain 'G' and resid 295 through 309 removed outlier: 3.548A pdb=" N ASN G 308 " --> pdb=" O ASN G 304 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N GLU G 309 " --> pdb=" O GLN G 305 " (cutoff:3.500A) Processing helix chain 'G' and resid 326 through 335 removed outlier: 3.639A pdb=" N SER G 334 " --> pdb=" O ILE G 330 " (cutoff:3.500A) Processing helix chain 'G' and resid 345 through 355 removed outlier: 3.599A pdb=" N GLU G 351 " --> pdb=" O ASP G 347 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N THR G 352 " --> pdb=" O ASP G 348 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N LEU G 353 " --> pdb=" O PHE G 349 " (cutoff:3.500A) removed outlier: 4.294A pdb=" N ASN G 354 " --> pdb=" O ASN G 350 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER G 355 " --> pdb=" O GLU G 351 " (cutoff:3.500A) Processing helix chain 'G' and resid 387 through 394 removed outlier: 4.237A pdb=" N LYS G 391 " --> pdb=" O PHE G 387 " (cutoff:3.500A) removed outlier: 4.265A pdb=" N GLU G 392 " --> pdb=" O ALA G 388 " (cutoff:3.500A) Processing helix chain 'H' and resid 153 through 155 No H-bonds generated for 'chain 'H' and resid 153 through 155' Processing helix chain 'H' and resid 156 through 169 removed outlier: 3.555A pdb=" N THR H 160 " --> pdb=" O GLN H 156 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N ILE H 161 " --> pdb=" O LYS H 157 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN H 162 " --> pdb=" O LYS H 158 " (cutoff:3.500A) removed outlier: 3.692A pdb=" N ILE H 163 " --> pdb=" O GLU H 159 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N ILE H 164 " --> pdb=" O THR H 160 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN H 166 " --> pdb=" O GLN H 162 " (cutoff:3.500A) removed outlier: 4.230A pdb=" N HIS H 167 " --> pdb=" O ILE H 163 " (cutoff:3.500A) Processing helix chain 'H' and resid 172 through 177 Processing helix chain 'H' and resid 178 through 192 removed outlier: 3.915A pdb=" N ASN H 182 " --> pdb=" O TYR H 178 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ARG H 185 " --> pdb=" O SER H 181 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N LYS H 186 " --> pdb=" O ASN H 182 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ILE H 190 " --> pdb=" O LYS H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 203 through 208 Processing helix chain 'H' and resid 224 through 232 removed outlier: 3.600A pdb=" N TYR H 228 " --> pdb=" O GLY H 224 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N LEU H 229 " --> pdb=" O ARG H 225 " (cutoff:3.500A) removed outlier: 4.264A pdb=" N ARG H 230 " --> pdb=" O LYS H 226 " (cutoff:3.500A) Processing helix chain 'H' and resid 232 through 237 removed outlier: 3.562A pdb=" N PHE H 236 " --> pdb=" O LEU H 232 " (cutoff:3.500A) Processing helix chain 'H' and resid 259 through 274 removed outlier: 3.832A pdb=" N VAL H 263 " --> pdb=" O ASP H 259 " (cutoff:3.500A) Processing helix chain 'H' and resid 295 through 309 removed outlier: 3.524A pdb=" N LEU H 302 " --> pdb=" O ASN H 298 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N PHE H 307 " --> pdb=" O LYS H 303 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ASN H 308 " --> pdb=" O ASN H 304 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU H 309 " --> pdb=" O GLN H 305 " (cutoff:3.500A) Processing helix chain 'H' and resid 325 through 334 removed outlier: 4.192A pdb=" N LEU H 329 " --> pdb=" O THR H 325 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N SER H 334 " --> pdb=" O ILE H 330 " (cutoff:3.500A) Processing helix chain 'H' and resid 345 through 355 removed outlier: 3.958A pdb=" N GLU H 351 " --> pdb=" O ASP H 347 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N THR H 352 " --> pdb=" O ASP H 348 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N ASN H 354 " --> pdb=" O ASN H 350 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N SER H 355 " --> pdb=" O GLU H 351 " (cutoff:3.500A) Processing helix chain 'H' and resid 387 through 392 removed outlier: 3.965A pdb=" N LYS H 391 " --> pdb=" O PHE H 387 " (cutoff:3.500A) removed outlier: 3.953A pdb=" N GLU H 392 " --> pdb=" O ALA H 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 387 through 392' Processing helix chain 'I' and resid 154 through 160 removed outlier: 3.589A pdb=" N LYS I 158 " --> pdb=" O ASP I 154 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR I 160 " --> pdb=" O GLN I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 169 Processing helix chain 'I' and resid 178 through 190 removed outlier: 3.589A pdb=" N ASN I 182 " --> pdb=" O TYR I 178 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N ALA I 183 " --> pdb=" O LEU I 179 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N PHE I 184 " --> pdb=" O TYR I 180 " (cutoff:3.500A) Processing helix chain 'I' and resid 203 through 209 Processing helix chain 'I' and resid 216 through 224 Processing helix chain 'I' and resid 224 through 234 removed outlier: 3.650A pdb=" N LEU I 229 " --> pdb=" O ARG I 225 " (cutoff:3.500A) Processing helix chain 'I' and resid 259 through 275 removed outlier: 3.936A pdb=" N VAL I 263 " --> pdb=" O ASP I 259 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N CYS I 266 " --> pdb=" O THR I 262 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N SER I 275 " --> pdb=" O GLN I 271 " (cutoff:3.500A) Processing helix chain 'I' and resid 295 through 309 removed outlier: 3.711A pdb=" N GLN I 305 " --> pdb=" O GLU I 301 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N ASN I 308 " --> pdb=" O ASN I 304 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N GLU I 309 " --> pdb=" O GLN I 305 " (cutoff:3.500A) Processing helix chain 'I' and resid 325 through 334 removed outlier: 4.259A pdb=" N LEU I 329 " --> pdb=" O THR I 325 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N SER I 334 " --> pdb=" O ILE I 330 " (cutoff:3.500A) Processing helix chain 'I' and resid 345 through 353 Processing helix chain 'I' and resid 354 through 356 No H-bonds generated for 'chain 'I' and resid 354 through 356' Processing helix chain 'I' and resid 387 through 392 removed outlier: 4.171A pdb=" N LYS I 391 " --> pdb=" O PHE I 387 " (cutoff:3.500A) removed outlier: 4.423A pdb=" N GLU I 392 " --> pdb=" O ALA I 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 387 through 392' Processing helix chain 'J' and resid 159 through 169 removed outlier: 3.942A pdb=" N ILE J 163 " --> pdb=" O GLU J 159 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N PHE J 168 " --> pdb=" O ILE J 164 " (cutoff:3.500A) Processing helix chain 'J' and resid 171 through 177 removed outlier: 3.950A pdb=" N GLU J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) Processing helix chain 'J' and resid 179 through 193 removed outlier: 4.391A pdb=" N ASN J 193 " --> pdb=" O ASP J 189 " (cutoff:3.500A) Processing helix chain 'J' and resid 201 through 209 removed outlier: 3.663A pdb=" N VAL J 205 " --> pdb=" O LYS J 201 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N GLU J 206 " --> pdb=" O SER J 202 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ILE J 208 " --> pdb=" O PHE J 204 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ASN J 209 " --> pdb=" O VAL J 205 " (cutoff:3.500A) Processing helix chain 'J' and resid 223 through 232 removed outlier: 4.212A pdb=" N GLU J 227 " --> pdb=" O GLU J 223 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N TYR J 228 " --> pdb=" O GLY J 224 " (cutoff:3.500A) Processing helix chain 'J' and resid 232 through 237 removed outlier: 3.601A pdb=" N PHE J 236 " --> pdb=" O LEU J 232 " (cutoff:3.500A) Processing helix chain 'J' and resid 259 through 274 Processing helix chain 'J' and resid 295 through 309 Processing helix chain 'J' and resid 325 through 334 removed outlier: 4.071A pdb=" N LEU J 329 " --> pdb=" O THR J 325 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N SER J 334 " --> pdb=" O ILE J 330 " (cutoff:3.500A) Processing helix chain 'J' and resid 345 through 356 removed outlier: 3.547A pdb=" N THR J 352 " --> pdb=" O ASP J 348 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N LEU J 353 " --> pdb=" O PHE J 349 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ASN J 354 " --> pdb=" O ASN J 350 " (cutoff:3.500A) removed outlier: 3.921A pdb=" N SER J 355 " --> pdb=" O GLU J 351 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N ILE J 356 " --> pdb=" O THR J 352 " (cutoff:3.500A) Processing helix chain 'J' and resid 387 through 392 removed outlier: 3.950A pdb=" N LYS J 391 " --> pdb=" O PHE J 387 " (cutoff:3.500A) removed outlier: 4.108A pdb=" N GLU J 392 " --> pdb=" O ALA J 388 " (cutoff:3.500A) No H-bonds generated for 'chain 'J' and resid 387 through 392' Processing helix chain 'K' and resid 152 through 169 removed outlier: 3.789A pdb=" N GLN K 156 " --> pdb=" O SER K 152 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N LYS K 157 " --> pdb=" O PHE K 153 " (cutoff:3.500A) removed outlier: 3.990A pdb=" N LYS K 158 " --> pdb=" O ASP K 154 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N ILE K 164 " --> pdb=" O THR K 160 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N ASN K 166 " --> pdb=" O GLN K 162 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N HIS K 167 " --> pdb=" O ILE K 163 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N PHE K 168 " --> pdb=" O ILE K 164 " (cutoff:3.500A) Processing helix chain 'K' and resid 172 through 177 removed outlier: 4.225A pdb=" N GLU K 176 " --> pdb=" O ASP K 172 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N HIS K 177 " --> pdb=" O TYR K 173 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 172 through 177' Processing helix chain 'K' and resid 179 through 192 removed outlier: 3.612A pdb=" N ARG K 185 " --> pdb=" O SER K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 200 through 207 removed outlier: 3.579A pdb=" N PHE K 204 " --> pdb=" O LYS K 200 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLU K 206 " --> pdb=" O SER K 202 " (cutoff:3.500A) Processing helix chain 'K' and resid 217 through 224 Processing helix chain 'K' and resid 227 through 232 Processing helix chain 'K' and resid 232 through 237 removed outlier: 3.987A pdb=" N PHE K 236 " --> pdb=" O LEU K 232 " (cutoff:3.500A) Processing helix chain 'K' and resid 259 through 274 removed outlier: 4.072A pdb=" N CYS K 266 " --> pdb=" O THR K 262 " (cutoff:3.500A) Processing helix chain 'K' and resid 295 through 308 Processing helix chain 'K' and resid 325 through 335 removed outlier: 3.902A pdb=" N LEU K 329 " --> pdb=" O THR K 325 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N SER K 334 " --> pdb=" O ILE K 330 " (cutoff:3.500A) Processing helix chain 'K' and resid 345 through 354 removed outlier: 3.709A pdb=" N ASN K 350 " --> pdb=" O ILE K 346 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N GLU K 351 " --> pdb=" O ASP K 347 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N THR K 352 " --> pdb=" O ASP K 348 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASN K 354 " --> pdb=" O ASN K 350 " (cutoff:3.500A) Processing helix chain 'K' and resid 387 through 394 removed outlier: 4.212A pdb=" N LYS K 391 " --> pdb=" O PHE K 387 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N GLU K 392 " --> pdb=" O ALA K 388 " (cutoff:3.500A) Processing helix chain 'L' and resid 161 through 169 removed outlier: 3.681A pdb=" N HIS L 167 " --> pdb=" O ILE L 163 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N PHE L 168 " --> pdb=" O ILE L 164 " (cutoff:3.500A) Processing helix chain 'L' and resid 179 through 193 removed outlier: 4.044A pdb=" N ILE L 190 " --> pdb=" O LYS L 186 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN L 193 " --> pdb=" O ASP L 189 " (cutoff:3.500A) Processing helix chain 'L' and resid 200 through 209 Processing helix chain 'L' and resid 217 through 222 removed outlier: 3.983A pdb=" N GLN L 221 " --> pdb=" O ILE L 217 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 222 " --> pdb=" O TRP L 218 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 217 through 222' Processing helix chain 'L' and resid 224 through 237 removed outlier: 3.562A pdb=" N TYR L 228 " --> pdb=" O GLY L 224 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N LEU L 229 " --> pdb=" O ARG L 225 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N SER L 235 " --> pdb=" O LYS L 231 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N PHE L 236 " --> pdb=" O LEU L 232 " (cutoff:3.500A) Processing helix chain 'L' and resid 259 through 274 removed outlier: 3.816A pdb=" N VAL L 263 " --> pdb=" O ASP L 259 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ASN L 273 " --> pdb=" O LYS L 269 " (cutoff:3.500A) Processing helix chain 'L' and resid 295 through 309 removed outlier: 3.708A pdb=" N GLU L 309 " --> pdb=" O GLN L 305 " (cutoff:3.500A) Processing helix chain 'L' and resid 325 through 334 removed outlier: 4.240A pdb=" N LEU L 329 " --> pdb=" O THR L 325 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER L 334 " --> pdb=" O ILE L 330 " (cutoff:3.500A) Processing helix chain 'L' and resid 345 through 356 removed outlier: 3.647A pdb=" N GLU L 351 " --> pdb=" O ASP L 347 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N THR L 352 " --> pdb=" O ASP L 348 " (cutoff:3.500A) removed outlier: 3.750A pdb=" N ASN L 354 " --> pdb=" O ASN L 350 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER L 355 " --> pdb=" O GLU L 351 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ILE L 356 " --> pdb=" O THR L 352 " (cutoff:3.500A) Processing helix chain 'L' and resid 387 through 394 removed outlier: 4.116A pdb=" N LYS L 391 " --> pdb=" O PHE L 387 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLU L 392 " --> pdb=" O ALA L 388 " (cutoff:3.500A) Processing helix chain 'M' and resid 226 through 236 removed outlier: 3.911A pdb=" N PHE M 236 " --> pdb=" O LEU M 232 " (cutoff:3.500A) Processing helix chain 'M' and resid 