Starting phenix.real_space_refine on Sat Sep 28 22:53:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/09_2024/7jtk_22475.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/09_2024/7jtk_22475.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/09_2024/7jtk_22475.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/09_2024/7jtk_22475.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/09_2024/7jtk_22475.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7jtk_22475/09_2024/7jtk_22475.cif" } resolution = 3.2 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= 0.000 sd= 0.001 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: 5 Type Number sf(0) Gaussians P 4 5.49 5 S 240 5.16 5 C 46302 2.51 5 N 12498 2.21 5 O 13763 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 378 residue(s): 0.19s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 72807 Number of models: 1 Model: "" Number of chains: 43 Chain: "A" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5698 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 59, 'TRANS': 689} Chain breaks: 3 Chain: "B" Number of atoms: 5698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 749, 5698 Classifications: {'peptide': 749} Link IDs: {'PTRANS': 59, 'TRANS': 689} Chain breaks: 3 Chain: "C" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3248 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 409} Chain breaks: 2 Chain: "D" Number of atoms: 3248 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3248 Classifications: {'peptide': 427} Link IDs: {'PCIS': 1, 'PTRANS': 16, 'TRANS': 409} Chain breaks: 2 Chain: "E" Number of atoms: 2216 Number of conformers: 1 Conformer: "" Number of residues, atoms: 284, 2216 Classifications: {'peptide': 284} Link IDs: {'PTRANS': 6, 'TRANS': 277} Chain breaks: 2 Chain: "F" Number of atoms: 2232 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2232 Classifications: {'peptide': 287} Link IDs: {'PTRANS': 6, 'TRANS': 280} Chain breaks: 2 Chain: "G" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3207 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 39, 'TRANS': 381} Chain breaks: 1 Chain: "H" Number of atoms: 3207 Number of conformers: 1 Conformer: "" Number of residues, atoms: 421, 3207 Classifications: {'peptide': 421} Link IDs: {'PTRANS': 39, 'TRANS': 381} Chain breaks: 1 Chain: "I" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3644 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 443} Chain breaks: 2 Chain: "J" Number of atoms: 3644 Number of conformers: 1 Conformer: "" Number of residues, atoms: 483, 3644 Classifications: {'peptide': 483} Link IDs: {'PCIS': 1, 'PTRANS': 38, 'TRANS': 443} Chain breaks: 2 Chain: "K" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3214 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 381} Chain breaks: 2 Chain: "L" Number of atoms: 3214 Number of conformers: 1 Conformer: "" Number of residues, atoms: 428, 3214 Classifications: {'peptide': 428} Link IDs: {'PCIS': 1, 'PTRANS': 45, 'TRANS': 381} Chain breaks: 2 Chain: "M" Number of atoms: 373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 47, 373 Classifications: {'peptide': 47} Link IDs: {'PTRANS': 4, 'TRANS': 42} Chain: "N" Number of atoms: 316 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 316 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 3, 'TRANS': 36} Chain: "O" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "P" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "Q" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "R" Number of atoms: 1930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 249, 1930 Classifications: {'peptide': 249} Link IDs: {'PTRANS': 10, 'TRANS': 238} Chain breaks: 1 Chain: "S" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1530 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Chain: "T" Number of atoms: 1530 Number of conformers: 1 Conformer: "" Number of residues, atoms: 199, 1530 Classifications: {'peptide': 199} Link IDs: {'PTRANS': 12, 'TRANS': 186} Chain breaks: 1 Chain: "U" Number of atoms: 382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 48, 382 Classifications: {'peptide': 48} Link IDs: {'PTRANS': 2, 'TRANS': 45} Chain: "V" Number of atoms: 1055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 182, 1055 Classifications: {'peptide': 182} Incomplete info: {'truncation_to_alanine': 103} Link IDs: {'PTRANS': 11, 'TRANS': 170} Chain breaks: 4 Unresolved chain link angles: 8 Unresolved non-hydrogen bonds: 335 Unresolved non-hydrogen angles: 429 Unresolved non-hydrogen dihedrals: 271 Unresolved non-hydrogen chiralities: 37 Planarities with less than four sites: {'GLN:plan1': 5, 'HIS:plan': 1, 'TYR:plan': 2, 'ASN:plan1': 2, 'ASP:plan': 9, 'PHE:plan': 7, 'GLU:plan': 8, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 161 Chain: "W" Number of atoms: 1241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 163, 1241 Classifications: {'peptide': 163} Link IDs: {'PTRANS': 13, 'TRANS': 149} Chain: "X" Number of atoms: 2787 Number of conformers: 1 Conformer: "" Number of residues, atoms: 379, 2787 Classifications: {'peptide': 379} Link IDs: {'PTRANS': 22, 'TRANS': 356} Chain: "Y" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 20, 'TRANS': 192} Chain: "Z" Number of atoms: 1693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1693 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 20, 'TRANS': 192} Chain: "a" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "b" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "c" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "d" Number of atoms: 686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 686 Classifications: {'peptide': 84} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "e" Number of atoms: 170 Number of conformers: 1 Conformer: "" Number of residues, atoms: 34, 170 Classifications: {'peptide': 34} Incomplete info: {'truncation_to_alanine': 34} Link IDs: {'TRANS': 33} Unresolved non-hydrogen bonds: 68 Unresolved non-hydrogen angles: 102 Unresolved non-hydrogen dihedrals: 34 Planarities with less than four sites: {'UNK:plan-1': 34} Unresolved non-hydrogen planarities: 34 Chain: "i" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1558 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 14, 'TRANS': 186} Chain: "j" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1558 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 14, 'TRANS': 186} Chain: "k" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1756 Classifications: {'peptide': 213} Link IDs: {'PTRANS': 17, 'TRANS': 195} Chain breaks: 1 Chain: "s" Number of atoms: 301 Number of conformers: 1 Conformer: "" Number of residues, atoms: 37, 301 Classifications: {'peptide': 37} Link IDs: {'PTRANS': 2, 'TRANS': 34} Chain: "u" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 427 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "v" Number of atoms: 427 Number of conformers: 1 Conformer: "" Number of residues, atoms: 50, 427 Classifications: {'peptide': 50} Link IDs: {'PTRANS': 3, 'TRANS': 46} Chain: "y" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "z" Number of atoms: 528 Number of conformers: 1 Conformer: "" Number of residues, atoms: 64, 528 Classifications: {'peptide': 64} Link IDs: {'PTRANS': 2, 'TRANS': 61} Chain: "G" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 5 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 5 Unusual residues: {'PO4': 1} Classifications: {'undetermined': 1} Time building chain proxies: 33.91, per 1000 atoms: 0.47 Number of scatterers: 72807 At special positions: 0 Unit cell: (289.94, 349.89, 332.45, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 240 16.00 P 4 15.00 O 13763 8.00 N 12498 7.00 C 46302 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS O 105 " - pdb=" SG CYS O 155 " distance=2.03 Simple disulfide: pdb=" SG CYS P 105 " - pdb=" SG CYS P 155 " distance=2.04 Simple disulfide: pdb=" SG CYS Q 105 " - pdb=" SG CYS Q 155 " distance=2.03 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 155 " distance=2.04 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=0, symmetry=0 Time building additional restraints: 14.94 Conformation dependent library (CDL) restraints added in 7.5 seconds 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 17614 Finding SS restraints... Secondary structure from input PDB file: 274 helices and 87 sheets defined 41.4% alpha, 19.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 8.18 Creating SS restraints... Processing helix chain 'A' and resid 86 through 89 Processing helix chain 'A' and resid 138 through 144 removed outlier: 3.996A pdb=" N GLN A 144 " --> pdb=" O PRO A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 180 through 195 removed outlier: 3.603A pdb=" N HIS A 195 " --> pdb=" O LEU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 204 Processing helix chain 'A' and resid 225 through 231 Processing helix chain 'A' and resid 360 through 362 No H-bonds generated for 'chain 'A' and resid 360 through 362' Processing helix chain 'A' and resid 405 through 415 Processing helix chain 'A' and resid 460 through 469 removed outlier: 3.664A pdb=" N GLY A 469 " --> pdb=" O PHE A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 479 Processing helix chain 'A' and resid 480 through 512 Processing helix chain 'A' and resid 539 through 542 Processing helix chain 'A' and resid 543 through 551 removed outlier: 3.968A pdb=" N LEU A 549 " --> pdb=" O ASP A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 711 through 714 removed outlier: 3.683A pdb=" N LEU A 714 " --> pdb=" O HIS A 711 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 711 through 714' Processing helix chain 'A' and resid 720 through 724 Processing helix chain 'B' and resid 138 through 143 Processing helix chain 'B' and resid 180 through 194 removed outlier: 3.565A pdb=" N ILE B 188 " --> pdb=" O LEU B 184 " (cutoff:3.500A) Processing helix chain 'B' and resid 199 through 205 Processing helix chain 'B' and resid 225 through 231 Processing helix chain 'B' and resid 405 through 415 Processing helix chain 'B' and resid 463 through 469 removed outlier: 3.680A pdb=" N ALA B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N GLY B 469 " --> pdb=" O PHE B 465 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 478 Processing helix chain 'B' and resid 480 through 512 removed outlier: 3.579A pdb=" N ILE B 484 " --> pdb=" O GLU B 480 " (cutoff:3.500A) Processing helix chain 'B' and resid 538 through 541 Processing helix chain 'B' and resid 542 through 551 Processing helix chain 'B' and resid 720 through 724 Processing helix chain 'C' and resid 9 through 32 removed outlier: 7.119A pdb=" N GLU C 19 " --> pdb=" O GLU C 15 " (cutoff:3.500A) removed outlier: 6.222A pdb=" N ALA C 20 " --> pdb=" O THR C 16 " (cutoff:3.500A) Processing helix chain 'C' and resid 35 through 99 removed outlier: 3.613A pdb=" N LEU C 96 " --> pdb=" O ALA C 92 " (cutoff:3.500A) removed outlier: 4.401A pdb=" N ALA C 97 " --> pdb=" O ALA C 93 " (cutoff:3.500A) removed outlier: 4.150A pdb=" N LEU C 98 " --> pdb=" O ASP C 94 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N VAL C 99 " --> pdb=" O ALA C 95 " (cutoff:3.500A) Processing helix chain 'C' and resid 102 through 118 Processing helix chain 'C' and resid 239 through 246 removed outlier: 4.151A pdb=" N LEU C 243 " --> pdb=" O SER C 239 " (cutoff:3.500A) Processing helix chain 'C' and resid 305 through 337 removed outlier: 3.990A pdb=" N THR C 337 " --> pdb=" O ALA C 333 " (cutoff:3.500A) Processing helix chain 'C' and resid 341 through 360 Processing helix chain 'C' and resid 435 through 475 removed outlier: 3.997A pdb=" N HIS C 475 " --> pdb=" O LEU C 471 " (cutoff:3.500A) Processing helix chain 'C' and resid 475 through 485 Processing helix chain 'C' and resid 490 through 504 Processing helix chain 'C' and resid 513 through 521 removed outlier: 4.367A pdb=" N SER C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N HIS C 520 " --> pdb=" O ARG C 516 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE C 521 " --> pdb=" O ALA C 517 " (cutoff:3.500A) Processing helix chain 'C' and resid 523 through 532 removed outlier: 3.955A pdb=" N GLU C 527 " --> pdb=" O PRO C 523 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N ALA C 530 " --> pdb=" O PHE C 526 " (cutoff:3.500A) Processing helix chain 'C' and resid 539 through 552 removed outlier: 3.791A pdb=" N ARG C 545 " --> pdb=" O ALA C 541 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL C 546 " --> pdb=" O VAL C 542 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ALA C 552 " --> pdb=" O SER C 548 " (cutoff:3.500A) Processing helix chain 'C' and resid 555 through 563 removed outlier: 4.389A pdb=" N MET C 563 " --> pdb=" O LEU C 559 " (cutoff:3.500A) Processing helix chain 'C' and resid 567 through 610 Processing helix chain 'D' and resid 9 through 32 removed outlier: 6.741A pdb=" N GLU D 19 " --> pdb=" O GLU D 15 " (cutoff:3.500A) removed outlier: 6.270A pdb=" N ALA D 20 " --> pdb=" O THR D 16 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N ARG D 23 " --> pdb=" O GLU D 19 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N GLN D 32 " --> pdb=" O ALA D 28 " (cutoff:3.500A) Processing helix chain 'D' and resid 35 through 97 Processing helix chain 'D' and resid 102 through 118 Processing helix chain 'D' and resid 239 through 245 removed outlier: 4.066A pdb=" N LEU D 243 " --> pdb=" O SER D 239 " (cutoff:3.500A) Processing helix chain 'D' and resid 305 through 335 removed outlier: 3.504A pdb=" N ALA D 335 " --> pdb=" O ALA D 331 " (cutoff:3.500A) Processing helix chain 'D' and resid 339 through 362 removed outlier: 3.917A pdb=" N GLU D 345 " --> pdb=" O GLU D 341 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N ALA D 362 " --> pdb=" O ALA D 358 " (cutoff:3.500A) Processing helix chain 'D' and resid 435 through 475 removed outlier: 3.998A pdb=" N HIS D 475 " --> pdb=" O LEU D 471 " (cutoff:3.500A) Processing helix chain 'D' and resid 475 through 485 Processing helix chain 'D' and resid 490 through 505 removed outlier: 3.561A pdb=" N GLY D 505 " --> pdb=" O LEU D 501 " (cutoff:3.500A) Processing helix chain 'D' and resid 513 through 518 Processing helix chain 'D' and resid 522 through 532 removed outlier: 3.875A pdb=" N PHE D 526 " --> pdb=" O SER D 522 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N ALA D 530 " --> pdb=" O PHE D 526 " (cutoff:3.500A) Processing helix chain 'D' and resid 539 through 552 removed outlier: 3.729A pdb=" N ALA D 552 " --> pdb=" O SER D 548 " (cutoff:3.500A) Processing helix chain 'D' and resid 555 through 561 Processing helix chain 'D' and resid 567 through 610 removed outlier: 4.119A pdb=" N VAL D 571 " --> pdb=" O LEU D 567 " (cutoff:3.500A) Processing helix chain 'E' and resid 153 through 261 removed outlier: 3.517A pdb=" N GLU E 157 " --> pdb=" O ASP E 153 " (cutoff:3.500A) Proline residue: E 160 - end of helix removed outlier: 3.778A pdb=" N ALA E 245 " --> pdb=" O ALA E 241 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N GLY E 251 " --> pdb=" O GLY E 247 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N VAL E 261 " --> pdb=" O PHE E 257 " (cutoff:3.500A) Processing helix chain 'E' and resid 269 through 361 removed outlier: 3.555A pdb=" N GLU E 273 " --> pdb=" O PRO E 269 " (cutoff:3.500A) Proline residue: E 280 - end of helix Proline residue: E 355 - end of helix Processing helix chain 'E' and resid 368 through 385 Processing helix chain 'E' and resid 471 through 483 Processing helix chain 'E' and resid 486 through 499 Processing helix chain 'E' and resid 500 through 503 Processing helix chain 'F' and resid 154 through 264 Proline residue: F 160 - end of helix removed outlier: 3.620A pdb=" N ARG F 226 " --> pdb=" O MET F 222 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N ALA F 240 " --> pdb=" O ARG F 236 " (cutoff:3.500A) Processing helix chain 'F' and resid 269 through 361 removed outlier: 3.603A pdb=" N GLU F 273 " --> pdb=" O PRO F 269 " (cutoff:3.500A) Proline residue: F 280 - end of helix Proline residue: F 355 - end of helix Processing helix chain 'F' and resid 368 through 386 Processing helix chain 'F' and resid 471 through 482 Processing helix chain 'F' and resid 486 through 499 removed outlier: 3.788A pdb=" N LEU F 499 " --> pdb=" O ALA F 495 " (cutoff:3.500A) Processing helix chain 'G' and resid 7 through 15 Processing helix chain 'G' and resid 24 through 39 removed outlier: 3.556A pdb=" N HIS G 28 " --> pdb=" O SER G 24 " (cutoff:3.500A) Processing helix chain 'G' and resid 46 through 58 Processing helix chain 'G' and resid 76 through 84 Processing helix chain 'G' and resid 113 through 125 Processing helix chain 'G' and resid 130 through 146 removed outlier: 3.662A pdb=" N ASP G 146 " --> pdb=" O ARG G 142 " (cutoff:3.500A) Processing helix chain 'G' and resid 211 through 216 removed outlier: 4.385A pdb=" N PHE G 216 " --> pdb=" O ALA G 213 " (cutoff:3.500A) Processing helix chain 'G' and resid 235 through 243 Processing helix chain 'G' and resid 266 through 283 Processing helix chain 'G' and resid 315 through 317 No H-bonds generated for 'chain 'G' and resid 315 through 317' Processing helix chain 'G' and resid 363 through 367 Processing helix chain 'H' and resid 7 through 15 Processing helix chain 'H' and resid 24 through 40 Processing helix chain 'H' and resid 46 through 58 Processing helix chain 'H' and resid 76 through 84 Processing helix chain 'H' and resid 113 through 125 Processing helix chain 'H' and resid 129 through 146 removed outlier: 3.647A pdb=" N ASP H 146 " --> pdb=" O ARG H 142 " (cutoff:3.500A) Processing helix chain 'H' and resid 211 through 215 removed outlier: 3.592A pdb=" N LYS H 215 " --> pdb=" O GLY H 212 " (cutoff:3.500A) Processing helix chain 'H' and resid 235 through 243 Processing helix chain 'H' and resid 266 through 283 Processing helix chain 'H' and resid 315 through 317 No H-bonds generated for 'chain 'H' and resid 315 through 317' Processing helix chain 'H' and resid 363 through 367 Processing helix chain 'I' and resid 18 through 26 Processing helix chain 'I' and resid 52 through 58 Processing helix chain 'I' and resid 84 through 96 removed outlier: 3.588A pdb=" N ASN I 88 " --> pdb=" O ALA I 84 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU I 90 " --> pdb=" O GLU I 86 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N VAL I 91 " --> pdb=" O TYR I 87 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ARG I 92 " --> pdb=" O ASN I 88 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ALA I 95 " --> pdb=" O VAL I 91 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N LYS I 96 " --> pdb=" O ARG I 92 " (cutoff:3.500A) Processing helix chain 'I' and resid 97 through 121 removed outlier: 3.571A pdb=" N LYS I 121 " --> pdb=" O VAL I 117 " (cutoff:3.500A) Processing helix chain 'I' and resid 122 through 155 removed outlier: 3.793A pdb=" N GLU I 126 " --> pdb=" O GLY I 122 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ALA I 127 " --> pdb=" O PRO I 123 " (cutoff:3.500A) removed outlier: 3.785A pdb=" N SER I 154 " --> pdb=" O LYS I 150 " (cutoff:3.500A) Processing helix chain 'I' and resid 161 through 174 removed outlier: 3.516A pdb=" N GLY I 174 " --> pdb=" O LEU I 170 " (cutoff:3.500A) Processing helix chain 'I' and resid 190 through 195 Processing helix chain 'I' and resid 208 through 225 Processing helix chain 'I' and resid 242 through 249 removed outlier: 3.528A pdb=" N GLY I 249 " --> pdb=" O TRP I 245 " (cutoff:3.500A) Processing helix chain 'I' and resid 249 through 269 Processing helix chain 'I' and resid 299 through 311 Processing helix chain 'I' and resid 340 through 349 Processing helix chain 'I' and resid 369 through 379 Processing helix chain 'I' and resid 414 through 426 Processing helix chain 'I' and resid 427 through 446 removed outlier: 3.616A pdb=" N HIS I 445 " --> pdb=" O ILE I 441 " (cutoff:3.500A) Processing helix chain 'I' and resid 450 through 460 Processing helix chain 'I' and resid 475 through 479 Processing helix chain 'I' and resid 485 through 490 Processing helix chain 'I' and resid 496 through 500 Processing helix chain 'I' and resid 507 through 518 removed outlier: 3.800A pdb=" N ALA I 518 " --> pdb=" O LEU I 514 " (cutoff:3.500A) Processing helix chain 'J' and resid 18 through 25 Processing helix chain 'J' and resid 52 through 57 Processing helix chain 'J' and resid 84 through 95 removed outlier: 3.544A pdb=" N ASN J 88 " --> pdb=" O ALA J 84 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N LEU J 90 " --> pdb=" O GLU J 86 " (cutoff:3.500A) removed outlier: 4.741A pdb=" N VAL J 91 " --> pdb=" O TYR J 87 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N ARG J 92 " --> pdb=" O ASN J 88 " (cutoff:3.500A) Processing helix chain 'J' and resid 97 through 121 Processing helix chain 'J' and resid 122 through 156 removed outlier: 4.009A pdb=" N GLU J 126 " --> pdb=" O GLY J 122 " (cutoff:3.500A) removed outlier: 4.071A pdb=" N ALA J 127 " --> pdb=" O PRO J 123 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N SER J 154 " --> pdb=" O LYS J 150 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N ASP J 156 " --> pdb=" O SER J 152 " (cutoff:3.500A) Processing helix chain 'J' and resid 161 through 174 removed outlier: 3.588A pdb=" N GLY J 174 " --> pdb=" O LEU J 170 " (cutoff:3.500A) Processing helix chain 'J' and resid 190 through 195 Processing helix chain 'J' and resid 208 through 225 Processing helix chain 'J' and resid 242 through 247 Processing helix chain 'J' and resid 249 through 269 Processing helix chain 'J' and resid 299 through 311 Processing helix chain 'J' and resid 340 through 350 Processing helix chain 'J' and resid 368 through 379 Processing helix chain 'J' and resid 414 through 425 Processing helix chain 'J' and resid 427 through 446 removed outlier: 3.673A pdb=" N HIS J 445 " --> pdb=" O ILE J 441 " (cutoff:3.500A) Processing helix chain 'J' and resid 448 through 460 removed outlier: 3.813A pdb=" N VAL J 452 " --> pdb=" O LYS J 448 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ALA J 453 " --> pdb=" O PRO J 449 " (cutoff:3.500A) Processing helix chain 'J' and resid 470 through 474 removed outlier: 3.647A pdb=" N VAL J 474 " --> pdb=" O SER J 471 " (cutoff:3.500A) Processing helix chain 'J' and resid 475 through 479 Processing helix chain 'J' and resid 485 through 490 Processing helix chain 'J' and resid 496 through 500 Processing helix chain 'J' and resid 507 through 517 Processing helix chain 'K' and resid 5 through 13 Processing helix chain 'K' and resid 22 through 38 Processing helix chain 'K' and resid 41 through 49 removed outlier: 4.022A pdb=" N GLU K 47 " --> pdb=" O VAL K 43 " (cutoff:3.500A) Processing helix chain 'K' and resid 68 through 80 Processing helix chain 'K' and resid 109 through 121 removed outlier: 3.527A pdb=" N ASP K 113 " --> pdb=" O ASP K 109 " (cutoff:3.500A) Processing helix chain 'K' and resid 125 through 142 removed outlier: 3.633A pdb=" N TYR K 130 " --> pdb=" O ARG K 126 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N ALA K 131 " --> pdb=" O GLN K 127 " (cutoff:3.500A) Processing helix chain 'K' and resid 215 through 223 Processing helix chain 'K' and resid 246 through 262 Processing helix chain 'K' and resid 289 through 297 removed outlier: 3.537A pdb=" N GLU K 292 " --> pdb=" O LYS K 289 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET K 293 " --> pdb=" O GLY K 290 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N LEU K 295 " --> pdb=" O GLU K 292 " (cutoff:3.500A) Proline residue: K 296 - end of helix Processing helix chain 'L' and resid 5 through 13 Processing helix chain 'L' and resid 22 through 38 Processing helix chain 'L' and resid 41 through 49 removed outlier: 3.789A pdb=" N GLU L 47 " --> pdb=" O VAL L 43 " (cutoff:3.500A) Processing helix chain 'L' and resid 68 through 81 removed outlier: 3.601A pdb=" N LEU L 81 " --> pdb=" O ALA L 77 " (cutoff:3.500A) Processing helix chain 'L' and resid 109 through 121 Processing helix chain 'L' and resid 125 through 142 removed outlier: 3.621A pdb=" N TYR L 130 " --> pdb=" O ARG L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 215 through 223 Processing helix chain 'L' and resid 246 through 263 Processing helix chain 'L' and resid 290 through 297 removed outlier: 3.833A pdb=" N MET L 293 " --> pdb=" O GLY L 290 " (cutoff:3.500A) Proline residue: L 296 - end of helix Processing helix chain 'M' and resid 14 through 30 removed outlier: 3.982A pdb=" N ILE M 18 " --> pdb=" O ASP M 14 " (cutoff:3.500A) Processing helix chain 'M' and resid 33 through 47 Processing helix chain 'N' and resid 14 through 30 removed outlier: 3.610A pdb=" N ILE N 18 " --> pdb=" O ASP N 14 " (cutoff:3.500A) Processing helix chain 'N' and resid 33 through 47 removed outlier: 3.530A pdb=" N GLY N 47 " --> pdb=" O SER N 43 " (cutoff:3.500A) Processing helix chain 'O' and resid 7 through 15 removed outlier: 3.699A pdb=" N VAL O 11 " --> pdb=" O ASN O 7 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N LEU O 12 " --> pdb=" O ILE O 8 " (cutoff:3.500A) Processing helix chain 'O' and resid 23 through 41 Proline residue: O 35 - end of helix Processing helix chain 'O' and resid 98 through 105 Processing helix chain 'O' and resid 149 through 165 Processing helix chain 'O' and resid 194 through 196 No H-bonds generated for 'chain 'O' and resid 194 through 196' Processing helix chain 'O' and resid 264 through 269 removed outlier: 3.779A pdb=" N MET O 268 " --> pdb=" O ASP O 264 " (cutoff:3.500A) Processing helix chain 'P' and resid 7 through 15 Processing helix chain 'P' and resid 23 through 41 Proline residue: P 35 - end of helix Processing helix chain 'P' and resid 98 through 106 Processing helix chain 'P' and resid 149 through 164 Processing helix chain 'P' and resid 194 through 196 No H-bonds generated for 'chain 'P' and resid 194 through 196' Processing helix