259 through 274 removed outlier: 3.705A pdb=" N VAL M 263 " --> pdb=" O ASP M 259 " (cutoff:3.500A) Processing helix chain 'M' and resid 295 through 309 Processing helix chain 'M' and resid 325 through 335 removed outlier: 4.146A pdb=" N LEU M 329 " --> pdb=" O THR M 325 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N SER M 334 " --> pdb=" O ILE M 330 " (cutoff:3.500A) Processing helix chain 'M' and resid 345 through 356 removed outlier: 3.509A pdb=" N ASN M 354 " --> pdb=" O ASN M 350 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N SER M 355 " --> pdb=" O GLU M 351 " (cutoff:3.500A) Processing helix chain 'M' and resid 387 through 391 removed outlier: 3.655A pdb=" N LYS M 391 " --> pdb=" O ALA M 388 " (cutoff:3.500A) Processing helix chain 'N' and resid 225 through 235 removed outlier: 3.555A pdb=" N LEU N 229 " --> pdb=" O ARG N 225 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N LYS N 231 " --> pdb=" O GLU N 227 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N LEU N 232 " --> pdb=" O TYR N 228 " (cutoff:3.500A) Processing helix chain 'N' and resid 259 through 274 removed outlier: 3.989A pdb=" N VAL N 263 " --> pdb=" O ASP N 259 " (cutoff:3.500A) Processing helix chain 'N' and resid 295 through 309 Processing helix chain 'N' and resid 325 through 335 removed outlier: 4.105A pdb=" N LEU N 329 " --> pdb=" O THR N 325 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N SER N 334 " --> pdb=" O ILE N 330 " (cutoff:3.500A) Processing helix chain 'N' and resid 345 through 356 Processing helix chain 'N' and resid 387 through 394 removed outlier: 4.393A pdb=" N LYS N 391 " --> pdb=" O PHE N 387 " (cutoff:3.500A) removed outlier: 4.393A pdb=" N GLU N 392 " --> pdb=" O ALA N 388 " (cutoff:3.500A) Processing helix chain 'O' and resid 226 through 236 removed outlier: 4.024A pdb=" N PHE O 236 " --> pdb=" O LEU O 232 " (cutoff:3.500A) Processing helix chain 'O' and resid 259 through 274 removed outlier: 3.706A pdb=" N VAL O 263 " --> pdb=" O ASP O 259 " (cutoff:3.500A) Processing helix chain 'O' and resid 295 through 309 removed outlier: 3.523A pdb=" N LEU O 299 " --> pdb=" O SER O 295 " (cutoff:3.500A) Processing helix chain 'O' and resid 325 through 335 removed outlier: 4.449A pdb=" N LEU O 329 " --> pdb=" O THR O 325 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N SER O 334 " --> pdb=" O ILE O 330 " (cutoff:3.500A) Processing helix chain 'O' and resid 345 through 354 removed outlier: 3.546A pdb=" N GLU O 351 " --> pdb=" O ASP O 347 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ASN O 354 " --> pdb=" O ASN O 350 " (cutoff:3.500A) Processing helix chain 'O' and resid 388 through 394 removed outlier: 4.090A pdb=" N GLU O 392 " --> pdb=" O ALA O 388 " (cutoff:3.500A) Processing helix chain 'P' and resid 225 through 237 removed outlier: 4.081A pdb=" N LEU P 229 " --> pdb=" O ARG P 225 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ARG P 230 " --> pdb=" O LYS P 226 " (cutoff:3.500A) removed outlier: 4.006A pdb=" N PHE P 236 " --> pdb=" O LEU P 232 " (cutoff:3.500A) Processing helix chain 'P' and resid 238 through 243 removed outlier: 3.760A pdb=" N ASN P 242 " --> pdb=" O ARG P 238 " (cutoff:3.500A) removed outlier: 4.146A pdb=" N THR P 243 " --> pdb=" O ARG P 239 " (cutoff:3.500A) No H-bonds generated for 'chain 'P' and resid 238 through 243' Processing helix chain 'P' and resid 259 through 274 removed outlier: 3.677A pdb=" N VAL P 263 " --> pdb=" O ASP P 259 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ASP P 265 " --> pdb=" O LYS P 261 " (cutoff:3.500A) Processing helix chain 'P' and resid 295 through 309 Processing helix chain 'P' and resid 327 through 335 removed outlier: 3.563A pdb=" N SER P 334 " --> pdb=" O ILE P 330 " (cutoff:3.500A) Processing helix chain 'P' and resid 345 through 354 removed outlier: 3.723A pdb=" N ASN P 354 " --> pdb=" O ASN P 350 " (cutoff:3.500A) Processing helix chain 'P' and resid 386 through 388 No H-bonds generated for 'chain 'P' and resid 386 through 388' Processing helix chain 'P' and resid 389 through 394 removed outlier: 3.590A pdb=" N ILE P 393 " --> pdb=" O ASP P 389 " (cutoff:3.500A) Processing helix chain 'Q' and resid 226 through 237 removed outlier: 3.906A pdb=" N LYS Q 231 " --> pdb=" O GLU Q 227 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N LEU Q 232 " --> pdb=" O TYR Q 228 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LYS Q 233 " --> pdb=" O LEU Q 229 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE Q 237 " --> pdb=" O LYS Q 233 " (cutoff:3.500A) Processing helix chain 'Q' and resid 259 through 274 removed outlier: 3.707A pdb=" N VAL Q 263 " --> pdb=" O ASP Q 259 " (cutoff:3.500A) Processing helix chain 'Q' and resid 295 through 309 Processing helix chain 'Q' and resid 325 through 335 removed outlier: 4.043A pdb=" N LEU Q 329 " --> pdb=" O THR Q 325 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N SER Q 334 " --> pdb=" O ILE Q 330 " (cutoff:3.500A) Processing helix chain 'Q' and resid 345 through 354 removed outlier: 3.782A pdb=" N ASN Q 354 " --> pdb=" O ASN Q 350 " (cutoff:3.500A) Processing helix chain 'Q' and resid 386 through 388 No H-bonds generated for 'chain 'Q' and resid 386 through 388' Processing helix chain 'Q' and resid 389 through 394 removed outlier: 3.632A pdb=" N ILE Q 393 " --> pdb=" O ASP Q 389 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 235 removed outlier: 3.708A pdb=" N ARG R 230 " --> pdb=" O LYS R 226 " (cutoff:3.500A) Processing helix chain 'R' and resid 259 through 274 Processing helix chain 'R' and resid 295 through 309 removed outlier: 3.544A pdb=" N LEU R 306 " --> pdb=" O LEU R 302 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE R 307 " --> pdb=" O LYS R 303 " (cutoff:3.500A) Processing helix chain 'R' and resid 325 through 334 removed outlier: 4.178A pdb=" N LEU R 329 " --> pdb=" O THR R 325 " (cutoff:3.500A) removed outlier: 3.986A pdb=" N SER R 334 " --> pdb=" O ILE R 330 " (cutoff:3.500A) Processing helix chain 'R' and resid 345 through 354 removed outlier: 3.759A pdb=" N ASN R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) Processing helix chain 'R' and resid 389 through 394 removed outlier: 3.702A pdb=" N ILE R 393 " --> pdb=" O ASP R 389 " (cutoff:3.500A) removed outlier: 3.536A pdb=" N VAL R 394 " --> pdb=" O ILE R 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 389 through 394' Processing sheet with id=AA1, first strand: chain 'A' and resid 9 through 14 removed outlier: 6.618A pdb=" N LYS A 20 " --> pdb=" O VAL A 12 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 19 through 23 current: chain 'A' and resid 50 through 62 removed outlier: 6.966A pdb=" N VAL A 50 " --> pdb=" O LYS A 82 " (cutoff:3.500A) removed outlier: 7.011A pdb=" N LYS A 82 " --> pdb=" O VAL A 50 " (cutoff:3.500A) removed outlier: 7.059A pdb=" N LEU A 52 " --> pdb=" O LEU A 80 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N LEU A 80 " --> pdb=" O LEU A 52 " (cutoff:3.500A) removed outlier: 7.291A pdb=" N ALA A 54 " --> pdb=" O ILE A 78 " (cutoff:3.500A) removed outlier: 6.254A pdb=" N ILE A 78 " --> pdb=" O ALA A 54 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N ILE A 56 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 6.611A pdb=" N SER A 76 " --> pdb=" O ILE A 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 85 through 88 current: chain 'B' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 19 through 23 current: chain 'B' and resid 50 through 62 removed outlier: 5.707A pdb=" N ILE B 56 " --> pdb=" O SER B 76 " (cutoff:3.500A) removed outlier: 6.711A pdb=" N SER B 76 " --> pdb=" O ILE B 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 70 through 77 current: chain 'B' and resid 85 through 88 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 85 through 88 current: chain 'C' and resid 19 through 26 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 19 through 26 current: chain 'C' and resid 50 through 62 removed outlier: 6.883A pdb=" N VAL C 50 " --> pdb=" O LYS C 82 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N LYS C 82 " --> pdb=" O VAL C 50 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N LEU C 52 " --> pdb=" O LEU C 80 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N LEU C 80 " --> pdb=" O LEU C 52 " (cutoff:3.500A) removed outlier: 7.200A pdb=" N ALA C 54 " --> pdb=" O ILE C 78 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ILE C 78 " --> pdb=" O ALA C 54 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N ILE C 56 " --> pdb=" O SER C 76 " (cutoff:3.500A) removed outlier: 5.939A pdb=" N SER C 76 " --> pdb=" O ILE C 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 85 through 88 current: chain 'D' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 19 through 23 current: chain 'D' and resid 50 through 62 removed outlier: 6.906A pdb=" N VAL D 50 " --> pdb=" O LYS D 82 " (cutoff:3.500A) removed outlier: 6.955A pdb=" N LYS D 82 " --> pdb=" O VAL D 50 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N LEU D 52 " --> pdb=" O LEU D 80 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU D 80 " --> pdb=" O LEU D 52 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ALA D 54 " --> pdb=" O ILE D 78 " (cutoff:3.500A) removed outlier: 6.236A pdb=" N ILE D 78 " --> pdb=" O ALA D 54 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ILE D 56 " --> pdb=" O SER D 76 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N SER D 76 " --> pdb=" O ILE D 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 85 through 87 current: chain 'E' and resid 19 through 23 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 19 through 23 current: chain 'E' and resid 50 through 62 removed outlier: 6.907A pdb=" N VAL E 50 " --> pdb=" O LYS E 82 " (cutoff:3.500A) removed outlier: 6.974A pdb=" N LYS E 82 " --> pdb=" O VAL E 50 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N LEU E 52 " --> pdb=" O LEU E 80 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N LEU E 80 " --> pdb=" O LEU E 52 " (cutoff:3.500A) removed outlier: 7.257A pdb=" N ALA E 54 " --> pdb=" O ILE E 78 " (cutoff:3.500A) removed outlier: 6.289A pdb=" N ILE E 78 " --> pdb=" O ALA E 54 " (cutoff:3.500A) removed outlier: 5.682A pdb=" N ILE E 56 " --> pdb=" O SER E 76 " (cutoff:3.500A) removed outlier: 6.587A pdb=" N SER E 76 " --> pdb=" O ILE E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 85 through 88 current: chain 'F' and resid 19 through 26 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 19 through 26 current: chain 'F' and resid 50 through 62 removed outlier: 6.780A pdb=" N VAL F 50 " --> pdb=" O LYS F 82 " (cutoff:3.500A) removed outlier: 6.778A pdb=" N LYS F 82 " --> pdb=" O VAL F 50 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N LEU F 52 " --> pdb=" O LEU F 80 " (cutoff:3.500A) removed outlier: 6.351A pdb=" N LEU F 80 " --> pdb=" O LEU F 52 " (cutoff:3.500A) removed outlier: 7.409A pdb=" N ALA F 54 " --> pdb=" O ILE F 78 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N ILE F 78 " --> pdb=" O ALA F 54 " (cutoff:3.500A) removed outlier: 5.904A pdb=" N ILE F 56 " --> pdb=" O SER F 76 " (cutoff:3.500A) removed outlier: 6.182A pdb=" N SER F 76 " --> pdb=" O ILE F 56 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 121 through 122 Processing sheet with id=AA3, first strand: chain 'A' and resid 125 through 127 removed outlier: 6.578A pdb=" N HIS A 146 " --> pdb=" O THR A 481 " (cutoff:3.500A) removed outlier: 8.025A pdb=" N ILE A 483 " --> pdb=" O HIS A 146 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N ALA A 148 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 6.622A pdb=" N ILE A 147 " --> pdb=" O LEU A 463 " (cutoff:3.500A) removed outlier: 8.015A pdb=" N SER A 465 " --> pdb=" O ILE A 147 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N ILE A 149 " --> pdb=" O SER A 465 " (cutoff:3.500A) removed outlier: 6.720A pdb=" N ILE A 184 " --> pdb=" O THR A 376 " (cutoff:3.500A) removed outlier: 7.440A pdb=" N LEU A 378 " --> pdb=" O ILE A 184 " (cutoff:3.500A) removed outlier: 6.547A pdb=" N ILE A 186 " --> pdb=" O LEU A 378 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 284 through 285 Processing sheet with id=AA5, first strand: chain 'A' and resid 299 through 301 Processing sheet with id=AA6, first strand: chain 'B' and resid 134 through 138 removed outlier: 4.188A pdb=" N SER B 125 " --> pdb=" O VAL B 135 " (cutoff:3.500A) removed outlier: 7.005A pdb=" N VAL B 137 " --> pdb=" O THR B 123 " (cutoff:3.500A) removed outlier: 5.182A pdb=" N THR B 123 " --> pdb=" O VAL B 137 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N SER B 530 " --> pdb=" O ILE B 521 " (cutoff:3.500A) removed outlier: 6.100A pdb=" N HIS B 146 " --> pdb=" O CYS B 479 " (cutoff:3.500A) removed outlier: 6.623A pdb=" N ILE B 185 " --> pdb=" O VAL B 424 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 284 through 285 Processing sheet with id=AA8, first strand: chain 'B' and resid 299 through 301 Processing sheet with id=AA9, first strand: chain 'C' and resid 134 through 138 removed outlier: 7.703A pdb=" N VAL C 135 " --> pdb=" O PHE C 124 " (cutoff:3.500A) removed outlier: 4.459A pdb=" N PHE C 124 " --> pdb=" O VAL C 135 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N ALA C 148 " --> pdb=" O ILE C 483 " (cutoff:3.500A) removed outlier: 6.598A pdb=" N ILE C 147 " --> pdb=" O LEU C 463 " (cutoff:3.500A) removed outlier: 7.797A pdb=" N SER C 465 " --> pdb=" O ILE C 147 " (cutoff:3.500A) removed outlier: 6.257A pdb=" N ILE C 149 " --> pdb=" O SER C 465 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N ILE C 185 " --> pdb=" O VAL C 424 " (cutoff:3.500A) removed outlier: 7.362A pdb=" N GLU C 426 " --> pdb=" O ILE C 185 " (cutoff:3.500A) removed outlier: 6.369A pdb=" N ILE C 184 " --> pdb=" O THR C 376 " (cutoff:3.500A) removed outlier: 7.617A pdb=" N LEU C 378 " --> pdb=" O ILE C 184 " (cutoff:3.500A) removed outlier: 6.879A