chain 'Q' and resid 8 through 15 Processing helix chain 'Q' and resid 23 through 41 Proline residue: Q 35 - end of helix Processing helix chain 'Q' and resid 98 through 105 Processing helix chain 'Q' and resid 149 through 165 Processing helix chain 'Q' and resid 194 through 196 No H-bonds generated for 'chain 'Q' and resid 194 through 196' Processing helix chain 'Q' and resid 215 through 217 No H-bonds generated for 'chain 'Q' and resid 215 through 217' Processing helix chain 'Q' and resid 264 through 269 removed outlier: 3.524A pdb=" N MET Q 268 " --> pdb=" O ASP Q 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 7 through 15 Processing helix chain 'R' and resid 23 through 42 Proline residue: R 35 - end of helix Processing helix chain 'R' and resid 98 through 107 removed outlier: 3.744A pdb=" N ARG R 107 " --> pdb=" O THR R 103 " (cutoff:3.500A) Processing helix chain 'R' and resid 149 through 164 Processing helix chain 'R' and resid 194 through 196 No H-bonds generated for 'chain 'R' and resid 194 through 196' Processing helix chain 'R' and resid 264 through 269 removed outlier: 3.724A pdb=" N MET R 268 " --> pdb=" O ASP R 264 " (cutoff:3.500A) Processing helix chain 'S' and resid 17 through 21 removed outlier: 3.636A pdb=" N GLY S 20 " --> pdb=" O ASP S 17 " (cutoff:3.500A) Processing helix chain 'S' and resid 170 through 174 Processing helix chain 'T' and resid 18 through 20 No H-bonds generated for 'chain 'T' and resid 18 through 20' Processing helix chain 'U' and resid 8 through 12 Processing helix chain 'U' and resid 17 through 33 removed outlier: 3.774A pdb=" N ILE U 21 " --> pdb=" O ASN U 17 " (cutoff:3.500A) Processing helix chain 'U' and resid 36 through 52 Processing helix chain 'V' and resid 17 through 33 Processing helix chain 'V' and resid 36 through 54 Processing helix chain 'V' and resid 61 through 73 Processing helix chain 'V' and resid 80 through 89 Processing helix chain 'V' and resid 96 through 107 Processing helix chain 'V' and resid 116 through 127 removed outlier: 3.543A pdb=" N SER V 126 " --> pdb=" O CYS V 122 " (cutoff:3.500A) Processing helix chain 'V' and resid 129 through 142 removed outlier: 3.966A pdb=" N SER V 142 " --> pdb=" O PHE V 138 " (cutoff:3.500A) Processing helix chain 'V' and resid 149 through 160 removed outlier: 3.527A pdb=" N LEU V 153 " --> pdb=" O ALA V 149 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N LEU V 159 " --> pdb=" O LEU V 155 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N GLY V 160 " --> pdb=" O ILE V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 168 through 179 Processing helix chain 'V' and resid 187 through 193 Processing helix chain 'W' and resid 44 through 57 Processing helix chain 'W' and resid 128 through 132 Processing helix chain 'W' and resid 143 through 155 removed outlier: 3.922A pdb=" N LEU W 147 " --> pdb=" O ASN W 143 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N THR W 155 " --> pdb=" O LEU W 151 " (cutoff:3.500A) Processing helix chain 'X' and resid 3 through 17 removed outlier: 3.665A pdb=" N PHE X 17 " --> pdb=" O HIS X 13 " (cutoff:3.500A) Processing helix chain 'X' and resid 35 through 37 No H-bonds generated for 'chain 'X' and resid 35 through 37' Processing helix chain 'X' and resid 38 through 47 Processing helix chain 'X' and resid 51 through 66 Processing helix chain 'X' and resid 68 through 78 Processing helix chain 'X' and resid 80 through 90 Processing helix chain 'X' and resid 93 through 108 removed outlier: 3.712A pdb=" N ARG X 97 " --> pdb=" O ASP X 93 " (cutoff:3.500A) Processing helix chain 'X' and resid 110 through 120 Processing helix chain 'X' and resid 121 through 130 removed outlier: 3.544A pdb=" N ALA X 125 " --> pdb=" O SER X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 135 through 149 Processing helix chain 'X' and resid 151 through 160 Processing helix chain 'X' and resid 165 through 179 Processing helix chain 'X' and resid 182 through 198 removed outlier: 4.209A pdb=" N ALA X 186 " --> pdb=" O ALA X 182 " (cutoff:3.500A) Processing helix chain 'X' and resid 202 through 214 Processing helix chain 'X' and resid 214 through 222 removed outlier: 3.980A pdb=" N HIS X 218 " --> pdb=" O GLN X 214 " (cutoff:3.500A) Processing helix chain 'X' and resid 228 through 243 Processing helix chain 'X' and resid 245 through 256 Processing helix chain 'X' and resid 257 through 264 removed outlier: 3.556A pdb=" N ALA X 264 " --> pdb=" O LEU X 260 " (cutoff:3.500A) Processing helix chain 'X' and resid 270 through 285 Processing helix chain 'X' and resid 287 through 297 Processing helix chain 'X' and resid 299 through 308 removed outlier: 3.956A pdb=" N LEU X 308 " --> pdb=" O LEU X 304 " (cutoff:3.500A) Processing helix chain 'X' and resid 312 through 327 Processing helix chain 'X' and resid 331 through 339 removed outlier: 3.562A pdb=" N ILE X 335 " --> pdb=" O GLU X 331 " (cutoff:3.500A) Processing helix chain 'X' and resid 340 through 352 Processing helix chain 'X' and resid 354 through 369 Processing helix chain 'Y' and resid 144 through 151 Processing helix chain 'Y' and resid 234 through 239 Processing helix chain 'Y' and resid 299 through 310 Processing helix chain 'Y' and resid 319 through 334 removed outlier: 3.502A pdb=" N LYS Y 323 " --> pdb=" O ASN Y 319 " (cutoff:3.500A) Processing helix chain 'Z' and resid 144 through 151 Processing helix chain 'Z' and resid 234 through 239 Processing helix chain 'Z' and resid 299 through 311 Processing helix chain 'Z' and resid 319 through 334 Processing helix chain 'a' and resid 16 through 32 removed outlier: 3.626A pdb=" N GLU a 32 " --> pdb=" O THR a 28 " (cutoff:3.500A) Processing helix chain 'a' and resid 36 through 52 Processing helix chain 'b' and resid 16 through 34 Processing helix chain 'b' and resid 36 through 52 removed outlier: 3.524A pdb=" N ILE b 40 " --> pdb=" O ILE b 36 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LYS b 51 " --> pdb=" O GLU b 47 " (cutoff:3.500A) Processing helix chain 'c' and resid 16 through 34 Processing helix chain 'c' and resid 36 through 51 Processing helix chain 'd' and resid 16 through 34 Processing helix chain 'd' and resid 36 through 52 Processing helix chain 'e' and resid 6 through 20 removed outlier: 4.505A pdb=" N UNK e 16 " --> pdb=" O UNK e 12 " (cutoff:3.500A) removed outlier: 5.968A pdb=" N UNK e 17 " --> pdb=" O UNK e 13 " (cutoff:3.500A) removed outlier: 4.223A pdb=" N UNK e 18 " --> pdb=" O UNK e 14 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N UNK e 20 " --> pdb=" O UNK e 16 " (cutoff:3.500A) Processing helix chain 'e' and resid 22 through 38 Processing helix chain 'i' and resid 13 through 18 removed outlier: 3.760A pdb=" N ALA i 18 " --> pdb=" O ASP i 14 " (cutoff:3.500A) Processing helix chain 'i' and resid 20 through 31 Processing helix chain 'i' and resid 44 through 52 Processing helix chain 'i' and resid 60 through 69 removed outlier: 3.731A pdb=" N THR i 69 " --> pdb=" O VAL i 65 " (cutoff:3.500A) Processing helix chain 'i' and resid 82 through 92 Processing helix chain 'i' and resid 95 through 103 Processing helix chain 'i' and resid 106 through 111 Processing helix chain 'i' and resid 125 through 137 Processing helix chain 'i' and resid 149 through 176 removed outlier: 3.844A pdb=" N GLN i 162 " --> pdb=" O THR i 158 " (cutoff:3.500A) Proline residue: i 163 - end of helix removed outlier: 4.947A pdb=" N ALA i 166 " --> pdb=" O GLN i 162 " (cutoff:3.500A) removed outlier: 5.537A pdb=" N LYS i 167 " --> pdb=" O PRO i 163 " (cutoff:3.500A) Processing helix chain 'i' and resid 180 through 195 removed outlier: 3.601A pdb=" N ALA i 184 " --> pdb=" O ASP i 180 " (cutoff:3.500A) Processing helix chain 'j' and resid 13 through 18 removed outlier: 3.530A pdb=" N ALA j 18 " --> pdb=" O ASP j 14 " (cutoff:3.500A) Processing helix chain 'j' and resid 20 through 31 Processing helix chain 'j' and resid 44 through 52 Processing helix chain 'j' and resid 60 through 69 removed outlier: 3.602A pdb=" N THR j 69 " --> pdb=" O VAL j 65 " (cutoff:3.500A) Processing helix chain 'j' and resid 82 through 92 Processing helix chain 'j' and resid 95 through 103 removed outlier: 3.703A pdb=" N ALA j 101 " --> pdb=" O PHE j 97 " (cutoff:3.500A) Processing helix chain 'j' and resid 106 through 112 Processing helix chain 'j' and resid 125 through 137 Processing helix chain 'j' and resid 149 through 160 Processing helix chain 'j' and resid 160 through 176 removed outlier: 4.535A pdb=" N ALA j 164 " --> pdb=" O ARG j 160 " (cutoff:3.500A) removed outlier: 3.910A pdb=" N LYS j 167 " --> pdb=" O PRO j 163 " (cutoff:3.500A) Processing helix chain 'j' and resid 180 through 195 removed outlier: 3.846A pdb=" N ALA j 184 " --> pdb=" O ASP j 180 " (cutoff:3.500A) Processing helix chain 'k' and resid 13 through 19 Processing helix chain 'k' and resid 37 through 44 Processing helix chain 'k' and resid 49 through 54 Processing helix chain 'k' and resid 114 through 119 Processing helix chain 'k' and resid 150 through 159 Processing helix chain 'k' and resid 201 through 208 Processing helix chain 'u' and resid 18 through 29 removed outlier: 3.507A pdb=" N MET u 24 " --> pdb=" O LEU u 20 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N TYR u 27 " --> pdb=" O LYS u 23 " (cutoff:3.500A) Processing helix chain 'u' and resid 30 through 48 removed outlier: 4.093A pdb=" N LYS u 39 " --> pdb=" O GLU u 35 " (cutoff:3.500A) Processing helix chain 'u' and resid 51 through 65 removed outlier: 3.720A pdb=" N TRP u 55 " --> pdb=" O ASP u 51 " (cutoff:3.500A) removed outlier: 3.946A pdb=" N LYS u 65 " --> pdb=" O SER u 61 " (cutoff:3.500A) Processing helix chain 'v' and resid 18 through 29 Processing helix chain 'v' and resid 30 through 48 removed outlier: 3.564A pdb=" N GLN v 34 " --> pdb=" O SER v 30 " (cutoff:3.500A) Processing helix chain 'v' and resid 51 through 65 removed outlier: 3.501A pdb=" N TRP v 55 " --> pdb=" O ASP v 51 " (cutoff:3.500A) Processing helix chain 'y' and resid 18 through 34 Processing helix chain 'y' and resid 40 through 59 removed outlier: 4.387A pdb=" N ASP y 59 " --> pdb=" O GLU y 55 " (cutoff:3.500A) Processing helix chain 'y' and resid 59 through 68 Processing helix chain 'z' and resid 18 through 33 Processing helix chain 'z' and resid 44 through 58 removed outlier: 3.748A pdb=" N LEU z 48 " --> pdb=" O GLY z 44 " (cutoff:3.500A) Processing helix chain 'z' and resid 59 through 69 Processing sheet with id=AA1, first strand: chain 'A' and resid 54 through 55 Processing sheet with id=AA2, first strand: chain 'A' and resid 44 through 47 removed outlier: 4.503A pdb=" N ASP A 46 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 153 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 100 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 151 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 44 through 47 removed outlier: 4.503A pdb=" N ASP A 46 " --> pdb=" O ALA A 37 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N ALA A 153 " --> pdb=" O PHE A 98 " (cutoff:3.500A) removed outlier: 6.824A pdb=" N ALA A 100 " --> pdb=" O ILE A 151 " (cutoff:3.500A) removed outlier: 5.616A pdb=" N ILE A 151 " --> pdb=" O ALA A 100 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 222 through 224 removed outlier: 6.049A pdb=" N LEU A 530 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 450 " --> pdb=" O LEU A 530 " (cutoff:3.500A) removed outlier: 6.194A pdb=" N LEU A 532 " --> pdb=" O VAL A 448 " (cutoff:3.500A) removed outlier: 4.194A pdb=" N VAL A 448 " --> pdb=" O LEU A 532 " (cutoff:3.500A) removed outlier: 5.211A pdb=" N ALA A 449 " --> pdb=" O VAL A 373 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N VAL A 373 " --> pdb=" O ALA A 449 " (cutoff:3.500A) removed outlier: 4.939A pdb=" N MET A 451 " --> pdb=" O LEU A 371 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N LEU A 371 " --> pdb=" O MET A 451 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N ARG A 367 " --> pdb=" O LYS A 455 " (cutoff:3.500A) removed outlier: 3.932A pdb=" N SER A 368 " --> pdb=" O TYR A 276 " (cutoff:3.500A) removed outlier: 6.996A pdb=" N TYR A 271 " --> pdb=" O SER A 287 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N SER A 287 " --> pdb=" O TYR A 271 " (cutoff:3.500A) removed outlier: 6.642A pdb=" N LEU A 273 " --> pdb=" O SER A 285 " (cutoff:3.500A) removed outlier: 4.670A pdb=" N SER A 285 " --> pdb=" O LEU A 273 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N MET A 275 " --> pdb=" O VAL A 283 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 353 through 358 removed outlier: 4.140A pdb=" N ASP A 353 " --> pdb=" O LEU A 246 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N LEU A 246 " --> pdb=" O ASP A 353 " (cutoff:3.500A) removed outlier: 4.198A pdb=" N ALA A 431 " --> pdb=" O LEU A 392 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N ASP A 394 " --> pdb=" O VAL A 429 " (cutoff:3.500A) removed outlier: 5.677A pdb=" N VAL A 429 " --> pdb=" O ASP A 394 