pdb=" N ILE C 186 " --> pdb=" O LEU C 378 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ASN C 201 " --> pdb=" O ILE C 377 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N ASP C 379 " --> pdb=" O ASN C 201 " (cutoff:3.500A) removed outlier: 6.523A pdb=" N LEU C 203 " --> pdb=" O ASP C 379 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 284 through 285 Processing sheet with id=AB2, first strand: chain 'C' and resid 299 through 301 Processing sheet with id=AB3, first strand: chain 'D' and resid 134 through 138 removed outlier: 7.886A pdb=" N VAL D 135 " --> pdb=" O PHE D 124 " (cutoff:3.500A) removed outlier: 4.497A pdb=" N PHE D 124 " --> pdb=" O VAL D 135 " (cutoff:3.500A) removed outlier: 3.594A pdb=" N SER D 530 " --> pdb=" O ILE D 521 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N ILE D 147 " --> pdb=" O LEU D 463 " (cutoff:3.500A) removed outlier: 7.584A pdb=" N SER D 465 " --> pdb=" O ILE D 147 " (cutoff:3.500A) removed outlier: 5.991A pdb=" N ILE D 149 " --> pdb=" O SER D 465 " (cutoff:3.500A) removed outlier: 6.324A pdb=" N ILE D 421 " --> pdb=" O THR D 460 " (cutoff:3.500A) removed outlier: 7.589A pdb=" N LEU D 462 " --> pdb=" O ILE D 421 " (cutoff:3.500A) removed outlier: 6.531A pdb=" N ILE D 423 " --> pdb=" O LEU D 462 " (cutoff:3.500A) removed outlier: 6.739A pdb=" N ALA D 464 " --> pdb=" O ILE D 423 " (cutoff:3.500A) removed outlier: 5.770A pdb=" N TYR D 425 " --> pdb=" O ALA D 464 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N HIS D 183 " --> pdb=" O LEU D 422 " (cutoff:3.500A) removed outlier: 7.566A pdb=" N VAL D 424 " --> pdb=" O HIS D 183 " (cutoff:3.500A) removed outlier: 6.451A pdb=" N ILE D 185 " --> pdb=" O VAL D 424 " (cutoff:3.500A) removed outlier: 6.941A pdb=" N GLU D 426 " --> pdb=" O ILE D 185 " (cutoff:3.500A) removed outlier: 6.263A pdb=" N ILE D 184 " --> pdb=" O THR D 376 " (cutoff:3.500A) removed outlier: 6.304A pdb=" N ASN D 201 " --> pdb=" O ILE D 377 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'D' and resid 284 through 285 Processing sheet with id=AB5, first strand: chain 'D' and resid 299 through 301 Processing sheet with id=AB6, first strand: chain 'E' and resid 134 through 138 removed outlier: 7.700A pdb=" N VAL E 135 " --> pdb=" O PHE E 124 " (cutoff:3.500A) removed outlier: 4.297A pdb=" N PHE E 124 " --> pdb=" O VAL E 135 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 201 through 203 removed outlier: 3.522A pdb=" N ASN E 201 " --> pdb=" O ILE E 375 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ILE E 184 " --> pdb=" O THR E 376 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N LEU E 378 " --> pdb=" O ILE E 184 " (cutoff:3.500A) removed outlier: 6.481A pdb=" N ILE E 186 " --> pdb=" O LEU E 378 " (cutoff:3.500A) removed outlier: 6.480A pdb=" N ILE E 185 " --> pdb=" O VAL E 424 " (cutoff:3.500A) removed outlier: 7.364A pdb=" N GLU E 426 " --> pdb=" O ILE E 185 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE E 187 " --> pdb=" O GLU E 426 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'E' and resid 284 through 285 Processing sheet with id=AB9, first strand: chain 'E' and resid 299 through 301 removed outlier: 3.515A pdb=" N TRP E 293 " --> pdb=" O PHE E 300 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'F' and resid 134 through 138 removed outlier: 7.848A pdb=" N VAL F 135 " --> pdb=" O PHE F 124 " (cutoff:3.500A) removed outlier: 4.677A pdb=" N PHE F 124 " --> pdb=" O VAL F 135 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N SER F 530 " --> pdb=" O ILE F 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ILE F 521 " --> pdb=" O SER F 530 " (cutoff:3.500A) removed outlier: 6.674A pdb=" N ILE F 147 " --> pdb=" O LEU F 463 " (cutoff:3.500A) removed outlier: 8.109A pdb=" N SER F 465 " --> pdb=" O ILE F 147 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N ILE F 149 " --> pdb=" O SER F 465 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N ILE F 185 " --> pdb=" O VAL F 424 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N GLU F 426 " --> pdb=" O ILE F 185 " (cutoff:3.500A) removed outlier: 6.049A pdb=" N PHE F 187 " --> pdb=" O GLU F 426 " (cutoff:3.500A) removed outlier: 6.383A pdb=" N ILE F 184 " --> pdb=" O THR F 376 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LEU F 378 " --> pdb=" O ILE F 184 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N ILE F 186 " --> pdb=" O LEU F 378 " (cutoff:3.500A) removed outlier: 6.296A pdb=" N ASN F 201 " --> pdb=" O ILE F 377 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP F 379 " --> pdb=" O ASN F 201 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'F' and resid 284 through 285 Processing sheet with id=AC3, first strand: chain 'F' and resid 299 through 301 removed outlier: 3.550A pdb=" N PHE F 300 " --> pdb=" O TRP F 293 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N TRP F 293 " --> pdb=" O PHE F 300 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE F 292 " --> pdb=" O ASP F 318 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain 'G' and resid 313 through 314 removed outlier: 5.980A pdb=" N THR G 314 " --> pdb=" O PHE G 342 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N PHE G 291 " --> pdb=" O ILE G 343 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'H' and resid 212 through 213 removed outlier: 6.276A pdb=" N ALA H 247 " --> pdb=" O GLU H 361 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N TYR H 363 " --> pdb=" O ALA H 247 " (cutoff:3.500A) removed outlier: 6.329A pdb=" N PHE H 249 " --> pdb=" O TYR H 363 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N PHE H 365 " --> pdb=" O PHE H 249 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ILE H 251 " --> pdb=" O PHE H 365 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N HIS H 292 " --> pdb=" O LEU H 252 " (cutoff:3.500A) removed outlier: 6.357A pdb=" N LEU H 289 " --> pdb=" O ILE H 343 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N THR H 314 " --> pdb=" O PHE H 342 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'I' and resid 313 through 314 removed outlier: 6.414A pdb=" N THR I 314 " --> pdb=" O PHE I 342 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N LEU I 289 " --> pdb=" O ILE I 343 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N ARG I 248 " --> pdb=" O PHE I 288 " (cutoff:3.500A) removed outlier: 8.018A pdb=" N LEU I 290 " --> pdb=" O ARG I 248 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N PHE I 250 " --> pdb=" O LEU I 290 " (cutoff:3.500A) removed outlier: 7.991A pdb=" N HIS I 292 " --> pdb=" O PHE I 250 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N LEU I 252 " --> pdb=" O HIS I 292 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ALA I 247 " --> pdb=" O GLU I 361 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N TYR I 363 " --> pdb=" O ALA I 247 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N PHE I 249 " --> pdb=" O TYR I 363 " (cutoff:3.500A) removed outlier: 7.349A pdb=" N PHE I 365 " --> pdb=" O PHE I 249 " (cutoff:3.500A) removed outlier: 5.959A pdb=" N ILE I 251 " --> pdb=" O PHE I 365 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'J' and resid 313 through 314 removed outlier: 6.235A pdb=" N THR J 314 " --> pdb=" O PHE J 342 " (cutoff:3.500A) removed outlier: 6.308A pdb=" N LEU J 289 " --> pdb=" O ILE J 343 " (cutoff:3.500A) removed outlier: 6.187A pdb=" N ALA J 247 " --> pdb=" O GLU J 361 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N TYR J 363 " --> pdb=" O ALA J 247 " (cutoff:3.500A) removed outlier: 6.453A pdb=" N PHE J 249 " --> pdb=" O TYR J 363 " (cutoff:3.500A) removed outlier: 7.165A pdb=" N PHE J 365 " --> pdb=" O PHE J 249 " (cutoff:3.500A) removed outlier: 6.197A pdb=" N ILE J 251 " --> pdb=" O PHE J 365 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'K' and resid 313 through 314 removed outlier: 6.342A pdb=" N THR K 314 " --> pdb=" O PHE K 342 " (cutoff:3.500A) removed outlier: 6.291A pdb=" N LEU K 289 " --> pdb=" O ILE K 343 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N HIS K 292 " --> pdb=" O LEU K 252 " (cutoff:3.500A) removed outlier: 6.366A pdb=" N ALA K 247 " --> pdb=" O GLU K 361 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N TYR K 363 " --> pdb=" O ALA K 247 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N PHE K 249 " --> pdb=" O TYR K 363 " (cutoff:3.500A) removed outlier: 7.402A pdb=" N PHE K 365 " --> pdb=" O PHE K 249 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ILE K 251 " --> pdb=" O PHE K 365 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain 'L' and resid 313 through 314 removed outlier: 6.288A pdb=" N THR L 314 " --> pdb=" O PHE L 342 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N PHE L 291 " --> pdb=" O ILE L 343 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ARG L 248 " --> pdb=" O PHE L 288 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N LEU L 290 " --> pdb=" O ARG L 248 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE L 250 " --> pdb=" O LEU L 290 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N HIS L 292 " --> pdb=" O PHE L 250 " (cutoff:3.500A) removed outlier: 7.151A pdb=" N LEU L 252 " --> pdb=" O HIS L 292 " (cutoff:3.500A) removed outlier: 5.884A pdb=" N ALA L 247 " --> pdb=" O GLU L 361 " (cutoff:3.500A) removed outlier: 7.536A pdb=" N TYR L 363 " --> pdb=" O ALA L 247 " (cutoff:3.500A) removed outlier: 6.447A pdb=" N PHE L 249 " --> pdb=" O TYR L 363 " (cutoff:3.500A) removed outlier: 7.209A pdb=" N PHE L 365 " --> pdb=" O PHE L 249 " (cutoff:3.500A) removed outlier: 5.851A pdb=" N ILE L 251 " --> pdb=" O PHE L 365 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain 'M' and resid 313 through 314 removed outlier: 5.958A pdb=" N THR M 314 " --> pdb=" O PHE M 342 " (cutoff:3.500A) removed outlier: 4.164A pdb=" N PHE M 291 " --> pdb=" O ILE M 343 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N ALA M 247 " --> pdb=" O GLU M 361 " (cutoff:3.500A) removed outlier: 7.551A pdb=" N TYR M 363 " --> pdb=" O ALA M 247 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N PHE M 249 " --> pdb=" O TYR M 363 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N PHE M 365 " --> pdb=" O PHE M 249 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ILE M 251 " --> pdb=" O PHE M 365 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'N' and resid 313 through 314 removed outlier: 6.076A pdb=" N THR N 314 " --> pdb=" O PHE N 342 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N PHE N 291 " --> pdb=" O ILE N 343 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N HIS N 292 " --> pdb=" O LEU N 252 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA N 247 " --> pdb=" O GLU N 361 " (cutoff:3.500A) removed outlier: 7.598A pdb=" N TYR N 363 " --> pdb=" O ALA N 247 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N PHE N 249 " --> pdb=" O TYR N 363 " (cutoff:3.500A) removed outlier: 7.472A pdb=" N PHE N 365 " --> pdb=" O PHE N 249 " (cutoff:3.500A) removed outlier: 6.154A pdb=" N ILE N 251 " --> pdb=" O PHE N 365 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain 'O' and resid 313 through 314 removed outlier: 6.220A pdb=" N THR O 314 " --> pdb=" O PHE O 342 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE O 291 " --> pdb=" O ILE O 343 " (cutoff:3.500A) removed outlier: 8.865A pdb=" N VAL O 380 " --> pdb=" O LYS O 360 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL O 362 " --> pdb=" O VAL O 380 " (cutoff:3.500A) removed outlier: 7.726A pdb=" N ILE O 382 " --> pdb=" O VAL O 362 " (cutoff:3.500A) removed outlier: 6.429A pdb=" N GLN O 364 " --> pdb=" O ILE O 382 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain 'P' and resid 313 through 314 removed outlier: 6.182A pdb=" N THR P 314 " --> pdb=" O PHE P 342 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N PHE P 291 " --> pdb=" O ILE P 343 " (cutoff:3.500A) removed outlier: 6.238A pdb=" N ALA P 247 " --> pdb=" O GLU P 361 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N TYR P 363 " --> pdb=" O ALA P 247 " (cutoff:3.500A) removed outlier: 6.057A pdb=" N PHE P 249 " --> pdb=" O TYR P 363 " (cutoff:3.500A) removed outlier: 7.344A pdb=" N PHE P 365 " --> pdb=" O PHE P 249 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ILE P 251 " --> pdb=" O PHE P 365 " (cutoff:3.500A) removed outlier: 8.895A pdb=" N VAL P 380 " --> pdb=" O LYS P 360 " (cutoff:3.500A) removed outlier: 6.810A pdb=" N VAL P 362 " --> pdb=" O VAL P 380 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ILE P 382 " --> pdb=" O VAL P 362 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N GLN P 364 " --> pdb=" O ILE P 382 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'Q' and resid 313 through 314 removed outlier: 6.100A pdb=" N THR Q 314 " --> pdb=" O PHE Q 342 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N PHE Q 291 " --> pdb=" O ILE Q 343 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'R' and resid 313 through 314 removed outlier: 6.161A pdb=" N THR R 314 " --> pdb=" O PHE R 342 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE R 291 " --> pdb=" O ILE R 343 " (cutoff:3.500A) removed outlier: 6.568A pdb=" N ALA R 247 " --> pdb=" O GLU R 361 " (cutoff:3.500A) removed outlier: 7.651A pdb=" N TYR R 363 " --> pdb=" O ALA R 247 " (cutoff:3.500A) removed outlier: 6.239A pdb=" N PHE R 249 " --> pdb=" O TYR R 363 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N PHE R 365 " --> pdb=" O PHE R 249 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE R 251 " --> pdb=" O PHE R 365 " (cutoff:3.500A) 1564 hydrogen bonds defined for protein. 4458 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: 17.27 Time building geometry restraints manager: 10.53 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 8751 1.32 - 1.45: 13105 1.45 - 1.58: 28000 1.58 - 1.70: 72 1.70 - 1.83: 114 Bond restraints: 50042 Sorted by residual: bond pdb=" N3B ANP A 601 " pdb=" PG ANP A 601 " ideal model delta sigma weight residual 1.795 1.626 0.169 2.00e-02 2.50e+03 7.11e+01 bond pdb=" O3A ANP B 601 " pdb=" PB ANP B 601 " ideal model delta sigma weight residual 1.700 1.557 0.143 2.00e-02 2.50e+03 5.12e+01 bond pdb=" O3A ANP C 601 " pdb=" PB ANP C 601 " ideal model delta sigma weight residual 1.700 1.558 0.142 2.00e-02 2.50e+03 5.04e+01 bond pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.67e+01 bond pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 1.795 1.692 0.103 2.00e-02 2.50e+03 2.64e+01 ... (remaining 50037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.69: 67102 3.69 - 7.38: 496 7.38 - 11.07: 52 11.07 - 14.76: 9 14.76 - 18.45: 3 Bond angle restraints: 67662 Sorted by residual: angle pdb=" CA PRO A 265 " pdb=" N PRO A 265 " pdb=" CD PRO A 265 " ideal model delta sigma weight residual 112.00 99.56 12.44 1.40e+00 5.10e-01 7.90e+01 angle pdb=" N ASN A 199 " pdb=" CA ASN A 199 " pdb=" C ASN A 199 " ideal model delta sigma weight residual 110.44 102.85 7.59 1.20e+00 6.94e-01 4.00e+01 angle pdb=" PB ANP B 601 " pdb=" N3B ANP B 601 " pdb=" PG ANP B 601 " ideal model delta sigma weight residual 126.95 108.50 18.45 3.00e+00 1.11e-01 3.78e+01 angle pdb=" CB LYS L 231 " pdb=" CG LYS L 231 " pdb=" CD LYS L 231 " ideal model delta sigma weight residual 111.30 124.54 -13.24 2.30e+00 1.89e-01 3.31e+01 angle pdb=" PB ANP C 601 " pdb=" N3B ANP C 601 " pdb=" PG ANP C 601 " ideal model delta sigma weight residual 126.95 109.75 17.20 3.00e+00 1.11e-01 3.29e+01 ... (remaining 67657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.27: 28920 35.27 - 70.53: 1346 70.53 - 105.80: 81 105.80 - 141.06: 5 141.06 - 176.33: 1 Dihedral angle restraints: 30353 sinusoidal: 12923 harmonic: 17430 Sorted by residual: dihedral pdb=" CA PRO A 540 " pdb=" C PRO A 540 " pdb=" N PRO A 541 " pdb=" CA PRO A 541 " ideal model delta harmonic sigma weight residual 180.00 146.64 33.36 0 5.00e+00 4.00e-02 4.45e+01 dihedral pdb=" O1B ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PB ADP E 601 " pdb=" PA ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 78.11 -138.12 1 2.00e+01 2.50e-03 4.19e+01 dihedral pdb=" O2A ADP E 601 " pdb=" O3A ADP E 601 " pdb=" PA ADP E 601 " pdb=" PB ADP E 601 " ideal model delta sinusoidal sigma weight residual -60.00 70.19 -130.19 1 2.00e+01 2.50e-03 3.95e+01 ... (remaining 30350 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 6680 0.087 - 0.173: 655 0.173 - 0.260: 30 0.260 - 0.347: 5 0.347 - 0.433: 3 Chirality restraints: 7373 Sorted by residual: chirality pdb=" CA GLU B 174 " pdb=" N GLU B 174 " pdb=" C GLU B 174 " pdb=" CB GLU B 174 " both_signs ideal model delta sigma weight residual False 2.51 2.08 0.43 2.00e-01 2.50e+01 4.69e+00 chirality pdb=" CA ASN A 289 " pdb=" N ASN A 289 " pdb=" C ASN A 289 " pdb=" CB ASN A 289 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.27e+00 chirality pdb=" C3' ANP A 601 " pdb=" C2' ANP A 601 " pdb=" C4' ANP A 601 " pdb=" O3' ANP A 601 " both_signs ideal model delta sigma weight residual False -2.36 -2.76 0.40 2.00e-01 2.50e+01 3.99e+00 ... (remaining 7370 not shown) Planarity restraints: 8639 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER F 264 " 0.087 5.00e-02 4.00e+02 1.33e-01 2.82e+01 pdb=" N PRO F 265 " -0.230 5.00e-02 4.00e+02 pdb=" CA PRO F 265 " 0.073 5.00e-02 4.00e+02 pdb=" CD PRO F 265 " 0.069 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 340 " 0.022 2.00e-02 2.50e+03 4.70e-02 2.21e+01 pdb=" C ILE A 340 " -0.081 2.00e-02 2.50e+03 pdb=" O ILE A 340 " 0.032 2.00e-02 2.50e+03 pdb=" N PHE A 341 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL F 333 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C VAL F 333 " 0.060 2.00e-02 2.50e+03 pdb=" O VAL F 333 " -0.023 2.00e-02 2.50e+03 pdb=" N ASP F 334 " -0.021 2.00e-02 2.50e+03 ... (remaining 8636 not shown) Histogram of nonbonded interaction distances: 2.07 - 2.63: 756 2.63 - 3.20: 41289 3.20 - 3.77: 78668 3.77 - 4.33: 112180 4.33 - 4.90: 182374 Nonbonded interactions: 415267 Sorted by model distance: nonbonded pdb=" NH2 ARG A 284 " pdb=" OP1 DG T 3 " model vdw 2.068 3.120 nonbonded pdb=" O ASN A 289 " pdb=" ND2 ASN A 289 " model vdw 2.075 3.120 nonbonded pdb=" OG SER C 158 " pdb="MG MG C 602 " model vdw 2.086 2.170 nonbonded pdb=" OG SER B 158 " pdb="MG MG B 602 " model vdw 2.090 2.170 nonbonded pdb=" O3G ANP C 601 " pdb="MG MG C 602 " model vdw 2.143 2.170 ... (remaining 415262 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 5 through 502 or resid 507 through 571)) selection = (chain 'B' and (resid 5 through 502 or resid 507 through 571)) selection = (chain 'C' and (resid 5 through 502 or resid 507 through 571)) selection = chain 'D' selection = (chain 'E' and (resid 5 through 502 or resid 507 through 571)) selection = (chain 'F' and (resid 5 through 502 or resid 507 through 571)) } ncs_group { reference = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = (chain 'N' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = (chain 'O' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = (chain 'P' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) selection = chain 'Q' selection = (chain 'R' and ((resid 225 and (name N or name CA or name C or name O or name CB \ )) or resid 226 through 394)) } 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=1.00 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: 0.010 Normalize map: mean=0, sd=1: 1.370 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 1.710 Check model and map are aligned: 0.330 Set scattering table: 0.400 Process input model: 84.370 Find NCS groups from input model: 2.050 Set up NCS constraints: 0.230 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: 0.010 Load rotamer database and sin/cos tables:11.140 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 101.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 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 0.169 50042 Z= 0.279 Angle : 0.812 18.448 67662 Z= 0.425 Chirality : 0.051 0.433 7373 Planarity : 0.006 0.133 8639 Dihedral : 18.851 176.330 19031 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.02 % Allowed : 3.35 % Favored : 96.63 % Rotamer: Outliers : 0.88 % Allowed : 32.70 % Favored : 66.42 % Cbeta Deviations : 0.04 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.48 % 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: -2.30 (0.10), residues: 5849 helix: -2.81 (0.08), residues: 2056 sheet: -0.08 (0.18), residues: 839 loop : -0.85 (0.10), residues: 2954 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.002 TRP D 556 HIS 0.010 0.001 HIS L 292 PHE 0.040 0.002 PHE O 319 TYR 0.038 0.002 TYR K 188 ARG 0.016 0.001 ARG B 498 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 735 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 687 time to evaluate : 4.260 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 563 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8022 (mtmt) REVERT: B 179 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8455 (pp) REVERT: B 261 SER cc_start: 0.8449 (OUTLIER) cc_final: 0.8242 (p) REVERT: C 188 ASP cc_start: 0.8181 (t0) cc_final: 0.7884 (p0) REVERT: C 437 LEU cc_start: 0.8572 (mp) cc_final: 0.8306 (mt) REVERT: D 64 LYS cc_start: 0.8245 (mttp) cc_final: 0.7941 (mttp) REVERT: D 74 GLU cc_start: 0.7687 (mt-10) cc_final: 0.7417 (mp0) REVERT: E 118 ILE cc_start: 0.8533 (tp) cc_final: 0.8278 (tt) REVERT: E 330 LEU cc_start: 0.8671 (tp) cc_final: 0.8468 (tt) REVERT: E 478 GLN cc_start: 0.7943 (mp10) cc_final: 0.7725 (mp10) REVERT: F 120 ASP cc_start: 0.7829 (m-30) cc_final: 0.7567 (m-30) REVERT: F 180 ASN cc_start: 0.7248 (p0) cc_final: 0.7028 (p0) REVERT: F 334 ASP cc_start: 0.8733 (OUTLIER) cc_final: 0.8471 (t0) REVERT: I 230 ARG cc_start: 0.7959 (ttp80) cc_final: 0.7610 (tmm160) REVERT: K 156 GLN cc_start: 0.5380 (pm20) cc_final: 0.5081 (pm20) REVERT: K 230 ARG cc_start: 0.7943 (ttp80) cc_final: 0.7251 (ttp80) REVERT: L 191 SER cc_start: 0.1957 (OUTLIER) cc_final: 0.1104 (m) REVERT: L 220 TYR cc_start: 0.5952 (t80) cc_final: 0.5692 (t80) REVERT: O 232 LEU cc_start: 0.7902 (mt) cc_final: 0.7656 (mm) REVERT: P 279 LYS cc_start: 0.8037 (mttm) cc_final: 0.7821 (mtpp) outliers start: 48 outliers final: 8 residues processed: 727 average time/residue: 1.1529 time to fit residues: 1075.8814 Evaluate side-chains 576 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 563 time to evaluate : 4.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 286 ASN Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 174 GLU Chi-restraints excluded: chain B residue 179 LEU Chi-restraints excluded: chain B residue 261 SER Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain E residue 548 TYR Chi-restraints excluded: chain F residue 334 ASP Chi-restraints excluded: chain H residue 334 SER Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 298 ASN Chi-restraints excluded: chain L residue 191 SER Chi-restraints excluded: chain Q residue 389 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 493 optimal weight: 5.9990 chunk 442 optimal weight: 5.9990 chunk 245 optimal weight: 8.9990 chunk 151 optimal weight: 4.9990 chunk 298 optimal weight: 4.9990 chunk 236 optimal weight: 0.7980 chunk 457 optimal weight: 0.4980 chunk 177 optimal weight: 0.9990 chunk 278 optimal weight: 0.7980 chunk 340 optimal weight: 4.9990 chunk 530 optimal weight: 6.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 240 GLN A 286 ASN A 466 GLN B 48 GLN B 183 HIS B 405 HIS B 494 ASN C 417 GLN C 466 GLN D 414 ASN E 232 HIS ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN F 326 ASN F 405 HIS F 478 GLN G 255 GLN G 305 GLN ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 221 GLN J 255 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 162 GLN K 216 ASN M 271 GLN N 255 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN Q 271 GLN R 298 ASN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 364 GLN Total number of N/Q/H flips: 27 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1567 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 50042 Z= 0.244 Angle : 0.562 7.807 67662 Z= 0.299 Chirality : 0.045 0.162 7373 Planarity : 0.005 0.095 8639 Dihedral : 9.672 168.856 6759 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 4.35 % Allowed : 29.23 % Favored : 66.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -1.24 (0.10), residues: 5849 helix: -0.97 (0.10), residues: 2127 sheet: -0.29 (0.17), residues: 951 loop : -0.74 (0.11), residues: 2771 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP D 556 HIS 0.006 0.001 HIS A 405 PHE 0.025 0.001 PHE B 385 TYR 0.021 0.001 TYR J 180 ARG 0.011 0.001 ARG E 239 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 883 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 238 poor density : 645 time to evaluate : 4.992 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8713 (OUTLIER) cc_final: 0.8459 (mp) REVERT: A 282 ASN cc_start: 0.8551 (OUTLIER) cc_final: 0.8340 (p0) REVERT: A 548 TYR cc_start: 0.8683 (OUTLIER) cc_final: 0.7912 (t80) REVERT: B 466 GLN cc_start: 0.8739 (OUTLIER) cc_final: 0.8517 (mt0) REVERT: C 548 TYR cc_start: 0.8936 (OUTLIER) cc_final: 0.8608 (t80) REVERT: D 417 GLN cc_start: 0.6936 (OUTLIER) cc_final: 0.5957 (tp40) REVERT: D 453 GLU cc_start: 0.8214 (OUTLIER) cc_final: 0.7999 (pt0) REVERT: D 515 LYS cc_start: 0.8265 (OUTLIER) cc_final: 0.7715 (mttp) REVERT: E 118 ILE cc_start: 0.8520 (tp) cc_final: 0.8288 (tt) REVERT: E 208 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8477 (tp) REVERT: F 120 ASP cc_start: 0.7876 (m-30) cc_final: 0.7598 (m-30) REVERT: F 180 ASN cc_start: 0.8079 (p0) cc_final: 0.7817 (p0) REVERT: G 217 ILE cc_start: 0.6711 (OUTLIER) cc_final: 0.6320 (mm) REVERT: H 240 SER cc_start: 0.8968 (OUTLIER) cc_final: 0.8736 (t) REVERT: I 230 ARG cc_start: 0.7896 (ttp80) cc_final: 0.7588 (tmm160) REVERT: L 220 TYR cc_start: 0.6125 (t80) cc_final: 0.5896 (t80) REVERT: L 308 ASN cc_start: 0.8660 (m-40) cc_final: 0.8404 (m110) REVERT: M 299 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8526 (tp) REVERT: N 253 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8147 (tt0) REVERT: N 376 GLN cc_start: 0.8366 (OUTLIER) cc_final: 0.7929 (pm20) REVERT: O 232 LEU cc_start: 0.8136 (mt) cc_final: 0.7912 (mm) REVERT: Q 392 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.7569 (mm-30) outliers start: 238 outliers final: 75 residues processed: 822 average time/residue: 1.2220 time to fit residues: 1277.2739 Evaluate side-chains 656 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 90 poor density : 566 time to evaluate : 4.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 282 ASN Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 390 ILE Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 431 TYR Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 202 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain C residue 567 GLN Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 453 GLU Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain G residue 208 ILE Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 240 SER Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 262 THR Chi-restraints excluded: chain J residue 379 GLN Chi-restraints excluded: chain K residue 346 ILE Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 391 LYS Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 279 LYS Chi-restraints excluded: chain O residue 325 THR Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 347 ASP Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 369 ASN Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 243 THR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 347 ASP Chi-restraints excluded: chain R residue 360 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 294 optimal weight: 6.9990 chunk 164 optimal weight: 2.9990 chunk 441 optimal weight: 3.9990 chunk 361 optimal weight: 10.0000 chunk 146 optimal weight: 7.9990 chunk 531 optimal weight: 0.8980 chunk 573 optimal weight: 5.9990 chunk 473 optimal weight: 6.9990 chunk 526 optimal weight: 2.9990 chunk 181 optimal weight: 0.8980 chunk 426 optimal weight: 6.