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 567 through 570 removed outlier: 3.629A pdb=" N THR A 576 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N PHE A 578 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER A 580 " --> pdb=" O PRO A 589 " (cutoff:3.500A) removed outlier: 4.828A pdb=" N ALA A 582 " --> pdb=" O HIS A 587 " (cutoff:3.500A) removed outlier: 5.492A pdb=" N HIS A 587 " --> pdb=" O ALA A 582 " (cutoff:3.500A) removed outlier: 5.658A pdb=" N ARG A 612 " --> pdb=" O GLU A 603 " (cutoff:3.500A) removed outlier: 4.655A pdb=" N ALA A 605 " --> pdb=" O HIS A 610 " (cutoff:3.500A) removed outlier: 5.039A pdb=" N HIS A 610 " --> pdb=" O ALA A 605 " (cutoff:3.500A) removed outlier: 5.470A pdb=" N GLN A 635 " --> pdb=" O GLU A 626 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N VAL A 628 " --> pdb=" O GLU A 633 " (cutoff:3.500A) removed outlier: 5.475A pdb=" N GLU A 633 " --> pdb=" O VAL A 628 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N GLY A 634 " --> pdb=" O TRP A 650 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N THR A 647 " --> pdb=" O VAL A 660 " (cutoff:3.500A) removed outlier: 4.893A pdb=" N ALA A 651 " --> pdb=" O HIS A 656 " (cutoff:3.500A) removed outlier: 6.001A pdb=" N HIS A 656 " --> pdb=" O ALA A 651 " (cutoff:3.500A) removed outlier: 4.684A pdb=" N GLU A 672 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 681 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG A 690 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 705 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU A 692 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 703 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 694 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N GLY A 702 " --> pdb=" O TYR A 738 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 677 through 678 removed outlier: 4.684A pdb=" N GLU A 672 " --> pdb=" O LYS A 681 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LYS A 681 " --> pdb=" O GLU A 672 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N ARG A 690 " --> pdb=" O THR A 705 " (cutoff:3.500A) removed outlier: 6.840A pdb=" N THR A 705 " --> pdb=" O ARG A 690 " (cutoff:3.500A) removed outlier: 7.781A pdb=" N GLU A 692 " --> pdb=" O THR A 703 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N THR A 703 " --> pdb=" O GLU A 692 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N GLU A 694 " --> pdb=" O ALA A 701 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 733 " --> pdb=" O GLY A 783 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.691A pdb=" N ILE B 19 " --> pdb=" O ASP B 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 44 through 48 removed outlier: 3.666A pdb=" N ASP B 46 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS B 35 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 153 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 100 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE B 151 " --> pdb=" O ALA B 100 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 44 through 48 removed outlier: 3.666A pdb=" N ASP B 46 " --> pdb=" O ALA B 37 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N CYS B 35 " --> pdb=" O LEU B 48 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA B 153 " --> pdb=" O PHE B 98 " (cutoff:3.500A) removed outlier: 6.704A pdb=" N ALA B 100 " --> pdb=" O ILE B 151 " (cutoff:3.500A) removed outlier: 5.477A pdb=" N ILE B 151 " --> pdb=" O ALA B 100 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N ASP B 170 " --> pdb=" O ILE B 151 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 221 through 224 removed outlier: 4.211A pdb=" N GLN B 221 " --> pdb=" O ALA B 529 " (cutoff:3.500A) removed outlier: 6.586A pdb=" N LEU B 371 " --> pdb=" O LEU B 450 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N VAL B 370 " --> pdb=" O VAL B 274 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N LEU B 372 " --> pdb=" O ASN B 272 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N TYR B 271 " --> pdb=" O SER B 287 " (cutoff:3.500A) removed outlier: 4.673A pdb=" N SER B 287 " --> pdb=" O TYR B 271 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU B 273 " --> pdb=" O SER B 285 " (cutoff:3.500A) removed outlier: 4.671A pdb=" N SER B 285 " --> pdb=" O LEU B 273 " (cutoff:3.500A) removed outlier: 6.870A pdb=" N MET B 275 " --> pdb=" O VAL B 283 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 221 through 224 removed outlier: 4.211A pdb=" N GLN B 221 " --> pdb=" O ALA B 529 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 353 through 358 removed outlier: 3.766A pdb=" N ALA B 431 " --> pdb=" O LEU B 392 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP B 394 " --> pdb=" O VAL B 429 " (cutoff:3.500A) removed outlier: 5.997A pdb=" N VAL B 429 " --> pdb=" O ASP B 394 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 552 through 553 removed outlier: 3.516A pdb=" N SER B 580 " --> pdb=" O PRO B 589 " (cutoff:3.500A) removed outlier: 4.981A pdb=" N ALA B 582 " --> pdb=" O HIS B 587 " (cutoff:3.500A) removed outlier: 5.427A pdb=" N HIS B 587 " --> pdb=" O ALA B 582 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N GLY B 599 " --> pdb=" O VAL B 614 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N VAL B 614 " --> pdb=" O GLY B 599 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N ALA B 601 " --> pdb=" O ARG B 612 " (cutoff:3.500A) removed outlier: 7.737A pdb=" N ARG B 612 " --> pdb=" O ALA B 601 " (cutoff:3.500A) removed outlier: 4.335A pdb=" N GLU B 603 " --> pdb=" O HIS B 610 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N HIS B 610 " --> pdb=" O GLU B 603 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N GLN B 635 " --> pdb=" O GLU B 626 " (cutoff:3.500A) removed outlier: 5.166A pdb=" N VAL B 628 " --> pdb=" O GLU B 633 " (cutoff:3.500A) removed outlier: 5.675A pdb=" N GLU B 633 " --> pdb=" O VAL B 628 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N VAL B 660 " --> pdb=" O THR B 647 " (cutoff:3.500A) removed outlier: 4.494A pdb=" N GLU B 672 " --> pdb=" O LYS B 681 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N LYS B 681 " --> pdb=" O GLU B 672 " (cutoff:3.500A) removed outlier: 6.680A pdb=" N ARG B 690 " --> pdb=" O THR B 705 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N THR B 705 " --> pdb=" O ARG B 690 " (cutoff:3.500A) removed outlier: 7.736A pdb=" N GLU B 692 " --> pdb=" O THR B 703 " (cutoff:3.500A) removed outlier: 7.624A pdb=" N THR B 703 " --> pdb=" O GLU B 692 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N GLU B 694 " --> pdb=" O ALA B 701 " (cutoff:3.500A) removed outlier: 3.681A pdb=" N GLY B 702 " --> pdb=" O TYR B 738 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 645 through 651 Processing sheet with id=AB7, first strand: chain 'B' and resid 668 through 674 Processing sheet with id=AB8, first strand: chain 'B' and resid 699 through 709 Processing sheet with id=AB9, first strand: chain 'C' and resid 122 through 126 removed outlier: 3.818A pdb=" N ALA C 288 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N LEU C 290 " --> pdb=" O CYS C 276 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N THR C 294 " --> pdb=" O SER C 272 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'D' and resid 122 through 126 removed outlier: 6.811A pdb=" N VAL D 278 " --> pdb=" O LYS D 287 " (cutoff:3.500A) removed outlier: 4.619A pdb=" N LEU D 289 " --> pdb=" O CYS D 276 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N CYS D 276 " --> pdb=" O LEU D 289 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ALA D 291 " --> pdb=" O GLN D 274 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N GLN D 274 " --> pdb=" O ALA D 291 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 140 through 143 removed outlier: 3.576A pdb=" N ALA E 142 " --> pdb=" O VAL b 68 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 140 through 141 Processing sheet with id=AC4, first strand: chain 'F' and resid 140 through 141 removed outlier: 7.268A pdb=" N ASN c 63 " --> pdb=" O ARG d 62 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N ARG d 62 " --> pdb=" O ASN c 63 " (cutoff:3.500A) removed outlier: 4.024A pdb=" N CYS d 58 " --> pdb=" O TYR c 67 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N VAL d 83 " --> pdb=" O LEU d 80 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N TYR d 79 " --> pdb=" O ILE d 10 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ILE d 10 " --> pdb=" O TYR d 79 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'G' and resid 103 through 104 Processing sheet with id=AC6, first strand: chain 'G' and resid 229 through 230 removed outlier: 6.282A pdb=" N TYR G 167 " --> pdb=" O LYS G 159 " (cutoff:3.500A) removed outlier: 4.148A pdb=" N LYS G 159 " --> pdb=" O TYR G 167 " (cutoff:3.500A) removed outlier: 6.826A pdb=" N VAL G 169 " --> pdb=" O PHE G 157 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N SER G 153 " --> pdb=" O ALA G 173 " (cutoff:3.500A) removed outlier: 17.656A pdb=" N TRP G 412 " --> pdb=" O SER G 153 " (cutoff:3.500A) removed outlier: 11.908A pdb=" N ARG G 155 " --> pdb=" O TRP G 412 " (cutoff:3.500A) removed outlier: 9.966A pdb=" N CYS G 414 " --> pdb=" O ARG G 155 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N PHE G 157 " --> pdb=" O CYS G 414 " (cutoff:3.500A) removed outlier: 5.406A pdb=" N ALA G 403 " --> pdb=" O SER G 397 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 284 through 286 Processing sheet with id=AC8, first strand: chain 'G' and resid 290 through 293 Processing sheet with id=AC9, first strand: chain 'H' and resid 103 through 104 Processing sheet with id=AD1, first strand: chain 'H' and resid 229 through 230 removed outlier: 6.829A pdb=" N TYR H 167 " --> pdb=" O GLY H 158 " (cutoff:3.500A) removed outlier: 6.515A pdb=" N GLY H 158 " --> pdb=" O TYR H 167 " (cutoff:3.500A) removed outlier: 7.546A pdb=" N VAL H 169 " --> pdb=" O PHE H 156 " (cutoff:3.500A) removed outlier: 5.306A pdb=" N PHE H 156 " --> pdb=" O VAL H 169 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLU H 171 " --> pdb=" O VAL H 154 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N VAL H 154 " --> pdb=" O GLU H 171 " (cutoff:3.500A) removed outlier: 6.489A pdb=" N ALA H 173 " --> pdb=" O ARG H 152 " (cutoff:3.500A) removed outlier: 17.913A pdb=" N TRP H 412 " --> pdb=" O SER H 153 " (cutoff:3.500A) removed outlier: 12.117A pdb=" N ARG H 155 " --> pdb=" O TRP H 412 " (cutoff:3.500A) removed outlier: 10.329A pdb=" N CYS H 414 " --> pdb=" O ARG H 155 " (cutoff:3.500A) removed outlier: 6.507A pdb=" N PHE H 157 " --> pdb=" O CYS H 414 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR H 416 " --> pdb=" O PHE H 157 " (cutoff:3.500A) Processing sheet with id=AD2, first strand: chain 'H' and resid 284 through 286 Processing sheet with id=AD3, first strand: chain 'H' and resid 290 through 293 Processing sheet with id=AD4, first strand: chain 'I' and resid 32 through 33 removed outlier: 4.549A pdb=" N VAL I 32 " --> pdb=" O LEU I 40 " (cutoff:3.500A) Processing sheet with id=AD5, first strand: chain 'I' and resid 178 through 180 removed outlier: 7.519A pdb=" N ILE I 334 " --> pdb=" O THR I 355 " (cutoff:3.500A) removed outlier: 6.716A pdb=" N VAL I 357 " --> pdb=" O ILE I 334 " (cutoff:3.500A) removed outlier: 6.685A pdb=" N LEU I 336 " --> pdb=" O VAL I 357 " (cutoff:3.500A) removed outlier: 6.183A pdb=" N VAL I 359 " --> pdb=" O LEU I 336 " (cutoff:3.500A) removed outlier: 6.106A pdb=" N VAL I 287 " --> pdb=" O GLY I 335 " (cutoff:3.500A) removed outlier: 7.485A pdb=" N VAL I 337 " --> pdb=" O VAL I 287 " (cutoff:3.500A) removed outlier: 6.801A pdb=" N LEU I 289 " --> pdb=" O VAL I 337 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'I' and resid 313 through 314 Processing sheet with id=AD7, first strand: chain 'J' and resid 32 through 33 removed outlier: 4.758A pdb=" N VAL J 32 " --> pdb=" O LEU J 40 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain 'J' and resid 44 through 46 removed outlier: 6.741A pdb=" N THR J 355 " --> pdb=" O LYS J 381 " (cutoff:3.500A) removed outlier: 8.165A pdb=" N LEU J 383 " --> pdb=" O THR J 355 " (cutoff:3.500A) removed outlier: 6.559A pdb=" N VAL J 357 " --> pdb=" O LEU J 383 " (cutoff:3.500A) removed outlier: 7.854A pdb=" N ARG J 385 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 7.019A pdb=" N VAL J 359 " --> pdb=" O ARG J 385 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N ILE J 334 " --> pdb=" O THR J 355 " (cutoff:3.500A) removed outlier: 6.594A pdb=" N VAL J 357 " --> pdb=" O ILE J 334 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N LEU J 336 " --> pdb=" O VAL J 357 " (cutoff:3.500A) removed outlier: 5.932A pdb=" N VAL J 359 " --> pdb=" O LEU J 336 " (cutoff:3.500A) removed outlier: 6.201A pdb=" N VAL J 287 " --> pdb=" O GLY J 335 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N VAL J 337 " --> pdb=" O VAL J 287 " (cutoff:3.500A) removed