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 466 GLN B 5 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN D 299 ASN D 414 ASN D 478 GLN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 201 ASN ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 240 GLN ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN E 478 GLN E 489 ASN F 306 ASN ** G 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN ** I 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 177 HIS I 216 ASN I 308 ASN I 383 GLN J 167 HIS J 255 GLN J 273 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN L 305 GLN ** L 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 383 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN P 305 GLN R 255 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 26 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8243 moved from start: 0.2317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 50042 Z= 0.311 Angle : 0.557 7.745 67662 Z= 0.294 Chirality : 0.046 0.178 7373 Planarity : 0.004 0.078 8639 Dihedral : 9.090 145.433 6733 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.96 % Favored : 97.04 % Rotamer: Outliers : 5.19 % Allowed : 28.33 % Favored : 66.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.87 (0.11), residues: 5849 helix: -0.34 (0.11), residues: 2203 sheet: -0.43 (0.17), residues: 949 loop : -0.70 (0.11), residues: 2697 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 556 HIS 0.006 0.001 HIS L 292 PHE 0.024 0.002 PHE H 184 TYR 0.017 0.002 TYR G 180 ARG 0.019 0.001 ARG E 239 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 902 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 284 poor density : 618 time to evaluate : 4.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8845 (OUTLIER) cc_final: 0.8595 (mp) REVERT: A 258 GLU cc_start: 0.7488 (OUTLIER) cc_final: 0.7221 (mm-30) REVERT: A 547 LYS cc_start: 0.8587 (OUTLIER) cc_final: 0.7871 (ttmm) REVERT: A 548 TYR cc_start: 0.8854 (OUTLIER) cc_final: 0.8104 (t80) REVERT: B 74 GLU cc_start: 0.7869 (OUTLIER) cc_final: 0.7516 (mp0) REVERT: B 109 ILE cc_start: 0.8222 (mp) cc_final: 0.7877 (mt) REVERT: B 250 PHE cc_start: 0.7779 (t80) cc_final: 0.7453 (t80) REVERT: C 35 LYS cc_start: 0.8960 (OUTLIER) cc_final: 0.8723 (mptp) REVERT: C 74 GLU cc_start: 0.7693 (mt-10) cc_final: 0.7488 (mp0) REVERT: C 394 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8626 (mt) REVERT: C 448 GLU cc_start: 0.7882 (mm-30) cc_final: 0.7597 (mt-10) REVERT: C 548 TYR cc_start: 0.8971 (OUTLIER) cc_final: 0.8576 (t80) REVERT: D 414 ASN cc_start: 0.7971 (t0) cc_final: 0.7714 (t0) REVERT: D 417 GLN cc_start: 0.7087 (OUTLIER) cc_final: 0.6094 (tp40) REVERT: D 515 LYS cc_start: 0.8380 (OUTLIER) cc_final: 0.7910 (mttp) REVERT: D 516 GLU cc_start: 0.7189 (tp30) cc_final: 0.6828 (tt0) REVERT: D 550 ASP cc_start: 0.7024 (m-30) cc_final: 0.6753 (m-30) REVERT: E 67 GLN cc_start: 0.8149 (OUTLIER) cc_final: 0.7930 (pt0) REVERT: E 69 GLN cc_start: 0.8546 (OUTLIER) cc_final: 0.7991 (tm-30) REVERT: E 118 ILE cc_start: 0.8586 (tp) cc_final: 0.8312 (tt) REVERT: E 208 LEU cc_start: 0.8892 (OUTLIER) cc_final: 0.8456 (tp) REVERT: E 253 ASP cc_start: 0.6988 (OUTLIER) cc_final: 0.6748 (t0) REVERT: E 515 LYS cc_start: 0.8433 (OUTLIER) cc_final: 0.8227 (mttm) REVERT: E 521 ILE cc_start: 0.8930 (OUTLIER) cc_final: 0.8549 (mm) REVERT: F 24 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8299 (m-30) REVERT: F 306 ASN cc_start: 0.8038 (OUTLIER) cc_final: 0.7824 (m-40) REVERT: G 217 ILE cc_start: 0.6992 (OUTLIER) cc_final: 0.6655 (mm) REVERT: G 385 LYS cc_start: 0.6305 (OUTLIER) cc_final: 0.5884 (ttmm) REVERT: I 230 ARG cc_start: 0.8035 (ttp80) cc_final: 0.7760 (tmm160) REVERT: K 151 LYS cc_start: 0.4686 (OUTLIER) cc_final: 0.3224 (tppt) REVERT: K 156 GLN cc_start: 0.5616 (pm20) cc_final: 0.5193 (pm20) REVERT: K 219 PHE cc_start: 0.7744 (m-10) cc_final: 0.7537 (m-10) REVERT: K 279 LYS cc_start: 0.8001 (OUTLIER) cc_final: 0.7771 (pttm) REVERT: L 220 TYR cc_start: 0.6306 (t80) cc_final: 0.6051 (t80) REVERT: L 221 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6628 (mm-40) REVERT: L 308 ASN cc_start: 0.8790 (m-40) cc_final: 0.8564 (m110) REVERT: L 373 ILE cc_start: 0.7605 (OUTLIER) cc_final: 0.7349 (pt) REVERT: M 253 GLU cc_start: 0.8521 (OUTLIER) cc_final: 0.8150 (tt0) REVERT: M 299 LEU cc_start: 0.8905 (OUTLIER) cc_final: 0.8574 (tp) REVERT: M 383 GLN cc_start: 0.8130 (OUTLIER) cc_final: 0.7903 (mm-40) REVERT: N 376 GLN cc_start: 0.8355 (OUTLIER) cc_final: 0.7956 (pm20) REVERT: O 227 GLU cc_start: 0.6142 (OUTLIER) cc_final: 0.5876 (pm20) REVERT: O 238 ARG cc_start: 0.6204 (OUTLIER) cc_final: 0.5342 (ptt-90) REVERT: O 280 ARG cc_start: 0.7576 (OUTLIER) cc_final: 0.6933 (ptm-80) REVERT: P 253 GLU cc_start: 0.8416 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: P 283 ARG cc_start: 0.8307 (OUTLIER) cc_final: 0.8057 (ttp-110) outliers start: 284 outliers final: 108 residues processed: 827 average time/residue: 1.2333 time to fit residues: 1298.5399 Evaluate side-chains 677 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 141 poor density : 536 time to evaluate : 4.478 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 131 THR Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 15 SER Chi-restraints excluded: chain B residue 27 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 126 SER Chi-restraints excluded: chain B residue 132 LYS Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 35 LYS Chi-restraints excluded: chain C residue 53 LEU Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 188 ASP Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 394 LEU Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 476 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 105 LEU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 292 ILE Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 67 GLN Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 253 ASP Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 366 ILE Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 515 LYS Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain F residue 24 ASP Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 323 VAL Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 283 ARG Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 217 ILE Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 279 LYS Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 373 ILE Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 280 ARG Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 283 ARG Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 369 ASN Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 323 VAL Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 524 optimal weight: 4.9990 chunk 399 optimal weight: 0.9990 chunk 275 optimal weight: 1.9990 chunk 58 optimal weight: 7.9990 chunk 253 optimal weight: 0.6980 chunk 356 optimal weight: 9.9990 chunk 533 optimal weight: 2.9990 chunk 564 optimal weight: 0.0770 chunk 278 optimal weight: 0.6980 chunk 505 optimal weight: 4.9990 chunk 152 optimal weight: 4.9990 overall best weight: 0.8942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 67 GLN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN A 509 ASN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 494 ASN ** B 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 232 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 67 GLN ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 279 ASN E 304 ASN E 478 GLN F 306 ASN ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 177 HIS I 298 ASN J 167 HIS J 255 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN K 364 GLN ** L 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 383 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN P 379 GLN P 383 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 50042 Z= 0.178 Angle : 0.491 7.382 67662 Z= 0.260 Chirality : 0.043 0.264 7373 Planarity : 0.004 0.058 8639 Dihedral : 8.819 143.280 6733 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.65 % Allowed : 29.54 % Favored : 66.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.59 (0.11), residues: 5849 helix: 0.04 (0.11), residues: 2209 sheet: -0.50 (0.17), residues: 924 loop : -0.58 (0.11), residues: 2716 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 556 HIS 0.004 0.001 HIS L 292 PHE 0.023 0.001 PHE H 184 TYR 0.015 0.001 TYR G 180 ARG 0.008 0.000 ARG Q 283 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 786 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 200 poor density : 586 time to evaluate : 4.473 Fit side-chains revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8775 (OUTLIER) cc_final: 0.8516 (mp) REVERT: A 258 GLU cc_start: 0.7456 (OUTLIER) cc_final: 0.7135 (mm-30) REVERT: A 467 ARG cc_start: 0.7951 (ttt90) cc_final: 0.7661 (tpt-90) REVERT: A 536 LYS cc_start: 0.6991 (mmmm) cc_final: 0.6535 (mtmm) REVERT: A 548 TYR cc_start: 0.8828 (OUTLIER) cc_final: 0.8061 (t80) REVERT: B 192 GLU cc_start: 0.8238 (OUTLIER) cc_final: 0.7981 (mt-10) REVERT: B 388 LEU cc_start: 0.8459 (OUTLIER) cc_final: 0.8192 (tp) REVERT: B 441 ARG cc_start: 0.8203 (ttp80) cc_final: 0.7594 (ttm-80) REVERT: B 442 THR cc_start: 0.8634 (t) cc_final: 0.8368 (p) REVERT: B 495 TYR cc_start: 0.7922 (t80) cc_final: 0.7702 (t80) REVERT: C 453 GLU cc_start: 0.7932 (OUTLIER) cc_final: 0.7673 (pm20) REVERT: C 548 TYR cc_start: 0.8959 (OUTLIER) cc_final: 0.8549 (t80) REVERT: D 272 GLU cc_start: 0.7779 (mt-10) cc_final: 0.7349 (mt-10) REVERT: D 480 ASN cc_start: 0.8400 (t0) cc_final: 0.7944 (m-40) REVERT: D 515 LYS cc_start: 0.8399 (OUTLIER) cc_final: 0.7987 (mttp) REVERT: D 516 GLU cc_start: 0.7145 (tp30) cc_final: 0.6814 (tt0) REVERT: D 550 ASP cc_start: 0.7029 (m-30) cc_final: 0.6756 (m-30) REVERT: E 118 ILE cc_start: 0.8585 (tp) cc_final: 0.8314 (tt) REVERT: E 208 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8416 (tp) REVERT: E 242 ILE cc_start: 0.8860 (OUTLIER) cc_final: 0.8531 (mp) REVERT: E 263 HIS cc_start: 0.7851 (OUTLIER) cc_final: 0.7352 (m-70) REVERT: F 180 ASN cc_start: 0.8263 (p0) cc_final: 0.7902 (p0) REVERT: F 306 ASN cc_start: 0.7877 (OUTLIER) cc_final: 0.7598 (m-40) REVERT: G 217 ILE cc_start: 0.6937 (OUTLIER) cc_final: 0.6600 (mm) REVERT: I 230 ARG cc_start: 0.7974 (ttp80) cc_final: 0.7684 (tmm160) REVERT: J 299 LEU cc_start: 0.8810 (OUTLIER) cc_final: 0.8601 (tp) REVERT: L 220 TYR cc_start: 0.6292 (t80) cc_final: 0.6067 (t80) REVERT: L 221 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6580 (mm-40) REVERT: L 308 ASN cc_start: 0.8764 (m-40) cc_final: 0.8497 (m110) REVERT: L 373 ILE cc_start: 0.7713 (OUTLIER) cc_final: 0.7428 (pt) REVERT: M 299 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8514 (tp) REVERT: N 283 ARG cc_start: 0.7898 (OUTLIER) cc_final: 0.7131 (ptp-170) REVERT: O 227 GLU cc_start: 0.6095 (OUTLIER) cc_final: 0.5841 (pm20) REVERT: P 361 GLU cc_start: 0.8508 (mt-10) cc_final: 0.8259 (mp0) REVERT: Q 363 TYR cc_start: 0.8800 (m-80) cc_final: 0.8525 (m-80) outliers start: 200 outliers final: 89 residues processed: 729 average time/residue: 1.2033 time to fit residues: 1117.9128 Evaluate side-chains 645 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 537 time to evaluate : 4.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 205 VAL Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 258 GLU Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain B residue 192 GLU Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 334 ASP Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 453 GLU Chi-restraints excluded: chain C residue 476 PHE Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 548 TYR Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 515 LYS Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 101 GLU Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 506 ASP Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 532 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain I residue 234 GLU Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain K residue 167 HIS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 373 ILE Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 347 ASP Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 275 SER Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 391 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 470 optimal weight: 9.9990 chunk 320 optimal weight: 6.9990 chunk 8 optimal weight: 6.9990 chunk 420 optimal weight: 0.0980 chunk 232 optimal weight: 0.4980 chunk 481 optimal weight: 6.9990 chunk 390 optimal weight: 9.9990 chunk 0 optimal weight: 5.9990 chunk 288 optimal weight: 4.9990 chunk 506 optimal weight: 6.9990 chunk 142 optimal weight: 5.9990 overall best weight: 3.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 166 GLN A 466 GLN B 567 GLN ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 281 ASN C 405 HIS C 466 GLN C 493 GLN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 47 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN F 48 GLN ** G 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN L 379 GLN L 383 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN R 255 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2970 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.077 50042 Z= 0.430 Angle : 0.592 8.495 67662 Z= 0.309 Chirality : 0.047 0.247 7373 Planarity : 0.004 0.059 8639 Dihedral : 9.080 138.932 6733 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 4.73 % Allowed : 28.17 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.64 (0.11), residues: 5849 helix: 0.11 (0.11), residues: 2200 sheet: -0.56 (0.16), residues: 946 loop : -0.70 (0.11), residues: 2703 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 568 HIS 0.009 0.001 HIS E 159 PHE 0.021 0.002 PHE H 184 TYR 0.020 0.002 TYR J 180 ARG 0.010 0.001 ARG E 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 829 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 259 poor density : 570 time to evaluate : 4.352 Fit side-chains revert: symmetry clash REVERT: A 547 LYS cc_start: 0.8681 (OUTLIER) cc_final: 0.8076 (ttmm) REVERT: A 548 TYR cc_start: 0.8948 (OUTLIER) cc_final: 0.8344 (t80) REVERT: A 563 LYS cc_start: 0.8434 (OUTLIER) cc_final: 0.8175 (mtmt) REVERT: B 28 GLU cc_start: 0.8237 (OUTLIER) cc_final: 0.7919 (tt0) REVERT: B 74 GLU cc_start: 0.7866 (OUTLIER) cc_final: 0.7489 (mp0) REVERT: B 250 PHE cc_start: 0.8057 (t80) cc_final: 0.7668 (t80) REVERT: B 388 LEU cc_start: 0.8493 (OUTLIER) cc_final: 0.8206 (tp) REVERT: B 441 ARG cc_start: 0.8177 (ttp80) cc_final: 0.7443 (ttm-80) REVERT: B 495 TYR cc_start: 0.8273 (t80) cc_final: 0.8067 (t80) REVERT: C 145 LYS cc_start: 0.8090 (OUTLIER) cc_final: 0.7541 (mmtp) REVERT: D 218 ASP cc_start: 0.7696 (m-30) cc_final: 0.7490 (m-30) REVERT: D 417 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.5822 (tp-100) REVERT: D 516 GLU cc_start: 0.7125 (tp30) cc_final: 0.6866 (tt0) REVERT: D 550 ASP cc_start: 0.7123 (m-30) cc_final: 0.6797 (m-30) REVERT: E 69 GLN cc_start: 0.8683 (OUTLIER) cc_final: 0.8101 (tm-30) REVERT: E 118 ILE cc_start: 0.8586 (tp) cc_final: 0.8302 (tt) REVERT: E 208 LEU cc_start: 0.8899 (OUTLIER) cc_final: 0.8461 (tp) REVERT: E 242 ILE cc_start: 0.8965 (OUTLIER) cc_final: 0.8624 (mp) REVERT: E 263 HIS cc_start: 0.8011 (OUTLIER) cc_final: 0.7372 (m-70) REVERT: E 521 ILE cc_start: 0.8929 (OUTLIER) cc_final: 0.8629 (mm) REVERT: F 306 ASN cc_start: 0.8050 (OUTLIER) cc_final: 0.7743 (m-40) REVERT: F 309 ARG cc_start: 0.8265 (ptp-170) cc_final: 0.8051 (pmm-80) REVERT: G 217 ILE cc_start: 0.7125 (OUTLIER) cc_final: 0.6837 (mm) REVERT: G 385 LYS cc_start: 0.6582 (OUTLIER) cc_final: 0.6181 (ttmm) REVERT: I 230 ARG cc_start: 0.8054 (ttp80) cc_final: 0.7780 (tmm160) REVERT: J 377 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6841 (pp) REVERT: K 151 LYS cc_start: 0.4399 (OUTLIER) cc_final: 0.3134 (tppt) REVERT: L 220 TYR cc_start: 0.6569 (t80) cc_final: 0.6329 (t80) REVERT: L 221 GLN cc_start: 0.7073 (OUTLIER) cc_final: 0.6514 (mm-40) REVERT: L 308 ASN cc_start: 0.8796 (m-40) cc_final: 0.8571 (m110) REVERT: M 253 GLU cc_start: 0.8620 (OUTLIER) cc_final: 0.8224 (tt0) REVERT: M 280 ARG cc_start: 0.7783 (OUTLIER) cc_final: 0.7444 (mtm110) REVERT: M 299 LEU cc_start: 0.8925 (OUTLIER) cc_final: 0.8613 (tp) REVERT: M 383 GLN cc_start: 0.8260 (OUTLIER) cc_final: 0.8004 (mm-40) REVERT: N 253 GLU cc_start: 0.8822 (OUTLIER) cc_final: 0.8070 (tt0) REVERT: N 376 GLN cc_start: 0.8325 (OUTLIER) cc_final: 0.7960 (pm20) REVERT: O 227 GLU cc_start: 0.6256 (OUTLIER) cc_final: 0.5862 (pm20) REVERT: O 238 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5238 (ptt-90) REVERT: P 253 GLU cc_start: 0.8471 (OUTLIER) cc_final: 0.7385 (tt0) REVERT: P 361 GLU cc_start: 0.8525 (mt-10) cc_final: 0.8286 (mt-10) REVERT: Q 237 ILE cc_start: 0.5142 (OUTLIER) cc_final: 0.4785 (tp) REVERT: Q 253 GLU cc_start: 0.8526 (OUTLIER) cc_final: 0.7914 (tm-30) outliers start: 259 outliers final: 139 residues processed: 763 average time/residue: 1.2524 time to fit residues: 1211.1369 Evaluate side-chains 695 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 169 poor density : 526 time to evaluate : 4.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 66 SER Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 28 GLU Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 106 ASP Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 524 ASP Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 145 LYS Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 419 ILE Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 476 PHE Chi-restraints excluded: chain C residue 503 THR Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 205 VAL Chi-restraints excluded: chain D residue 225 LEU Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 413 SER Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain D residue 559 SER Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 68 LYS Chi-restraints excluded: chain E residue 69 GLN Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 150 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 242 ILE Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 409 ILE Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 521 ILE Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 81 VAL Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 306 ASN Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 160 THR Chi-restraints excluded: chain J residue 243 THR Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 167 HIS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 253 GLU Chi-restraints excluded: chain M residue 280 ARG Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 253 GLU Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 253 GLU Chi-restraints excluded: chain P residue 330 ILE Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 253 GLU Chi-restraints excluded: chain Q residue 286 SER Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 361 GLU Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 189 optimal weight: 1.9990 chunk 508 optimal weight: 0.8980 chunk 111 optimal weight: 0.2980 chunk 331 optimal weight: 0.6980 chunk 139 optimal weight: 3.9990 chunk 565 optimal weight: 6.9990 chunk 469 optimal weight: 3.9990 chunk 261 optimal weight: 5.9990 chunk 46 optimal weight: 4.9990 chunk 186 optimal weight: 2.9990 chunk 296 optimal weight: 0.9980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN D 199 ASN D 232 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 478 GLN E 47 ASN ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 306 ASN G 364 GLN ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 379 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN L 255 GLN L 379 GLN L 383 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN P 369 ASN R 255 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 18 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3010 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 50042 Z= 0.187 Angle : 0.500 7.519 67662 Z= 0.264 Chirality : 0.043 0.224 7373 Planarity : 0.004 0.055 8639 Dihedral : 8.850 139.701 6733 Min Nonbonded Distance : 1.993 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 3.84 % Allowed : 29.23 % Favored : 66.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.44 (0.11), residues: 5849 helix: 0.35 (0.11), residues: 2197 sheet: -0.61 (0.17), residues: 943 loop : -0.59 (0.11), residues: 2709 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 213 HIS 0.005 0.001 HIS D 232 PHE 0.021 0.001 PHE H 184 TYR 0.024 0.001 TYR K 188 ARG 0.015 0.001 ARG E 239 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 781 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 210 poor density : 571 time to evaluate : 4.534 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 52 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8633 (mp) REVERT: A 548 TYR cc_start: 0.8879 (OUTLIER) cc_final: 0.8276 (t80) REVERT: A 563 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8110 (mtmt) REVERT: B 20 LYS cc_start: 0.8648 (OUTLIER) cc_final: 0.8445 (mppt) REVERT: B 74 GLU cc_start: 0.7757 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: B 250 PHE cc_start: 0.7997 (t80) cc_final: 0.7742 (t80) REVERT: B 388 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8249 (tp) REVERT: B 441 ARG cc_start: 0.8128 (ttp80) cc_final: 0.7476 (ttm-80) REVERT: B 442 THR cc_start: 0.8631 (t) cc_final: 0.8351 (p) REVERT: B 445 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7898 (mp0) REVERT: B 466 GLN cc_start: 0.8943 (OUTLIER) cc_final: 0.8546 (mt0) REVERT: D 438 SER cc_start: 0.8436 (OUTLIER) cc_final: 0.7929 (p) REVERT: D 516 GLU cc_start: 0.7117 (tp30) cc_final: 0.6839 (tt0) REVERT: D 550 ASP cc_start: 0.7087 (m-30) cc_final: 0.6781 (m-30) REVERT: E 118 ILE cc_start: 0.8589 (tp) cc_final: 0.8309 (tt) REVERT: E 263 HIS cc_start: 0.8075 (OUTLIER) cc_final: 0.7400 (m-70) REVERT: E 330 LEU cc_start: 0.8620 (tp) cc_final: 0.8370 (tt) REVERT: G 179 LEU cc_start: 0.6697 (OUTLIER) cc_final: 0.6264 (mm) REVERT: G 217 ILE cc_start: 0.7078 (OUTLIER) cc_final: 0.6753 (mm) REVERT: I 230 ARG cc_start: 0.8048 (ttp80) cc_final: 0.7760 (tmm160) REVERT: J 162 GLN cc_start: 0.7320 (OUTLIER) cc_final: 0.6616 (mp10) REVERT: J 180 TYR cc_start: 0.7748 (t80) cc_final: 0.5795 (t80) REVERT: J 299 LEU cc_start: 0.8834 (OUTLIER) cc_final: 0.8577 (tp) REVERT: J 377 LEU cc_start: 0.7292 (OUTLIER) cc_final: 0.6740 (pp) REVERT: L 220 TYR cc_start: 0.6427 (t80) cc_final: 0.6194 (t80) REVERT: L 221 GLN cc_start: 0.7028 (OUTLIER) cc_final: 0.6454 (mm-40) REVERT: L 308 ASN cc_start: 0.8737 (m-40) cc_final: 0.8528 (m110) REVERT: M 264 LYS cc_start: 0.9292 (OUTLIER) cc_final: 0.8605 (mtmt) REVERT: M 383 GLN cc_start: 0.8156 (OUTLIER) cc_final: 0.7943 (mm-40) REVERT: N 275 SER cc_start: 0.9230 (p) cc_final: 0.8934 (p) REVERT: N 283 ARG cc_start: 0.7972 (OUTLIER) cc_final: 0.7194 (ptp-170) REVERT: O 227 GLU cc_start: 0.6312 (OUTLIER) cc_final: 0.6020 (pm20) REVERT: O 238 ARG cc_start: 0.5998 (OUTLIER) cc_final: 0.5155 (ptt-90) REVERT: Q 226 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7286 (pmmt) REVERT: Q 237 ILE cc_start: 0.4941 (OUTLIER) cc_final: 0.4510 (mm) REVERT: Q 392 GLU cc_start: 0.8103 (OUTLIER) cc_final: 0.7701 (mm-30) outliers start: 210 outliers final: 106 residues processed: 729 average time/residue: 1.2830 time to fit residues: 1198.3883 Evaluate side-chains 652 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 522 time to evaluate : 4.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 544 ILE Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 445 GLU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 ILE Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 476 PHE Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 518 GLU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 391 CYS Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain E residue 13 SER Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain I residue 386 ASP Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 167 HIS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 264 LYS Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 227 GLU Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain Q residue 226 LYS Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 278 SER Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 310 ASP Chi-restraints excluded: chain R residue 360 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 544 optimal weight: 0.9980 chunk 63 optimal weight: 0.4980 chunk 321 optimal weight: 5.9990 chunk 412 optimal weight: 20.0000 chunk 319 optimal weight: 6.9990 chunk 475 optimal weight: 0.9990 chunk 315 optimal weight: 6.9990 chunk 562 optimal weight: 9.9990 chunk 352 optimal weight: 0.9980 chunk 343 optimal weight: 9.9990 chunk 259 optimal weight: 2.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN A 67 GLN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 249 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 216 ASN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 381 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 166 ASN K 216 ASN L 379 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN R 255 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.3086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 50042 Z= 0.210 Angle : 0.505 9.156 67662 Z= 0.265 Chirality : 0.043 0.219 7373 Planarity : 0.004 0.059 8639 Dihedral : 8.789 139.258 6733 Min Nonbonded Distance : 1.975 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 3.71 % Allowed : 29.61 % Favored : 66.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.34 (0.11), residues: 5849 helix: 0.47 (0.11), residues: 2200 sheet: -0.64 (0.17), residues: 938 loop : -0.53 (0.12), residues: 2711 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 568 HIS 0.005 0.001 HIS L 292 PHE 0.022 0.001 PHE H 184 TYR 0.022 0.001 TYR K 222 ARG 0.011 0.000 ARG I 283 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 755 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 203 poor density : 552 time to evaluate : 4.533 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8875 (tt0) cc_final: 0.8598 (tt0) REVERT: A 52 LEU cc_start: 0.8937 (OUTLIER) cc_final: 0.8654 (mp) REVERT: A 475 ILE cc_start: 0.9337 (mt) cc_final: 0.9134 (mp) REVERT: A 548 TYR cc_start: 0.8909 (OUTLIER) cc_final: 0.8257 (t80) REVERT: A 563 LYS cc_start: 0.8403 (OUTLIER) cc_final: 0.8128 (mtmt) REVERT: B 20 LYS cc_start: 0.8674 (OUTLIER) cc_final: 0.8466 (mppt) REVERT: B 74 GLU cc_start: 0.7764 (OUTLIER) cc_final: 0.7430 (mp0) REVERT: B 250 PHE cc_start: 0.8041 (t80) cc_final: 0.7833 (t80) REVERT: B 388 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8226 (tp) REVERT: B 408 LYS cc_start: 0.7889 (mmmt) cc_final: 0.7665 (mmpt) REVERT: B 441 ARG cc_start: 0.8121 (ttp80) cc_final: 0.7484 (ttm-80) REVERT: B 442 THR cc_start: 0.8647 (t) cc_final: 0.8393 (p) REVERT: B 466 GLN cc_start: 0.8936 (OUTLIER) cc_final: 0.8573 (mt0) REVERT: B 495 TYR cc_start: 0.8110 (t80) cc_final: 0.7901 (t80) REVERT: D 74 GLU cc_start: 0.7888 (mt-10) cc_final: 0.7684 (mp0) REVERT: D 438 SER cc_start: 0.8476 (OUTLIER) cc_final: 0.7944 (p) REVERT: D 516 GLU cc_start: 0.7114 (tp30) cc_final: 0.6851 (tt0) REVERT: D 550 ASP cc_start: 0.7066 (m-30) cc_final: 0.6764 (m-30) REVERT: E 118 ILE cc_start: 0.8591 (tp) cc_final: 0.8308 (tt) REVERT: E 208 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8447 (tp) REVERT: E 263 HIS cc_start: 0.8161 (OUTLIER) cc_final: 0.7427 (m-70) REVERT: G 179 LEU cc_start: 0.6635 (OUTLIER) cc_final: 0.6192 (mm) REVERT: G 217 ILE cc_start: 0.7087 (OUTLIER) cc_final: 0.6787 (mm) REVERT: G 226 LYS cc_start: 0.8303 (OUTLIER) cc_final: 0.7968 (tttm) REVERT: G 369 ASN cc_start: 0.7138 (m110) cc_final: 0.6908 (m-40) REVERT: G 385 LYS cc_start: 0.6415 (OUTLIER) cc_final: 0.6054 (ttmm) REVERT: G 391 LYS cc_start: 0.8902 (ttpp) cc_final: 0.8626 (tttm) REVERT: I 217 ILE cc_start: 0.7835 (OUTLIER) cc_final: 0.7381 (mt) REVERT: I 230 ARG cc_start: 0.8060 (ttp80) cc_final: 0.7769 (tmm160) REVERT: J 162 GLN cc_start: 0.7307 (OUTLIER) cc_final: 0.6588 (mp10) REVERT: J 299 LEU cc_start: 0.8823 (OUTLIER) cc_final: 0.8551 (tp) REVERT: J 377 LEU cc_start: 0.7273 (OUTLIER) cc_final: 0.6724 (pp) REVERT: L 220 TYR cc_start: 0.6503 (t80) cc_final: 0.6269 (t80) REVERT: L 221 GLN cc_start: 0.7002 (OUTLIER) cc_final: 0.6431 (mm-40) REVERT: L 308 ASN cc_start: 0.8757 (m-40) cc_final: 0.8539 (m110) REVERT: M 264 LYS cc_start: 0.9300 (OUTLIER) cc_final: 0.8503 (mtmt) REVERT: M 299 LEU cc_start: 0.8886 (OUTLIER) cc_final: 0.8633 (tp) REVERT: M 383 GLN cc_start: 0.8154 (OUTLIER) cc_final: 0.7951 (mm-40) REVERT: N 275 SER cc_start: 0.9197 (p) cc_final: 0.8916 (p) REVERT: N 376 GLN cc_start: 0.8309 (OUTLIER) cc_final: 0.7945 (pm20) REVERT: O 238 ARG cc_start: 0.6031 (OUTLIER) cc_final: 0.5205 (ptt-90) REVERT: O 253 GLU cc_start: 0.8653 (OUTLIER) cc_final: 0.7778 (tt0) REVERT: P 361 GLU cc_start: 0.8492 (mt-10) cc_final: 0.8257 (mp0) REVERT: Q 226 LYS cc_start: 0.7687 (OUTLIER) cc_final: 0.7296 (pmmt) REVERT: Q 237 ILE cc_start: 0.4990 (OUTLIER) cc_final: 0.4537 (mm) REVERT: Q 392 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7730 (mm-30) outliers start: 203 outliers final: 117 residues processed: 711 average time/residue: 1.2569 time to fit residues: 1135.1343 Evaluate side-chains 648 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 145 poor density : 503 time to evaluate : 4.