outlier: 6.706A pdb=" N LEU J 289 " --> pdb=" O VAL J 337 " (cutoff:3.500A) Processing sheet with id=AD9, first strand: chain 'K' and resid 209 through 210 removed outlier: 6.885A pdb=" N TYR K 163 " --> pdb=" O GLY K 154 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N GLY K 154 " --> pdb=" O TYR K 163 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N VAL K 165 " --> pdb=" O PHE K 152 " (cutoff:3.500A) removed outlier: 5.081A pdb=" N PHE K 152 " --> pdb=" O VAL K 165 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N GLU K 167 " --> pdb=" O VAL K 150 " (cutoff:3.500A) removed outlier: 4.614A pdb=" N VAL K 150 " --> pdb=" O GLU K 167 " (cutoff:3.500A) removed outlier: 6.829A pdb=" N THR K 169 " --> pdb=" O SER K 148 " (cutoff:3.500A) removed outlier: 22.424A pdb=" N PHE K 400 " --> pdb=" O VAL K 147 " (cutoff:3.500A) removed outlier: 16.086A pdb=" N THR K 149 " --> pdb=" O PHE K 400 " (cutoff:3.500A) removed outlier: 15.066A pdb=" N SER K 402 " --> pdb=" O THR K 149 " (cutoff:3.500A) removed outlier: 9.598A pdb=" N ARG K 151 " --> pdb=" O SER K 402 " (cutoff:3.500A) removed outlier: 10.024A pdb=" N TYR K 404 " --> pdb=" O ARG K 151 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N PHE K 153 " --> pdb=" O TYR K 404 " (cutoff:3.500A) removed outlier: 8.455A pdb=" N GLY K 406 " --> pdb=" O PHE K 153 " (cutoff:3.500A) removed outlier: 6.086A pdb=" N LYS K 155 " --> pdb=" O GLY K 406 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N CYS K 395 " --> pdb=" O ALA K 381 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ALA K 381 " --> pdb=" O CYS K 395 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'K' and resid 264 through 266 Processing sheet with id=AE2, first strand: chain 'K' and resid 270 through 272 Processing sheet with id=AE3, first strand: chain 'L' and resid 147 through 150 removed outlier: 6.726A pdb=" N THR L 169 " --> pdb=" O SER L 148 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL L 150 " --> pdb=" O GLU L 167 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU L 167 " --> pdb=" O VAL L 150 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain 'L' and resid 147 through 150 removed outlier: 6.726A pdb=" N THR L 169 " --> pdb=" O SER L 148 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N VAL L 150 " --> pdb=" O GLU L 167 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N GLU L 167 " --> pdb=" O VAL L 150 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N VAL L 165 " --> pdb=" O GLY L 154 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N GLY L 154 " --> pdb=" O VAL L 165 " (cutoff:3.500A) removed outlier: 5.105A pdb=" N ALA L 391 " --> pdb=" O SER L 385 " (cutoff:3.500A) removed outlier: 3.878A pdb=" N CYS L 395 " --> pdb=" O ALA L 381 " (cutoff:3.500A) removed outlier: 3.784A pdb=" N ALA L 381 " --> pdb=" O CYS L 395 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'L' and resid 264 through 266 Processing sheet with id=AE6, first strand: chain 'L' and resid 270 through 272 Processing sheet with id=AE7, first strand: chain 'O' and resid 92 through 94 removed outlier: 4.780A pdb=" N TYR O 82 " --> pdb=" O LEU O 94 " (cutoff:3.500A) removed outlier: 6.331A pdb=" N ALA O 75 " --> pdb=" O SER O 71 " (cutoff:3.500A) removed outlier: 4.604A pdb=" N SER O 71 " --> pdb=" O ALA O 75 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N VAL O 77 " --> pdb=" O ALA O 69 " (cutoff:3.500A) removed outlier: 4.512A pdb=" N ALA O 69 " --> pdb=" O VAL O 77 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N GLU O 79 " --> pdb=" O ASN O 67 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ASN O 67 " --> pdb=" O GLU O 79 " (cutoff:3.500A) removed outlier: 5.856A pdb=" N GLU O 64 " --> pdb=" O LEU O 48 " (cutoff:3.500A) removed outlier: 5.361A pdb=" N LEU O 48 " --> pdb=" O GLU O 64 " (cutoff:3.500A) removed outlier: 11.318A pdb=" N THR O 47 " --> pdb=" O TRP O 251 " (cutoff:3.500A) removed outlier: 9.879A pdb=" N SER O 253 " --> pdb=" O THR O 47 " (cutoff:3.500A) removed outlier: 6.063A pdb=" N TRP O 49 " --> pdb=" O SER O 253 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N TYR O 255 " --> pdb=" O TRP O 49 " (cutoff:3.500A) removed outlier: 4.867A pdb=" N TYR O 240 " --> pdb=" O SER O 234 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 'O' and resid 119 through 122 Processing sheet with id=AE9, first strand: chain 'O' and resid 166 through 168 Processing sheet with id=AF1, first strand: chain 'O' and resid 172 through 174 Processing sheet with id=AF2, first strand: chain 'P' and resid 45 through 52 removed outlier: 5.384A pdb=" N LEU P 46 " --> pdb=" O TYR P 66 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N TYR P 66 " --> pdb=" O LEU P 46 " (cutoff:3.500A) removed outlier: 5.335A pdb=" N LEU P 48 " --> pdb=" O GLU P 64 " (cutoff:3.500A) removed outlier: 5.670A pdb=" N GLU P 64 " --> pdb=" O LEU P 48 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASN P 67 " --> pdb=" O GLU P 79 " (cutoff:3.500A) removed outlier: 8.193A pdb=" N GLU P 79 " --> pdb=" O ASN P 67 " (cutoff:3.500A) removed outlier: 5.546A pdb=" N ALA P 69 " --> pdb=" O VAL P 77 " (cutoff:3.500A) removed outlier: 6.516A pdb=" N VAL P 77 " --> pdb=" O ALA P 69 " (cutoff:3.500A) Processing sheet with id=AF3, first strand: chain 'P' and resid 119 through 122 Processing sheet with id=AF4, first strand: chain 'P' and resid 166 through 168 Processing sheet with id=AF5, first strand: chain 'P' and resid 172 through 173 Processing sheet with id=AF6, first strand: chain 'P' and resid 219 through 224 removed outlier: 4.817A pdb=" N TYR P 240 " --> pdb=" O SER P 234 " (cutoff:3.500A) Processing sheet with id=AF7, first strand: chain 'Q' and resid 46 through 52 removed outlier: 6.013A pdb=" N LEU Q 46 " --> pdb=" O TYR Q 66 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N TYR Q 66 " --> pdb=" O LEU Q 46 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N LEU Q 48 " --> pdb=" O GLU Q 64 " (cutoff:3.500A) removed outlier: 5.919A pdb=" N GLU Q 64 " --> pdb=" O LEU Q 48 " (cutoff:3.500A) removed outlier: 4.414A pdb=" N ASN Q 67 " --> pdb=" O GLU Q 79 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N GLU Q 79 " --> pdb=" O ASN Q 67 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N ALA Q 69 " --> pdb=" O VAL Q 77 " (cutoff:3.500A) removed outlier: 6.120A pdb=" N VAL Q 77 " --> pdb=" O ALA Q 69 " (cutoff:3.500A) removed outlier: 4.560A pdb=" N SER Q 71 " --> pdb=" O ALA Q 75 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ALA Q 75 " --> pdb=" O SER Q 71 " (cutoff:3.500A) removed outlier: 4.753A pdb=" N TYR Q 82 " --> pdb=" O LEU Q 94 " (cutoff:3.500A) Processing sheet with id=AF8, first strand: chain 'Q' and resid 119 through 122 Processing sheet with id=AF9, first strand: chain 'Q' and resid 166 through 168 Processing sheet with id=AG1, first strand: chain 'Q' and resid 172 through 174 Processing sheet with id=AG2, first strand: chain 'Q' and resid 219 through 224 removed outlier: 4.812A pdb=" N TYR Q 240 " --> pdb=" O SER Q 234 " (cutoff:3.500A) Processing sheet with id=AG3, first strand: chain 'R' and resid 92 through 93 removed outlier: 6.033A pdb=" N ALA R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER R 71 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL R 77 " --> pdb=" O ALA R 69 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA R 69 " --> pdb=" O VAL R 77 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU R 79 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN R 67 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 14.846A pdb=" N ASN R 67 " --> pdb=" O PRO R 182 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ALA R 69 " --> pdb=" O VAL R 180 " (cutoff:3.500A) Processing sheet with id=AG4, first strand: chain 'R' and resid 92 through 93 removed outlier: 6.033A pdb=" N ALA R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 4.498A pdb=" N SER R 71 " --> pdb=" O ALA R 75 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL R 77 " --> pdb=" O ALA R 69 " (cutoff:3.500A) removed outlier: 4.816A pdb=" N ALA R 69 " --> pdb=" O VAL R 77 " (cutoff:3.500A) removed outlier: 8.252A pdb=" N GLU R 79 " --> pdb=" O ASN R 67 " (cutoff:3.500A) removed outlier: 4.324A pdb=" N ASN R 67 " --> pdb=" O GLU R 79 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N GLU R 64 " --> pdb=" O LEU R 48 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N LEU R 48 " --> pdb=" O GLU R 64 " (cutoff:3.500A) removed outlier: 7.670A pdb=" N TYR R 66 " --> pdb=" O LEU R 46 " (cutoff:3.500A) removed outlier: 5.482A pdb=" N LEU R 46 " --> pdb=" O TYR R 66 " (cutoff:3.500A) removed outlier: 16.151A pdb=" N TRP R 251 " --> pdb=" O SER R 45 " (cutoff:3.500A) removed outlier: 11.611A pdb=" N THR R 47 " --> pdb=" O TRP R 251 " (cutoff:3.500A) removed outlier: 9.856A pdb=" N SER R 253 " --> pdb=" O THR R 47 " (cutoff:3.500A) removed outlier: 6.286A pdb=" N TRP R 49 " --> pdb=" O SER R 253 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N TYR R 255 " --> pdb=" O TRP R 49 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N THR R 250 " --> pdb=" O ALA R 245 " (cutoff:3.500A) removed outlier: 4.856A pdb=" N TYR R 240 " --> pdb=" O SER R 234 " (cutoff:3.500A) Processing sheet with id=AG5, first strand: chain 'R' and resid 119 through 122 Processing sheet with id=AG6, first strand: chain 'R' and resid 166 through 168 Processing sheet with id=AG7, first strand: chain 'S' and resid 11 through 13 removed outlier: 6.638A pdb=" N LYS S 47 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR S 62 " --> pdb=" O LYS S 47 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU S 49 " --> pdb=" O LYS S 60 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LYS S 60 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR S 51 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS S 86 " --> pdb=" O THR S 73 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN S 107 " --> pdb=" O ASP S 98 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL S 100 " --> pdb=" O GLN S 105 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN S 105 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA S 121 " --> pdb=" O LYS S 130 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS S 130 " --> pdb=" O ALA S 121 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN S 141 " --> pdb=" O TRP S 156 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP S 156 " --> pdb=" O GLN S 141 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL S 143 " --> pdb=" O GLY S 154 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY S 154 " --> pdb=" O VAL S 143 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP S 145 " --> pdb=" O THR S 152 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR S 152 " --> pdb=" O PHE S 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 179 " --> pdb=" O LYS S 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR S 178 " --> pdb=" O PHE S 195 " (cutoff:3.500A) Processing sheet with id=AG8, first strand: chain 'S' and resid 11 through 13 removed outlier: 6.638A pdb=" N LYS S 47 " --> pdb=" O THR S 62 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N THR S 62 " --> pdb=" O LYS S 47 " (cutoff:3.500A) removed outlier: 7.516A pdb=" N GLU S 49 " --> pdb=" O LYS S 60 " (cutoff:3.500A) removed outlier: 7.460A pdb=" N LYS S 60 " --> pdb=" O GLU S 49 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N THR S 51 " --> pdb=" O THR S 58 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N LYS S 86 " --> pdb=" O THR S 73 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N GLN S 107 " --> pdb=" O ASP S 98 " (cutoff:3.500A) removed outlier: 5.023A pdb=" N VAL S 100 " --> pdb=" O GLN S 105 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N GLN S 105 " --> pdb=" O VAL S 100 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ALA S 121 " --> pdb=" O LYS S 130 " (cutoff:3.500A) removed outlier: 5.602A pdb=" N LYS S 130 " --> pdb=" O ALA S 121 " (cutoff:3.500A) removed outlier: 6.433A pdb=" N GLN S 141 " --> pdb=" O TRP S 156 " (cutoff:3.500A) removed outlier: 4.381A pdb=" N TRP S 156 " --> pdb=" O GLN S 141 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N VAL S 143 " --> pdb=" O GLY S 154 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N GLY S 154 " --> pdb=" O VAL S 143 " (cutoff:3.500A) removed outlier: 6.844A pdb=" N ASP S 145 " --> pdb=" O THR S 152 " (cutoff:3.500A) removed outlier: 4.582A pdb=" N THR S 152 " --> pdb=" O PHE S 168 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N ALA S 179 " --> pdb=" O LYS S 167 " (cutoff:3.500A) removed outlier: 6.665A pdb=" N THR S 178 " --> pdb=" O PHE S 195 " (cutoff:3.500A) Processing sheet with id=AG9, first strand: chain 'S' and resid 76 through 77 Processing sheet with id=AH1, first strand: chain 'T' and resid 16 through 17 removed outlier: 4.186A pdb=" N THR T 51 " --> pdb=" O LYS T 60 " (cutoff:3.500A) removed outlier: 5.822A pdb=" N LYS T 60 " --> pdb=" O THR T 51 " (cutoff:3.500A) removed outlier: 6.890A pdb=" N VAL T 71 " --> pdb=" O LYS T 86 " (cutoff:3.500A) removed outlier: 6.807A pdb=" N LYS T 86 " --> pdb=" O VAL T 71 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N THR T 73 " --> pdb=" O LYS T 84 " (cutoff:3.500A) removed outlier: 7.713A pdb=" N LYS T 84 " --> pdb=" O THR T 73 " (cutoff:3.500A) removed outlier: 5.111A pdb=" N ASP T 75 " --> pdb=" O HIS T 82 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N HIS T 82 " --> pdb=" O ASP T 75 " (cutoff:3.500A) removed outlier: 5.828A pdb=" N GLN T 107 " --> pdb=" O ASP T 98 " (cutoff:3.500A) removed outlier: 5.802A pdb=" N LYS T 130 " --> pdb=" O ALA T 121 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N TRP T 123 " --> pdb=" O HIS T 128 " (cutoff:3.500A) removed outlier: 5.972A pdb=" N HIS T 128 " --> pdb=" O TRP T 123 " (cutoff:3.500A) removed outlier: 6.348A pdb=" N GLN T 141 " --> pdb=" O TRP T 156 " (cutoff:3.500A) removed outlier: 4.244A pdb=" N TRP T 156 " --> pdb=" O GLN T 141 " (cutoff:3.500A) removed outlier: 6.612A pdb=" N VAL T 143 " --> pdb=" O GLY T 154 " (cutoff:3.500A) removed outlier: 4.552A pdb=" N GLY T 154 " --> pdb=" O VAL T 143 " (cutoff:3.500A) removed outlier: 6.912A pdb=" N ASP T 145 " --> pdb=" O THR T 152 " (cutoff:3.500A) removed outlier: 4.914A pdb=" N THR T 152 " --> pdb=" O PHE T 168 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N THR T 178 " --> pdb=" O PHE T 195 " (cutoff:3.500A) Processing sheet with id=AH2, first strand: chain 'T' and resid 11 through 13 Processing sheet with id=AH3, first strand: chain 'T' and resid 56 through 57 Processing sheet with id=AH4, first strand: chain 'T' and resid 201 through 203 Processing sheet with id=AH5, first strand: chain 'V' and resid 147 through 148 removed outlier: 3.869A pdb=" N LEU V 147 " --> pdb=" O VAL V 186 " (cutoff:3.500A) Processing sheet with id=AH6, first strand: chain 'W' and resid 139 through 141 removed outlier: 5.362A pdb=" N LEU W 31 " --> pdb=" O GLN W 27 " (cutoff:3.500A) removed outlier: 6.219A pdb=" N GLN W 27 " --> pdb=" O LEU W 31 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N THR W 19 " --> pdb=" O LEU W 39 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N TYR W 20 " --> pdb=" O ILE W 176 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER W 172 " --> pdb=" O SER W 24 " (cutoff:3.500A) removed outlier: 6.765A pdb=" N GLN W 26 " --> pdb=" O ILE W 170 " (cutoff:3.500A) removed outlier: 5.297A pdb=" N ILE W 170 " --> pdb=" O GLN W 26 " (cutoff:3.500A) Processing sheet with id=AH7, first strand: chain 'W' and resid 72 through 75 Processing sheet with id=AH8, first strand: chain 'W' and resid 159 through 160 Processing sheet with id=AH9, first strand: chain 'Y' and resid 137 through 143 removed outlier: 6.286A pdb=" N LYS Y 137 " --> pdb=" O VAL Y 208 " (cutoff:3.500A) removed outlier: 7.583A pdb=" N VAL Y 210 " --> pdb=" O LYS Y 137 " (cutoff:3.500A) removed outlier: 6.455A pdb=" N TYR Y 139 " --> pdb=" O VAL Y 210 " (cutoff:3.500A) removed outlier: 7.252A pdb=" N LYS Y 212 " --> pdb=" O TYR Y 139 " (cutoff:3.500A) removed outlier: 5.660A pdb=" N LEU Y 141 " --> pdb=" O LYS Y 212 " (cutoff:3.500A) Processing sheet with id=AI1, first strand: chain 'Y' and resid 153 through 162 Processing sheet with id=AI2, first strand: chain 'Y' and resid 219 through 222 Processing sheet with id=AI3, first strand: chain 'Y' and resid 242 through 246 Processing sheet with id=AI4, first strand: chain 'Z' and resid 137 through 143 removed outlier: 6.075A pdb=" N LYS Z 137 " --> pdb=" O VAL Z 208 " (cutoff:3.500A) removed outlier: 7.370A pdb=" N VAL Z 210 " --> pdb=" O LYS Z 137 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N TYR Z 139 " --> pdb=" O VAL Z 210 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N LYS Z 212 " --> pdb=" O TYR Z 139 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N LEU Z 141 " --> pdb=" O LYS Z 212 " (cutoff:3.500A) Processing sheet with id=AI5, first strand: chain 'Z' and resid 154 through 162 removed outlier: 3.662A pdb=" N VAL Z 170 " --> pdb=" O VAL Z 162 " (cutoff:3.500A) Processing sheet with id=AI6, first strand: chain 'Z' and resid 219 through 222 removed outlier: 3.683A pdb=" N ASP Z 225 " --> pdb=" O ARG Z 222 " (cutoff:3.500A) removed outlier: 6.550A pdb=" N LEU Z 226 " --> pdb=" O VAL Z 287 " (cutoff:3.500A) removed outlier: 7.469A pdb=" N GLU Z 289 " --> pdb=" O LEU Z 226 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N HIS Z 228 " --> pdb=" O GLU Z 289 " (cutoff:3.500A) removed outlier: 7.435A pdb=" N ASP Z 291 " --> pdb=" O HIS Z 228 " (cutoff:3.500A) removed outlier: 6.495A pdb=" N VAL Z 230 " --> pdb=" O ASP Z 291 " (cutoff:3.500A) removed outlier: 7.107A pdb=" N LEU Z 293 " --> pdb=" O VAL Z 230 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU Z 232 " --> pdb=" O LEU Z 293 " (cutoff:3.500A) removed outlier: 6.142A pdb=" N GLY Z 284 " --> pdb=" O GLY Z 271 " (cutoff:3.500A) Processing sheet with id=AI7, first strand: chain 'Z' and resid 242 through 246 Processing sheet with id=AI8, first strand: chain 'b' and resid 9 through 13 removed outlier: 5.395A pdb=" N ILE b 10 " --> pdb=" O TYR b 79 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR b 79 " --> pdb=" O ILE b 10 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS b 58 " --> pdb=" O TYR a 67 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN a 63 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE b 64 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY a 61 " --> pdb=" O PHE b 64 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N THR s 371 " --> pdb=" O SER a 66 " (cutoff:3.500A) removed outlier: 3.699A pdb=" N ARG s 367 " --> pdb=" O HIS a 70 " (cutoff:3.500A) Processing sheet with id=AI9, first strand: chain 'b' and resid 9 through 13 removed outlier: 5.395A pdb=" N ILE b 10 " --> pdb=" O TYR b 79 " (cutoff:3.500A) removed outlier: 6.815A pdb=" N TYR b 79 " --> pdb=" O ILE b 10 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N CYS b 58 " --> pdb=" O TYR a 67 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N ASN a 63 " --> pdb=" O ARG b 62 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N PHE b 64 " --> pdb=" O GLY a 61 " (cutoff:3.500A) removed outlier: 7.074A pdb=" N GLY a 61 " --> pdb=" O PHE b 64 " (cutoff:3.500A) removed outlier: 7.012A pdb=" N TYR a 79 " --> pdb=" O ILE a 10 " (cutoff:3.500A) removed outlier: 5.655A pdb=" N ILE a 10 " --> pdb=" O TYR a 79 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ALA a 8 " --> pdb=" O VAL s 388 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS s 386 " --> pdb=" O ILE a 10 " (cutoff:3.500A) Processing sheet with id=AJ1, first strand: chain 'c' and resid 10 through 14 removed outlier: 6.429A pdb=" N ILE c 10 " --> pdb=" O TYR c 79 " (cutoff:3.500A) removed outlier: 6.659A pdb=" N TYR c 79 " --> pdb=" O ILE c 10 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N TRP c 56 " --> pdb=" O THR d 69 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR d 69 " --> pdb=" O TRP c 56 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N CYS c 58 " --> pdb=" O TYR d 67 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N VAL d 68 " --> pdb=" O HIS s 361 " (cutoff:3.500A) removed outlier: 4.204A pdb=" N HIS s 361 " --> pdb=" O VAL d 68 " (cutoff:3.500A) Processing sheet with id=AJ2, first strand: chain 'i' and resid 34 through 41 removed outlier: 5.920A pdb=" N ILE i 35 " --> pdb=" O ALA i 79 " (cutoff:3.500A) removed outlier: 7.097A pdb=" N ALA i 79 " --> pdb=" O ILE i 35 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N ALA i 37 " --> pdb=" O VAL i 77 " (cutoff:3.500A) Processing sheet with id=AJ3, first strand: chain 'j' and resid 35 through 41 removed outlier: 6.548A pdb=" N VAL j 77 " --> pdb=" O ILE j 36 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N LYS j 38 " --> pdb=" O ALA j 75 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N ALA j 75 " --> pdb=" O LYS j 38 " (cutoff:3.500A) removed outlier: 4.535A pdb=" N LYS j 40 " --> pdb=" O ILE j 73 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N ILE j 73 " --> pdb=" O LYS j 40 " (cutoff:3.500A) Processing sheet with id=AJ4, first strand: chain 'k' and resid 27 through 30 Processing sheet with id=AJ5, first strand: chain 'k' and resid 73 through 75 Processing sheet with id=AJ6, first strand: chain 'k' and resid 139 through 146 removed outlier: 3.734A pdb=" N GLN k 139 " --> pdb=" O ASN k 134 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ASN k 134 " --> pdb=" O GLN k 139 " (cutoff:3.500A) removed outlier: 7.895A pdb=" N VAL k 218 " --> pdb=" O LEU k 173 " (cutoff:3.500A) removed outlier: 4.527A pdb=" N LEU k 173 " --> pdb=" O VAL k 218 " (cutoff:3.500A) 3801 hydrogen bonds defined for protein. 10779 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: 41.15 Time building geometry restraints manager: 17.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 15307 1.33 - 1.45: 16699 1.45 - 1.57: 42090 1.57 - 1.70: 1 1.70 - 1.82: 378 Bond restraints: 74475 Sorted by residual: bond pdb=" CA PRO H 432 " pdb=" C PRO H 432 " ideal model delta sigma weight residual 1.514 1.536 -0.022 5.50e-03 3.31e+04 1.54e+01 bond pdb=" C PRO H 432 " pdb=" O PRO H 432 " ideal model delta sigma weight residual 1.246 1.215 0.031 8.50e-03 1.38e+04 1.31e+01 bond pdb=" N TYR O 191 " pdb=" CA TYR O 191 " ideal model delta sigma weight residual 1.458 1.483 -0.025 7.40e-03 1.83e+04 1.18e+01 bond pdb=" N ILE W 176 " pdb=" CA ILE W 176 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.14e-02 7.69e+03 1.16e+01 bond pdb=" N GLN j 162 " pdb=" CA GLN j 162 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.04e-02 9.25e+03 1.14e+01 ... (remaining 74470 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.52: 99316 2.52 - 5.04: 1808 5.04 - 7.56: 87 7.56 - 10.08: 10 10.08 - 12.60: 3 Bond angle restraints: 101224 Sorted by residual: angle pdb=" CA GLY H 129 " pdb=" C GLY H 129 " pdb=" O GLY H 129 " ideal model delta sigma weight residual 122.23 117.91 4.32 6.90e-01 2.10e+00 3.93e+01 angle pdb=" CA GLY O 188 " pdb=" C GLY O 188 " pdb=" O GLY O 188 " ideal model delta sigma weight residual 122.45 118.27 4.18 7.20e-01 1.93e+00 3.37e+01 angle pdb=" N ALA K 239 " pdb=" CA ALA K 239 " pdb=" C ALA K 239 " ideal model delta sigma weight residual 113.12 106.34 6.78 1.25e+00 6.40e-01 2.94e+01 angle pdb=" N PRO H 432 " pdb=" CA PRO H 432 " pdb=" C PRO H 432 " ideal model delta sigma weight residual 110.47 115.58 -5.11 9.60e-01 1.09e+00 2.83e+01 angle pdb=" N VAL G 322 " pdb=" CA VAL G 322 " pdb=" C VAL G 322 " ideal model delta sigma weight residual 113.71 108.78 4.93 9.50e-01 1.11e+00 2.69e+01 ... (remaining 101219 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 40936 17.99 - 35.98: 3214 35.98 - 53.97: 509 53.97 - 71.96: 94 71.96 - 89.95: 55 Dihedral angle restraints: 44808 sinusoidal: 17436 harmonic: 27372 Sorted by residual: dihedral pdb=" CB CYS R 105 " pdb=" SG CYS R 105 " pdb=" SG CYS R 155 " pdb=" CB CYS R 155 " ideal model delta sinusoidal sigma weight residual 93.00 31.41 61.59 1 1.00e+01 1.00e-02 5.03e+01 dihedral pdb=" CA HIS X 312 " pdb=" C HIS X 312 " pdb=" N GLU X 313 " pdb=" CA GLU X 313 " ideal model delta harmonic sigma weight residual -180.00 -152.02 -27.98 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA ASN b 53 " pdb=" C ASN b 53 " pdb=" N PRO b 54 " pdb=" CA PRO b 54 " ideal model delta harmonic sigma weight residual -180.00 -152.10 -27.90 0 5.00e+00 4.00e-02 3.11e+01 ... (remaining 44805 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.082: 10080 0.082 - 0.164: 991 0.164 - 0.247: 87 0.247 - 0.329: 13 0.329 - 0.411: 1 Chirality restraints: 11172 Sorted by residual: chirality pdb=" CA THR A 517 " pdb=" N THR A 517 " pdb=" C THR A 517 " pdb=" CB THR A 517 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.23e+00 chirality pdb=" CA TYR W 177 " pdb=" N TYR W 177 " pdb=" C TYR W 177 " pdb=" CB TYR W 177 " both_signs ideal model delta sigma weight residual False 2.51 2.18 0.33 2.00e-01 2.50e+01 2.68e+00 chirality pdb=" CA ASP A 471 " pdb=" N ASP A 471 " pdb=" C ASP A 471 " pdb=" CB ASP A 471 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.15e+00 ... (remaining 11169 not shown) Planarity restraints: 13313 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 199 " 0.029 2.00e-02 2.50e+03 5.76e-02 3.32e+01 pdb=" C LEU A 199 " -0.100 2.00e-02 2.50e+03 pdb=" O LEU A 199 " 0.037 2.00e-02 2.50e+03 pdb=" N ASP A 200 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 199 " 0.025 2.00e-02 2.50e+03 4.90e-02 2.40e+01 pdb=" C LEU B 199 " -0.085 2.00e-02 2.50e+03 pdb=" O LEU B 199 " 0.032 2.00e-02 2.50e+03 pdb=" N ASP B 200 " 0.028 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG X 200 " 0.021 2.00e-02 2.50e+03 4.28e-02 1.83e+01 pdb=" C ARG X 200 " -0.074 2.00e-02 2.50e+03 pdb=" O ARG X 200 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS X 201 " 0.026 2.00e-02 2.50e+03 ... (remaining 13310 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 