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 292 ILE Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 466 GLN Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 476 PHE Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 316 THR Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 49 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 179 LEU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 162 GLN Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 167 HIS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 264 LYS Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 253 GLU Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 289 LEU Chi-restraints excluded: chain P residue 347 ASP Chi-restraints excluded: chain Q residue 226 LYS Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 237 ILE Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 348 optimal weight: 0.9980 chunk 224 optimal weight: 3.9990 chunk 336 optimal weight: 2.9990 chunk 169 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 109 optimal weight: 0.9980 chunk 357 optimal weight: 7.9990 chunk 383 optimal weight: 8.9990 chunk 278 optimal weight: 5.9990 chunk 52 optimal weight: 1.9990 chunk 442 optimal weight: 4.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN B 429 HIS ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 199 ASN D 232 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 304 ASN F 144 ASN ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 381 ASN L 379 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN P 369 ASN R 255 GLN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8278 moved from start: 0.3282 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 50042 Z= 0.292 Angle : 0.538 8.180 67662 Z= 0.281 Chirality : 0.045 0.215 7373 Planarity : 0.004 0.060 8639 Dihedral : 8.889 135.589 6733 Min Nonbonded Distance : 1.937 Molprobity Statistics. All-atom Clashscore : 8.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.91 % Allowed : 29.48 % Favored : 66.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.38 (0.11), residues: 5849 helix: 0.44 (0.11), residues: 2210 sheet: -0.64 (0.17), residues: 941 loop : -0.57 (0.12), residues: 2698 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 568 HIS 0.005 0.001 HIS E 159 PHE 0.023 0.001 PHE H 184 TYR 0.025 0.001 TYR K 188 ARG 0.013 0.001 ARG H 283 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 745 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 214 poor density : 531 time to evaluate : 4.534 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8932 (tt0) cc_final: 0.8682 (tt0) REVERT: A 548 TYR cc_start: 0.8955 (OUTLIER) cc_final: 0.8422 (t80) REVERT: A 563 LYS cc_start: 0.8423 (OUTLIER) cc_final: 0.8173 (mtmt) REVERT: B 20 LYS cc_start: 0.8726 (OUTLIER) cc_final: 0.8416 (mppt) REVERT: B 35 LYS cc_start: 0.8851 (OUTLIER) cc_final: 0.8613 (mmtp) REVERT: B 74 GLU cc_start: 0.7807 (OUTLIER) cc_final: 0.7463 (mp0) REVERT: B 250 PHE cc_start: 0.8153 (t80) cc_final: 0.7870 (t80) REVERT: B 388 LEU cc_start: 0.8476 (OUTLIER) cc_final: 0.8209 (tp) REVERT: B 408 LYS cc_start: 0.8038 (mmmt) cc_final: 0.7812 (mmpt) REVERT: B 441 ARG cc_start: 0.8097 (ttp80) cc_final: 0.7556 (ttm-80) REVERT: B 442 THR cc_start: 0.8663 (t) cc_final: 0.8373 (p) REVERT: D 74 GLU cc_start: 0.7909 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: D 417 GLN cc_start: 0.7092 (OUTLIER) cc_final: 0.5747 (tp-100) REVERT: D 438 SER cc_start: 0.8519 (OUTLIER) cc_final: 0.8015 (p) REVERT: D 516 GLU cc_start: 0.7167 (tp30) cc_final: 0.6893 (tt0) REVERT: D 550 ASP cc_start: 0.7029 (m-30) cc_final: 0.6698 (m-30) REVERT: E 118 ILE cc_start: 0.8605 (tp) cc_final: 0.8327 (tt) REVERT: E 208 LEU cc_start: 0.8885 (OUTLIER) cc_final: 0.8452 (tp) REVERT: E 263 HIS cc_start: 0.8223 (OUTLIER) cc_final: 0.7358 (m-70) REVERT: E 330 LEU cc_start: 0.8694 (tp) cc_final: 0.8431 (tt) REVERT: E 449 ARG cc_start: 0.7772 (ttt90) cc_final: 0.7561 (ttp-110) REVERT: G 217 ILE cc_start: 0.7117 (OUTLIER) cc_final: 0.6820 (mm) REVERT: G 226 LYS cc_start: 0.8324 (OUTLIER) cc_final: 0.7982 (tttm) REVERT: G 385 LYS cc_start: 0.6472 (OUTLIER) cc_final: 0.6102 (ttmm) REVERT: G 391 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8662 (tttm) REVERT: I 217 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7389 (mt) REVERT: I 230 ARG cc_start: 0.8038 (ttp80) cc_final: 0.7760 (tmm160) REVERT: J 377 LEU cc_start: 0.7326 (OUTLIER) cc_final: 0.6763 (pp) REVERT: K 151 LYS cc_start: 0.4203 (OUTLIER) cc_final: 0.3139 (tppt) REVERT: K 230 ARG cc_start: 0.8015 (ttp80) cc_final: 0.7446 (ttp80) REVERT: L 220 TYR cc_start: 0.6553 (t80) cc_final: 0.6288 (t80) REVERT: L 308 ASN cc_start: 0.8778 (m-40) cc_final: 0.8559 (m110) REVERT: M 264 LYS cc_start: 0.9314 (OUTLIER) cc_final: 0.8437 (mtmt) REVERT: M 283 ARG cc_start: 0.8106 (mtm180) cc_final: 0.7874 (mtm180) REVERT: M 299 LEU cc_start: 0.8890 (OUTLIER) cc_final: 0.8617 (tp) REVERT: M 383 GLN cc_start: 0.8245 (OUTLIER) cc_final: 0.8000 (mm-40) REVERT: N 275 SER cc_start: 0.9251 (p) cc_final: 0.8945 (p) REVERT: N 376 GLN cc_start: 0.8307 (OUTLIER) cc_final: 0.7949 (pm20) REVERT: O 238 ARG cc_start: 0.6020 (OUTLIER) cc_final: 0.5186 (ptt-90) REVERT: P 361 GLU cc_start: 0.8515 (mt-10) cc_final: 0.8259 (mp0) REVERT: Q 226 LYS cc_start: 0.7695 (OUTLIER) cc_final: 0.7310 (pmmt) REVERT: Q 392 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7714 (mm-30) outliers start: 214 outliers final: 127 residues processed: 697 average time/residue: 1.3077 time to fit residues: 1178.4200 Evaluate side-chains 647 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 151 poor density : 496 time to evaluate : 4.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 LEU Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 343 LYS Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 6 ASP Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 404 TYR Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 80 LEU Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 488 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 151 LYS Chi-restraints excluded: chain K residue 167 HIS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 264 LYS Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 232 LEU Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 347 ASP Chi-restraints excluded: chain P residue 380 VAL Chi-restraints excluded: chain Q residue 226 LYS Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 512 optimal weight: 0.8980 chunk 539 optimal weight: 3.9990 chunk 491 optimal weight: 4.9990 chunk 524 optimal weight: 3.9990 chunk 315 optimal weight: 6.9990 chunk 228 optimal weight: 4.9990 chunk 411 optimal weight: 20.0000 chunk 160 optimal weight: 0.9990 chunk 473 optimal weight: 1.9990 chunk 496 optimal weight: 0.9990 chunk 522 optimal weight: 8.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 17 ASN ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS D 236 ASN ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 379 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN ** P 292 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8269 moved from start: 0.3308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 50042 Z= 0.254 Angle : 0.528 8.811 67662 Z= 0.277 Chirality : 0.044 0.208 7373 Planarity : 0.004 0.060 8639 Dihedral : 8.862 135.260 6733 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 3.34 % Allowed : 30.25 % Favored : 66.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.37 (0.11), residues: 5849 helix: 0.45 (0.11), residues: 2225 sheet: -0.69 (0.17), residues: 934 loop : -0.55 (0.12), residues: 2690 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 568 HIS 0.007 0.001 HIS B 405 PHE 0.024 0.001 PHE H 184 TYR 0.023 0.001 TYR K 222 ARG 0.013 0.001 ARG I 283 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 696 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 183 poor density : 513 time to evaluate : 4.438 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8904 (tt0) cc_final: 0.8651 (tt0) REVERT: A 548 TYR cc_start: 0.8953 (OUTLIER) cc_final: 0.8500 (t80) REVERT: A 563 LYS cc_start: 0.8410 (OUTLIER) cc_final: 0.8159 (mtmt) REVERT: B 20 LYS cc_start: 0.8693 (OUTLIER) cc_final: 0.8384 (mppt) REVERT: B 35 LYS cc_start: 0.8831 (OUTLIER) cc_final: 0.8597 (mmtp) REVERT: B 74 GLU cc_start: 0.7794 (OUTLIER) cc_final: 0.7454 (mp0) REVERT: B 250 PHE cc_start: 0.8158 (t80) cc_final: 0.7879 (t80) REVERT: B 388 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8221 (tp) REVERT: B 441 ARG cc_start: 0.8096 (ttp80) cc_final: 0.7542 (ttm-80) REVERT: B 442 THR cc_start: 0.8657 (t) cc_final: 0.8365 (p) REVERT: C 244 LEU cc_start: 0.8770 (OUTLIER) cc_final: 0.8527 (tp) REVERT: D 74 GLU cc_start: 0.7903 (OUTLIER) cc_final: 0.7663 (mp0) REVERT: D 417 GLN cc_start: 0.7042 (OUTLIER) cc_final: 0.5666 (tp-100) REVERT: D 438 SER cc_start: 0.8504 (OUTLIER) cc_final: 0.8005 (p) REVERT: D 516 GLU cc_start: 0.7095 (tp30) cc_final: 0.6836 (tt0) REVERT: D 550 ASP cc_start: 0.7054 (m-30) cc_final: 0.6751 (m-30) REVERT: E 35 LYS cc_start: 0.8682 (OUTLIER) cc_final: 0.8050 (mtpp) REVERT: E 118 ILE cc_start: 0.8615 (tp) cc_final: 0.8316 (tt) REVERT: E 208 LEU cc_start: 0.8877 (OUTLIER) cc_final: 0.8444 (tp) REVERT: E 263 HIS cc_start: 0.8220 (OUTLIER) cc_final: 0.7341 (m-70) REVERT: E 330 LEU cc_start: 0.8695 (tp) cc_final: 0.8434 (tt) REVERT: E 449 ARG cc_start: 0.7811 (ttt90) cc_final: 0.7589 (ttp-110) REVERT: G 217 ILE cc_start: 0.7121 (OUTLIER) cc_final: 0.6823 (mm) REVERT: G 226 LYS cc_start: 0.8337 (OUTLIER) cc_final: 0.7987 (tttm) REVERT: G 385 LYS cc_start: 0.6478 (OUTLIER) cc_final: 0.6150 (ttmm) REVERT: G 391 LYS cc_start: 0.8934 (ttpp) cc_final: 0.8665 (tttm) REVERT: I 217 ILE cc_start: 0.7843 (OUTLIER) cc_final: 0.7389 (mt) REVERT: I 230 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7730 (tmm160) REVERT: I 283 ARG cc_start: 0.8115 (ttm110) cc_final: 0.7809 (ttp-110) REVERT: J 299 LEU cc_start: 0.8812 (OUTLIER) cc_final: 0.8554 (tp) REVERT: J 377 LEU cc_start: 0.7321 (OUTLIER) cc_final: 0.6770 (pp) REVERT: K 230 ARG cc_start: 0.8028 (ttp80) cc_final: 0.7484 (ttp80) REVERT: L 221 GLN cc_start: 0.6619 (OUTLIER) cc_final: 0.6288 (mm-40) REVERT: M 264 LYS cc_start: 0.9312 (OUTLIER) cc_final: 0.8447 (mtmt) REVERT: M 283 ARG cc_start: 0.8111 (mtm180) cc_final: 0.7890 (mtm180) REVERT: M 299 LEU cc_start: 0.8896 (OUTLIER) cc_final: 0.8641 (tp) REVERT: M 383 GLN cc_start: 0.8198 (OUTLIER) cc_final: 0.7997 (mm-40) REVERT: N 275 SER cc_start: 0.9240 (p) cc_final: 0.8948 (p) REVERT: N 281 THR cc_start: 0.8631 (p) cc_final: 0.8147 (t) REVERT: N 376 GLN cc_start: 0.8297 (OUTLIER) cc_final: 0.7941 (pm20) REVERT: O 238 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5188 (ptt-90) REVERT: P 361 GLU cc_start: 0.8490 (mt-10) cc_final: 0.8260 (mp0) REVERT: Q 226 LYS cc_start: 0.7726 (OUTLIER) cc_final: 0.7342 (pmmt) REVERT: Q 392 GLU cc_start: 0.8108 (OUTLIER) cc_final: 0.7717 (mm-30) outliers start: 183 outliers final: 123 residues processed: 653 average time/residue: 1.2117 time to fit residues: 1008.7600 Evaluate side-chains 648 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 150 poor density : 498 time to evaluate : 4.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 177 LYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 205 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 305 GLU Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 101 GLU Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 244 LEU Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 466 GLN Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 502 ASP Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 378 LEU Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 263 HIS Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 520 LEU Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 371 ASP Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 226 LYS Chi-restraints excluded: chain G residue 282 ASP Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 167 HIS Chi-restraints excluded: chain K residue 217 ILE Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 264 LYS Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain M residue 383 GLN Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 259 ASP Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 361 GLU Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 347 ASP Chi-restraints excluded: chain Q residue 226 LYS Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 344 optimal weight: 0.4980 chunk 554 optimal weight: 1.9990 chunk 338 optimal weight: 8.9990 chunk 263 optimal weight: 0.8980 chunk 385 optimal weight: 0.5980 chunk 581 optimal weight: 10.0000 chunk 535 optimal weight: 4.9990 chunk 463 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 357 optimal weight: 10.0000 chunk 284 optimal weight: 3.9990 overall best weight: 1.