453 2.54 - 3.13: 56551 3.13 - 3.72: 111336 3.72 - 4.31: 149059 4.31 - 4.90: 254131 Nonbonded interactions: 571530 Sorted by model distance: nonbonded pdb=" NH2 ARG A 300 " pdb=" OE1 GLU A 351 " model vdw 1.951 3.120 nonbonded pdb=" OE2 GLU H 99 " pdb=" O HIS Z 297 " model vdw 1.971 3.040 nonbonded pdb=" NH1 ARG B 300 " pdb=" OE2 GLU B 351 " model vdw 2.048 3.120 nonbonded pdb=" NH2 ARG A 300 " pdb=" OE2 GLU A 351 " model vdw 2.054 3.120 nonbonded pdb=" OG SER C 300 " pdb=" OE2 GLU S 212 " model vdw 2.069 3.040 ... (remaining 571525 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' selection = chain 'B' } ncs_group { reference = chain 'C' selection = chain 'D' } ncs_group { reference = chain 'E' selection = (chain 'F' and (resid 139 through 261 or resid 268 through 509)) } ncs_group { reference = chain 'G' selection = chain 'H' } ncs_group { reference = chain 'I' selection = chain 'J' } ncs_group { reference = chain 'K' selection = chain 'L' } ncs_group { reference = (chain 'M' and resid 8 through 47) selection = chain 'N' } ncs_group { reference = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' } ncs_group { reference = chain 'S' selection = chain 'T' } ncs_group { reference = chain 'Y' selection = chain 'Z' } ncs_group { reference = chain 'a' selection = chain 'b' selection = chain 'c' selection = chain 'd' } ncs_group { reference = chain 'i' selection = chain 'j' } ncs_group { reference = chain 'u' selection = chain 'v' } ncs_group { reference = chain 'y' selection = chain 'z' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.53 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.090 Extract box with map and model: 2.840 Check model and map are aligned: 0.450 Set scattering table: 0.560 Process input model: 150.640 Find NCS groups from input model: 2.820 Set up NCS constraints: 0.930 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: 0.040 Load rotamer database and sin/cos tables:2.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 176.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 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 : 0.005 0.086 74475 Z= 0.316 Angle : 0.751 12.600 101224 Z= 0.476 Chirality : 0.049 0.411 11172 Planarity : 0.005 0.091 13313 Dihedral : 13.431 89.954 27182 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.51 % Allowed : 0.72 % Favored : 98.77 % Cbeta Deviations : 0.02 % Peptide Plane: Cis-proline : 0.96 % 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: -0.30 (0.09), residues: 9336 helix: 1.44 (0.09), residues: 3529 sheet: -0.94 (0.13), residues: 1545 loop : -1.31 (0.09), residues: 4262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 673 HIS 0.013 0.001 HIS C 502 PHE 0.033 0.002 PHE a 48 TYR 0.026 0.002 TYR c 67 ARG 0.019 0.001 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 737 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 699 time to evaluate : 6.503 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 348 PHE cc_start: 0.7532 (t80) cc_final: 0.7296 (t80) REVERT: Q 111 MET cc_start: 0.8617 (ttm) cc_final: 0.8409 (ttp) REVERT: b 73 LYS cc_start: 0.5842 (tptp) cc_final: 0.5608 (tptt) REVERT: i 14 ASP cc_start: 0.8031 (p0) cc_final: 0.7815 (p0) REVERT: j 161 ILE cc_start: 0.7945 (OUTLIER) cc_final: 0.7111 (pt) outliers start: 38 outliers final: 10 residues processed: 729 average time/residue: 0.7361 time to fit residues: 919.0997 Evaluate side-chains 536 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 525 time to evaluate : 7.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 470 VAL Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain J residue 419 LEU Chi-restraints excluded: chain W residue 131 LEU Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain j residue 161 ILE Chi-restraints excluded: chain k residue 75 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 787 optimal weight: 0.3980 chunk 706 optimal weight: 6.9990 chunk 391 optimal weight: 5.9990 chunk 241 optimal weight: 3.9990 chunk 476 optimal weight: 0.9990 chunk 377 optimal weight: 0.9990 chunk 730 optimal weight: 1.9990 chunk 282 optimal weight: 8.9990 chunk 444 optimal weight: 0.9990 chunk 543 optimal weight: 3.9990 chunk 846 optimal weight: 4.9990 overall best weight: 1.0788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 290 ASN A 472 ASN A 479 GLN B 290 ASN D 32 GLN F 506 ASN ** I 358 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 134 ASN J 183 GLN J 423 ASN N 30 GLN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 65 HIS X 367 GLN Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Z 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** b 52 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN ** i 162 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.0892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 74475 Z= 0.244 Angle : 0.595 11.946 101224 Z= 0.307 Chirality : 0.042 0.186 11172 Planarity : 0.005 0.065 13313 Dihedral : 4.707 49.013 10246 Min Nonbonded Distance : 2.263 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.76 % Allowed : 6.94 % Favored : 92.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: -0.05 (0.09), residues: 9336 helix: 1.58 (0.09), residues: 3614 sheet: -0.86 (0.13), residues: 1557 loop : -1.14 (0.09), residues: 4165 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 470 HIS 0.008 0.001 HIS d 52 PHE 0.023 0.001 PHE a 48 TYR 0.034 0.001 TYR W 177 ARG 0.007 0.000 ARG X 6 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 620 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 563 time to evaluate : 6.607 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 275 MET cc_start: 0.7217 (mmm) cc_final: 0.7012 (mmm) REVERT: F 357 PHE cc_start: 0.6868 (t80) cc_final: 0.6655 (t80) REVERT: Q 111 MET cc_start: 0.8630 (ttm) cc_final: 0.8300 (ttp) REVERT: W 113 GLN cc_start: 0.6104 (mm-40) cc_final: 0.5858 (mm-40) REVERT: i 45 ARG cc_start: 0.8049 (tpp80) cc_final: 0.7810 (tpp80) outliers start: 57 outliers final: 41 residues processed: 594 average time/residue: 0.7067 time to fit residues: 727.2041 Evaluate side-chains 554 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 513 time to evaluate : 6.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 35 CYS Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 506 ASN Chi-restraints excluded: chain H residue 223 SER Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 65 HIS Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 167 LEU Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain c residue 29 GLN Chi-restraints excluded: chain c residue 72 THR Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 174 ARG Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain v residue 18 THR Chi-restraints excluded: chain y residue 13 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 470 optimal weight: 0.5980 chunk 262 optimal weight: 0.9990 chunk 704 optimal weight: 8.9990 chunk 576 optimal weight: 0.9980 chunk 233 optimal weight: 6.9990 chunk 847 optimal weight: 5.9990 chunk 915 optimal weight: 0.0970 chunk 755 optimal weight: 4.9990 chunk 840 optimal weight: 1.9990 chunk 289 optimal weight: 4.9990 chunk 680 optimal weight: 4.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 358 GLN J 313 GLN N 30 GLN Q 222 GLN ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** W 60 GLN W 65 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** Z 216 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** c 29 GLN i 162 GLN i 194 GLN j 162 GLN ** k 44 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.1142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 74475 Z= 0.216 Angle : 0.559 11.647 101224 Z= 0.286 Chirality : 0.041 0.184 11172 Planarity : 0.004 0.074 13313 Dihedral : 4.496 51.617 10237 Min Nonbonded Distance : 2.307 Molprobity Statistics. All-atom Clashscore : 6.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.01 % Allowed : 9.18 % Favored : 89.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.12 (0.09), residues: 9336 helix: 1.73 (0.09), residues: 3622 sheet: -0.79 (0.13), residues: 1569 loop : -1.05 (0.09), residues: 4145 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 470 HIS 0.006 0.001 HIS b 52 PHE 0.017 0.001 PHE C 521 TYR 0.027 0.001 TYR W 177 ARG 0.006 0.000 ARG E 354 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 628 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 553 time to evaluate : 6.535 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5759 (OUTLIER) cc_final: 0.5474 (mp0) REVERT: L 113 ASP cc_start: 0.7349 (p0) cc_final: 0.7109 (p0) REVERT: S 28 MET cc_start: 0.6956 (ttm) cc_final: 0.6654 (mtp) REVERT: Y 304 MET cc_start: 0.8257 (tmm) cc_final: 0.7997 (tmm) REVERT: i 45 ARG cc_start: 0.8055 (tpp80) cc_final: 0.7826 (tpp80) REVERT: k 144 GLU cc_start: 0.3040 (mp0) cc_final: 0.2807 (mp0) outliers start: 75 outliers final: 46 residues processed: 599 average time/residue: 0.7021 time to fit residues: 732.5155 Evaluate side-chains 557 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 510 time to evaluate : 6.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 291 ASP Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain a residue 47 GLU Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 174 ARG Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain k residue 227 LEU Chi-restraints excluded: chain u residue 35 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 837 optimal weight: 6.9990 chunk 637 optimal weight: 4.9990 chunk 440 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 404 optimal weight: 4.9990 chunk 569 optimal weight: 0.8980 chunk 850 optimal weight: 3.9990 chunk 900 optimal weight: 0.5980 chunk 444 optimal weight: 6.9990 chunk 806 optimal weight: 0.8980 chunk 242 optimal weight: 0.8980 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: J 134 ASN ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** V 47 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** W 113 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS Z 216 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7213 moved from start: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 74475 Z= 0.232 Angle : 0.553 11.493 101224 Z= 0.282 Chirality : 0.041 0.205 11172 Planarity : 0.004 0.076 13313 Dihedral : 4.406 53.501 10229 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.34 % Allowed : 10.30 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.24 (0.09), residues: 9336 helix: 1.81 (0.09), residues: 3626 sheet: -0.70 (0.13), residues: 1549 loop : -0.98 (0.10), residues: 4161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 470 HIS 0.006 0.001 HIS b 52 PHE 0.023 0.001 PHE B 21 TYR 0.026 0.001 TYR c 43 ARG 0.007 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 635 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 100 poor density : 535 time to evaluate : 6.586 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5794 (OUTLIER) cc_final: 0.5497 (mp0) REVERT: D 53 VAL cc_start: 0.8225 (OUTLIER) cc_final: 0.8002 (p) REVERT: E 257 PHE cc_start: 0.5498 (OUTLIER) cc_final: 0.5225 (t80) REVERT: E 279 MET cc_start: 0.5993 (mmt) cc_final: 0.5747 (mmt) REVERT: G 72 VAL cc_start: 0.8742 (OUTLIER) cc_final: 0.8481 (m) REVERT: Y 304 MET cc_start: 0.8278 (tmm) cc_final: 0.8025 (tmm) REVERT: i 45 ARG cc_start: 0.8041 (tpp80) cc_final: 0.7833 (tpp80) REVERT: k 144 GLU cc_start: 0.2836 (mp0) cc_final: 0.2289 (mp0) REVERT: u 40 MET cc_start: 0.6484 (tpp) cc_final: 0.6265 (tpp) REVERT: u 62 GLU cc_start: 0.7691 (OUTLIER) cc_final: 0.6628 (mp0) outliers start: 100 outliers final: 61 residues processed: 606 average time/residue: 0.7399 time to fit residues: 789.2609 Evaluate side-chains 565 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 499 time to evaluate : 6.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 118 LEU Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 605 ASP Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain P residue 111 MET Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 291 ASP Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain a residue 19 MET Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain u residue 62 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 750 optimal weight: 3.9990 chunk 511 optimal weight: 9.9990 chunk 13 optimal weight: 1.9990 chunk 670 optimal weight: 0.4980 chunk 371 optimal weight: 2.9990 chunk 768 optimal weight: 2.9990 chunk 622 optimal weight: 3.9990 chunk 1 optimal weight: 4.9990 chunk 460 optimal weight: 2.9990 chunk 808 optimal weight: 0.0770 chunk 227 optimal weight: 0.5980 overall best weight: 1.2342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 26 GLN Q 67 ASN ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 47 ASN ** W 65 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 GLN Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7225 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 74475 Z= 0.256 Angle : 0.559 11.406 101224 Z= 0.285 Chirality : 0.041 0.210 11172 Planarity : 0.004 0.075 13313 Dihedral : 4.415 56.127 10229 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 1.69 % Allowed : 11.18 % Favored : 87.