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 466 GLN ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 216 ASN L 308 ASN L 379 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN P 292 HIS P 369 ASN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.3355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 50042 Z= 0.238 Angle : 0.527 9.171 67662 Z= 0.276 Chirality : 0.044 0.208 7373 Planarity : 0.004 0.066 8639 Dihedral : 8.834 134.944 6733 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.97 % Favored : 97.03 % Rotamer: Outliers : 2.94 % Allowed : 30.62 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.34 (0.11), residues: 5849 helix: 0.48 (0.11), residues: 2221 sheet: -0.72 (0.17), residues: 928 loop : -0.52 (0.12), residues: 2700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 568 HIS 0.005 0.001 HIS L 292 PHE 0.024 0.001 PHE H 184 TYR 0.024 0.001 TYR K 188 ARG 0.015 0.001 ARG H 283 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 11698 Ramachandran restraints generated. 5849 Oldfield, 0 Emsley, 5849 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 674 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 161 poor density : 513 time to evaluate : 4.363 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8875 (tt0) cc_final: 0.8630 (tt0) REVERT: A 548 TYR cc_start: 0.8951 (OUTLIER) cc_final: 0.8495 (t80) REVERT: A 563 LYS cc_start: 0.8392 (OUTLIER) cc_final: 0.8139 (mtmt) REVERT: B 20 LYS cc_start: 0.8687 (OUTLIER) cc_final: 0.8382 (mppt) REVERT: B 35 LYS cc_start: 0.8827 (OUTLIER) cc_final: 0.8586 (mmtp) REVERT: B 74 GLU cc_start: 0.7785 (OUTLIER) cc_final: 0.7456 (mp0) REVERT: B 250 PHE cc_start: 0.8161 (t80) cc_final: 0.7883 (t80) REVERT: B 388 LEU cc_start: 0.8495 (OUTLIER) cc_final: 0.8239 (tp) REVERT: B 441 ARG cc_start: 0.8052 (ttp80) cc_final: 0.7511 (ttm-80) REVERT: B 442 THR cc_start: 0.8656 (t) cc_final: 0.8361 (p) REVERT: D 74 GLU cc_start: 0.7894 (OUTLIER) cc_final: 0.7658 (mp0) REVERT: D 417 GLN cc_start: 0.7033 (OUTLIER) cc_final: 0.5647 (tp-100) REVERT: D 438 SER cc_start: 0.8518 (OUTLIER) cc_final: 0.8017 (p) REVERT: D 516 GLU cc_start: 0.7099 (tp30) cc_final: 0.6849 (tt0) REVERT: D 550 ASP cc_start: 0.7050 (m-30) cc_final: 0.6731 (m-30) REVERT: E 35 LYS cc_start: 0.8677 (OUTLIER) cc_final: 0.8036 (mtpp) REVERT: E 118 ILE cc_start: 0.8611 (tp) cc_final: 0.8318 (tt) REVERT: E 208 LEU cc_start: 0.8881 (OUTLIER) cc_final: 0.8446 (tp) REVERT: E 330 LEU cc_start: 0.8700 (tp) cc_final: 0.8436 (tt) REVERT: E 449 ARG cc_start: 0.7810 (ttt90) cc_final: 0.7579 (ttp-110) REVERT: G 217 ILE cc_start: 0.7077 (OUTLIER) cc_final: 0.6781 (mm) REVERT: G 385 LYS cc_start: 0.6483 (OUTLIER) cc_final: 0.6160 (ttmm) REVERT: G 391 LYS cc_start: 0.8930 (ttpp) cc_final: 0.8664 (tttm) REVERT: I 217 ILE cc_start: 0.7846 (OUTLIER) cc_final: 0.7391 (mt) REVERT: I 230 ARG cc_start: 0.7994 (ttp80) cc_final: 0.7733 (tmm160) REVERT: J 299 LEU cc_start: 0.8826 (OUTLIER) cc_final: 0.8589 (tp) REVERT: J 377 LEU cc_start: 0.7307 (OUTLIER) cc_final: 0.6746 (pp) REVERT: K 230 ARG cc_start: 0.8034 (ttp80) cc_final: 0.7219 (ttp80) REVERT: L 221 GLN cc_start: 0.6598 (OUTLIER) cc_final: 0.6269 (mm-40) REVERT: M 264 LYS cc_start: 0.9308 (OUTLIER) cc_final: 0.8441 (mtmt) REVERT: M 299 LEU cc_start: 0.8893 (OUTLIER) cc_final: 0.8649 (tp) REVERT: N 275 SER cc_start: 0.9218 (p) cc_final: 0.8937 (p) REVERT: N 281 THR cc_start: 0.8639 (p) cc_final: 0.8180 (t) REVERT: N 376 GLN cc_start: 0.8291 (OUTLIER) cc_final: 0.7936 (pm20) REVERT: O 238 ARG cc_start: 0.6016 (OUTLIER) cc_final: 0.5181 (ptt-90) REVERT: Q 226 LYS cc_start: 0.7704 (OUTLIER) cc_final: 0.7328 (pmmt) REVERT: Q 392 GLU cc_start: 0.8104 (OUTLIER) cc_final: 0.7719 (mm-30) outliers start: 161 outliers final: 117 residues processed: 636 average time/residue: 1.2138 time to fit residues: 985.2049 Evaluate side-chains 636 residues out of total 5475 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 140 poor density : 496 time to evaluate : 4.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 LYS Chi-restraints excluded: chain A residue 206 ASP Chi-restraints excluded: chain A residue 209 THR Chi-restraints excluded: chain A residue 353 SER Chi-restraints excluded: chain A residue 357 THR Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 442 THR Chi-restraints excluded: chain A residue 473 GLU Chi-restraints excluded: chain A residue 474 THR Chi-restraints excluded: chain A residue 537 CYS Chi-restraints excluded: chain A residue 547 LYS Chi-restraints excluded: chain A residue 548 TYR Chi-restraints excluded: chain A residue 563 LYS Chi-restraints excluded: chain B residue 20 LYS Chi-restraints excluded: chain B residue 35 LYS Chi-restraints excluded: chain B residue 74 GLU Chi-restraints excluded: chain B residue 105 LEU Chi-restraints excluded: chain B residue 113 SER Chi-restraints excluded: chain B residue 133 VAL Chi-restraints excluded: chain B residue 227 THR Chi-restraints excluded: chain B residue 294 SER Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 388 LEU Chi-restraints excluded: chain B residue 394 LEU Chi-restraints excluded: chain B residue 436 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 548 TYR Chi-restraints excluded: chain C residue 205 VAL Chi-restraints excluded: chain C residue 207 THR Chi-restraints excluded: chain C residue 356 VAL Chi-restraints excluded: chain C residue 387 VAL Chi-restraints excluded: chain C residue 389 SER Chi-restraints excluded: chain C residue 418 ASP Chi-restraints excluded: chain C residue 474 THR Chi-restraints excluded: chain C residue 510 LEU Chi-restraints excluded: chain C residue 542 SER Chi-restraints excluded: chain C residue 557 VAL Chi-restraints excluded: chain D residue 13 SER Chi-restraints excluded: chain D residue 15 SER Chi-restraints excluded: chain D residue 74 GLU Chi-restraints excluded: chain D residue 83 ASN Chi-restraints excluded: chain D residue 113 SER Chi-restraints excluded: chain D residue 117 ASP Chi-restraints excluded: chain D residue 204 ASN Chi-restraints excluded: chain D residue 320 SER Chi-restraints excluded: chain D residue 375 ILE Chi-restraints excluded: chain D residue 383 VAL Chi-restraints excluded: chain D residue 390 ILE Chi-restraints excluded: chain D residue 417 GLN Chi-restraints excluded: chain D residue 435 SER Chi-restraints excluded: chain D residue 438 SER Chi-restraints excluded: chain D residue 499 LEU Chi-restraints excluded: chain D residue 528 ILE Chi-restraints excluded: chain D residue 538 THR Chi-restraints excluded: chain E residue 14 VAL Chi-restraints excluded: chain E residue 35 LYS Chi-restraints excluded: chain E residue 46 ASP Chi-restraints excluded: chain E residue 63 VAL Chi-restraints excluded: chain E residue 106 ASP Chi-restraints excluded: chain E residue 110 SER Chi-restraints excluded: chain E residue 115 SER Chi-restraints excluded: chain E residue 133 VAL Chi-restraints excluded: chain E residue 208 LEU Chi-restraints excluded: chain E residue 316 THR Chi-restraints excluded: chain E residue 356 VAL Chi-restraints excluded: chain E residue 373 SER Chi-restraints excluded: chain E residue 386 GLU Chi-restraints excluded: chain E residue 388 LEU Chi-restraints excluded: chain E residue 474 THR Chi-restraints excluded: chain E residue 496 VAL Chi-restraints excluded: chain E residue 538 THR Chi-restraints excluded: chain E residue 555 GLU Chi-restraints excluded: chain F residue 53 LEU Chi-restraints excluded: chain F residue 60 SER Chi-restraints excluded: chain F residue 157 LYS Chi-restraints excluded: chain F residue 205 VAL Chi-restraints excluded: chain F residue 366 ILE Chi-restraints excluded: chain F residue 386 GLU Chi-restraints excluded: chain G residue 203 ASP Chi-restraints excluded: chain G residue 217 ILE Chi-restraints excluded: chain G residue 334 SER Chi-restraints excluded: chain G residue 385 LYS Chi-restraints excluded: chain H residue 232 LEU Chi-restraints excluded: chain H residue 238 ARG Chi-restraints excluded: chain H residue 263 VAL Chi-restraints excluded: chain H residue 290 LEU Chi-restraints excluded: chain H residue 355 SER Chi-restraints excluded: chain I residue 217 ILE Chi-restraints excluded: chain I residue 258 THR Chi-restraints excluded: chain I residue 377 LEU Chi-restraints excluded: chain J residue 241 VAL Chi-restraints excluded: chain J residue 299 LEU Chi-restraints excluded: chain J residue 334 SER Chi-restraints excluded: chain J residue 377 LEU Chi-restraints excluded: chain K residue 240 SER Chi-restraints excluded: chain L residue 160 THR Chi-restraints excluded: chain L residue 214 LEU Chi-restraints excluded: chain L residue 221 GLN Chi-restraints excluded: chain L residue 263 VAL Chi-restraints excluded: chain L residue 281 THR Chi-restraints excluded: chain L residue 286 SER Chi-restraints excluded: chain L residue 334 SER Chi-restraints excluded: chain M residue 232 LEU Chi-restraints excluded: chain M residue 244 SER Chi-restraints excluded: chain M residue 264 LYS Chi-restraints excluded: chain M residue 299 LEU Chi-restraints excluded: chain M residue 302 LEU Chi-restraints excluded: chain M residue 334 SER Chi-restraints excluded: chain M residue 376 GLN Chi-restraints excluded: chain M residue 380 VAL Chi-restraints excluded: chain N residue 237 ILE Chi-restraints excluded: chain N residue 243 THR Chi-restraints excluded: chain N residue 258 THR Chi-restraints excluded: chain N residue 272 SER Chi-restraints excluded: chain N residue 283 ARG Chi-restraints excluded: chain N residue 322 SER Chi-restraints excluded: chain N residue 334 SER Chi-restraints excluded: chain N residue 355 SER Chi-restraints excluded: chain N residue 375 SER Chi-restraints excluded: chain N residue 376 GLN Chi-restraints excluded: chain N residue 380 VAL Chi-restraints excluded: chain O residue 238 ARG Chi-restraints excluded: chain O residue 244 SER Chi-restraints excluded: chain O residue 272 SER Chi-restraints excluded: chain O residue 277 LEU Chi-restraints excluded: chain O residue 355 SER Chi-restraints excluded: chain O residue 356 ILE Chi-restraints excluded: chain P residue 347 ASP Chi-restraints excluded: chain Q residue 226 LYS Chi-restraints excluded: chain Q residue 228 TYR Chi-restraints excluded: chain Q residue 334 SER Chi-restraints excluded: chain Q residue 347 ASP Chi-restraints excluded: chain Q residue 380 VAL Chi-restraints excluded: chain Q residue 383 GLN Chi-restraints excluded: chain Q residue 392 GLU Chi-restraints excluded: chain R residue 228 TYR Chi-restraints excluded: chain R residue 289 LEU Chi-restraints excluded: chain R residue 302 LEU Chi-restraints excluded: chain R residue 360 LYS Chi-restraints excluded: chain R residue 380 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 584 random chunks: chunk 368 optimal weight: 0.3980 chunk 493 optimal weight: 5.9990 chunk 141 optimal weight: 0.9980 chunk 427 optimal weight: 5.9990 chunk 68 optimal weight: 4.9990 chunk 128 optimal weight: 3.9990 chunk 464 optimal weight: 10.0000 chunk 194 optimal weight: 2.9990 chunk 476 optimal weight: 0.9980 chunk 58 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 466 GLN ** B 489 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 567 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 232 HIS ** D 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 405 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 138 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 159 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 234 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 245 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 233 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 376 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 255 GLN ** J 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 364 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 308 ASN L 379 GLN O 255 GLN ** O 335 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** P 273 ASN ** R 341 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3763 r_free = 0.3763 target = 0.145955 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.105967 restraints weight = 62543.318| |-----------------------------------------------------------------------------| r_work (start): 0.3248 rms_B_bonded: 2.32 r_work: 0.3103 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 50042 Z= 0.263 Angle : 0.536 8.879 67662 Z= 0.280 Chirality : 0.044 0.203 7373 Planarity : 0.004 0.064 8639 Dihedral : 8.844 134.089 6733 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 3.00 % Allowed : 30.62 % Favored : 66.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -0.36 (0.11), residues: 5849 helix: 0.46 (0.11), residues: 2233 sheet: -0.67 (0.17), residues: 941 loop : -0.56 (0.12), residues: 2675 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP D 568 HIS 0.005 0.001 HIS L 292 PHE 0.025 0.001 PHE H 184 TYR 0.024 0.001 TYR K 222 ARG 0.014 0.001 ARG I 283 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 17336.42 seconds wall clock time: 297 minutes 52.18 seconds (17872.18 seconds total)