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.30 (0.09), residues: 9336 helix: 1.85 (0.09), residues: 3626 sheet: -0.70 (0.13), residues: 1577 loop : -0.92 (0.10), residues: 4133 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP J 470 HIS 0.015 0.001 HIS W 65 PHE 0.024 0.001 PHE B 21 TYR 0.023 0.001 TYR U 25 ARG 0.010 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 659 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 126 poor density : 533 time to evaluate : 6.532 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5898 (OUTLIER) cc_final: 0.5605 (mp0) REVERT: D 53 VAL cc_start: 0.8254 (OUTLIER) cc_final: 0.8028 (p) REVERT: E 257 PHE cc_start: 0.5514 (OUTLIER) cc_final: 0.5269 (t80) REVERT: E 271 MET cc_start: 0.6139 (mmm) cc_final: 0.4931 (mmm) REVERT: G 72 VAL cc_start: 0.8705 (OUTLIER) cc_final: 0.8455 (m) REVERT: H 348 PHE cc_start: 0.7543 (t80) cc_final: 0.7324 (t80) REVERT: Y 304 MET cc_start: 0.8280 (tmm) cc_final: 0.8032 (tmm) REVERT: i 73 ILE cc_start: 0.9225 (OUTLIER) cc_final: 0.8893 (pt) REVERT: j 68 MET cc_start: 0.8359 (tpp) cc_final: 0.8054 (mmt) REVERT: k 144 GLU cc_start: 0.2945 (mp0) cc_final: 0.2567 (mp0) REVERT: u 62 GLU cc_start: 0.7685 (OUTLIER) cc_final: 0.6627 (mp0) outliers start: 126 outliers final: 79 residues processed: 626 average time/residue: 0.6714 time to fit residues: 738.1080 Evaluate side-chains 588 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 85 poor density : 503 time to evaluate : 6.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 448 THR Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 257 PHE Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 303 optimal weight: 2.9990 chunk 811 optimal weight: 0.5980 chunk 178 optimal weight: 0.8980 chunk 528 optimal weight: 4.9990 chunk 222 optimal weight: 4.9990 chunk 901 optimal weight: 2.9990 chunk 748 optimal weight: 0.9990 chunk 417 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 chunk 298 optimal weight: 0.7980 chunk 473 optimal weight: 3.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 329 GLN H 94 ASN ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 54 HIS ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 113 GLN Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.1535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 74475 Z= 0.259 Angle : 0.564 11.331 101224 Z= 0.287 Chirality : 0.041 0.208 11172 Planarity : 0.004 0.075 13313 Dihedral : 4.379 56.980 10227 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 1.74 % Allowed : 12.28 % Favored : 85.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.31 (0.09), residues: 9336 helix: 1.86 (0.09), residues: 3628 sheet: -0.69 (0.13), residues: 1561 loop : -0.91 (0.10), residues: 4147 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP J 103 HIS 0.006 0.001 HIS b 52 PHE 0.024 0.001 PHE B 21 TYR 0.021 0.001 TYR U 25 ARG 0.007 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 651 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 521 time to evaluate : 6.565 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 716 MET cc_start: 0.8103 (mtt) cc_final: 0.7467 (mtm) REVERT: C 527 GLU cc_start: 0.5910 (OUTLIER) cc_final: 0.5604 (mp0) REVERT: D 53 VAL cc_start: 0.8273 (OUTLIER) cc_final: 0.8037 (p) REVERT: G 72 VAL cc_start: 0.8699 (OUTLIER) cc_final: 0.8456 (m) REVERT: H 348 PHE cc_start: 0.7521 (t80) cc_final: 0.7314 (t80) REVERT: I 24 LEU cc_start: 0.8257 (OUTLIER) cc_final: 0.7937 (mp) REVERT: K 424 VAL cc_start: 0.7236 (m) cc_final: 0.7025 (m) REVERT: W 48 CYS cc_start: 0.5413 (m) cc_final: 0.5045 (m) REVERT: Y 304 MET cc_start: 0.8311 (tmm) cc_final: 0.8057 (tmm) REVERT: i 73 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8865 (pt) REVERT: j 73 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8822 (pt) REVERT: k 144 GLU cc_start: 0.3103 (mp0) cc_final: 0.2499 (mp0) REVERT: u 24 MET cc_start: 0.7373 (mtm) cc_final: 0.7166 (mtp) REVERT: u 62 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.6647 (mp0) outliers start: 130 outliers final: 90 residues processed: 621 average time/residue: 0.6667 time to fit residues: 730.1070 Evaluate side-chains 598 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 97 poor density : 501 time to evaluate : 6.583 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain j residue 73 ILE Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 869 optimal weight: 5.9990 chunk 101 optimal weight: 3.9990 chunk 513 optimal weight: 1.9990 chunk 658 optimal weight: 1.9990 chunk 510 optimal weight: 5.9990 chunk 759 optimal weight: 0.9990 chunk 503 optimal weight: 1.9990 chunk 898 optimal weight: 0.7980 chunk 562 optimal weight: 2.9990 chunk 547 optimal weight: 2.9990 chunk 414 optimal weight: 0.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 329 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** d 57 HIS u 64 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 74475 Z= 0.275 Angle : 0.574 11.299 101224 Z= 0.292 Chirality : 0.042 0.214 11172 Planarity : 0.004 0.074 13313 Dihedral : 4.413 58.041 10227 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 6.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.86 % Allowed : 12.83 % Favored : 85.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.32 (0.09), residues: 9336 helix: 1.86 (0.09), residues: 3628 sheet: -0.69 (0.13), residues: 1565 loop : -0.91 (0.10), residues: 4143 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP J 103 HIS 0.006 0.001 HIS b 52 PHE 0.022 0.002 PHE B 21 TYR 0.025 0.001 TYR c 43 ARG 0.006 0.000 ARG E 272 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 655 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 139 poor density : 516 time to evaluate : 6.711 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 716 MET cc_start: 0.8140 (mtt) cc_final: 0.7807 (mtt) REVERT: C 527 GLU cc_start: 0.5885 (OUTLIER) cc_final: 0.5592 (mp0) REVERT: D 53 VAL cc_start: 0.8292 (OUTLIER) cc_final: 0.8060 (p) REVERT: E 279 MET cc_start: 0.6287 (mmp) cc_final: 0.5524 (mmt) REVERT: G 72 VAL cc_start: 0.8692 (OUTLIER) cc_final: 0.8456 (m) REVERT: I 24 LEU cc_start: 0.8251 (OUTLIER) cc_final: 0.7943 (mp) REVERT: J 185 TRP cc_start: 0.9297 (OUTLIER) cc_final: 0.8834 (t-100) REVERT: W 48 CYS cc_start: 0.5462 (m) cc_final: 0.5110 (m) REVERT: Y 304 MET cc_start: 0.8293 (tmm) cc_final: 0.8019 (tmm) REVERT: i 73 ILE cc_start: 0.9207 (OUTLIER) cc_final: 0.8864 (pt) REVERT: j 73 ILE cc_start: 0.9142 (OUTLIER) cc_final: 0.8835 (pt) REVERT: k 144 GLU cc_start: 0.3318 (mp0) cc_final: 0.2307 (mp0) REVERT: s 367 ARG cc_start: 0.6110 (OUTLIER) cc_final: 0.5756 (ptt180) REVERT: u 24 MET cc_start: 0.7379 (mtm) cc_final: 0.7172 (mtp) REVERT: u 62 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.6609 (mp0) REVERT: v 62 GLU cc_start: 0.7261 (pp20) cc_final: 0.6949 (pp20) outliers start: 139 outliers final: 99 residues processed: 625 average time/residue: 0.6699 time to fit residues: 737.8757 Evaluate side-chains 609 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 108 poor density : 501 time to evaluate : 6.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 477 ILE Chi-restraints excluded: chain A residue 673 TRP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 345 GLU Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 177 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 271 MET Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain F residue 368 SER Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain K residue 418 CYS Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 112 LEU Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 34 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 291 ASP Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 65 VAL Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 73 ILE Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 367 ARG Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 555 optimal weight: 2.9990 chunk 358 optimal weight: 0.7980 chunk 536 optimal weight: 0.7980 chunk 270 optimal weight: 3.9990 chunk 176 optimal weight: 2.9990 chunk 174 optimal weight: 6.9990 chunk 571 optimal weight: 0.9990 chunk 612 optimal weight: 3.9990 chunk 444 optimal weight: 6.9990 chunk 83 optimal weight: 0.0670 chunk 706 optimal weight: 10.0000 overall best weight: 1.1322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 30 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 183 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** W 178 ASN X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Z 158 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 57 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 74475 Z= 0.240 Angle : 0.563 11.633 101224 Z= 0.286 Chirality : 0.041 0.209 11172 Planarity : 0.004 0.075 13313 Dihedral : 4.356 58.543 10227 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.48 % Favored : 96.52 % Rotamer: Outliers : 1.74 % Allowed : 13.37 % Favored : 84.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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 (0.09), residues: 9336 helix: 1.92 (0.09), residues: 3630 sheet: -0.64 (0.13), residues: 1551 loop : -0.89 (0.10), residues: 4155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP J 103 HIS 0.006 0.001 HIS b 52 PHE 0.018 0.001 PHE B 21 TYR 0.028 0.001 TYR c 43 ARG 0.009 0.000 ARG i 160 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 646 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 130 poor density : 516 time to evaluate : 6.589 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5854 (OUTLIER) cc_final: 0.5569 (mp0) REVERT: D 53 VAL cc_start: 0.8305 (OUTLIER) cc_final: 0.8072 (p) REVERT: E 279 MET cc_start: 0.6245 (mmp) cc_final: 0.5509 (mmt) REVERT: G 72 VAL cc_start: 0.8687 (OUTLIER) cc_final: 0.8458 (m) REVERT: I 24 LEU cc_start: 0.8236 (OUTLIER) cc_final: 0.7920 (mp) REVERT: J 185 TRP cc_start: 0.9276 (OUTLIER) cc_final: 0.8926 (t-100) REVERT: L 336 MET cc_start: 0.6468 (mmt) cc_final: 0.6215 (mmt) REVERT: L 407 TRP cc_start: 0.8728 (OUTLIER) cc_final: 0.8142 (m100) REVERT: W 48 CYS cc_start: 0.5223 (m) cc_final: 0.4889 (m) REVERT: Y 304 MET cc_start: 0.8324 (tmm) cc_final: 0.8061 (tmm) REVERT: i 73 ILE cc_start: 0.9202 (OUTLIER) cc_final: 0.8858 (pt) REVERT: j 73 ILE cc_start: 0.9140 (OUTLIER) cc_final: 0.8845 (pt) REVERT: k 144 GLU cc_start: 0.3333 (mp0) cc_final: 0.2354 (mp0) REVERT: s 367 ARG cc_start: 0.5973 (OUTLIER) cc_final: 0.5639 (ptt180) REVERT: u 24 MET cc_start: 0.7358 (mtm) cc_final: 0.7144 (mtp) REVERT: u 62 GLU cc_start: 0.7619 (OUTLIER) cc_final: 0.6551 (mp0) outliers start: 130 outliers final: 99 residues processed: 618 average time/residue: 0.6746 time to fit residues: 736.7080 Evaluate side-chains 615 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 109 poor density : 506 time to evaluate : 6.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 361 ASP Chi-restraints excluded: chain B residue 540 GLU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 249 MET Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 158 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 271 MET Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain F residue 343 LEU Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 437 GLU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain H residue 204 VAL Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 280 SER Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 193 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 407 TRP Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 444 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 8 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 87 MET Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 4 GLU Chi-restraints excluded: chain V residue 6 ILE Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 86 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 291 ASP Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 48 PHE Chi-restraints excluded: chain d residue 31 LEU Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain i residue 158 THR Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 73 ILE Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 367 ARG Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain u residue 62 GLU Chi-restraints excluded: chain z residue 37 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 817 optimal weight: 0.5980 chunk 860 optimal weight: 4.9990 chunk 785 optimal weight: 0.7980 chunk 837 optimal weight: 6.9990 chunk 503 optimal weight: 0.0770 chunk 364 optimal weight: 0.9990 chunk 657 optimal weight: 8.9990 chunk 256 optimal weight: 6.9990 chunk 756 optimal weight: 2.9990 chunk 791 optimal weight: 4.9990 chunk 834 optimal weight: 0.6980 overall best weight: 0.6340 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN F 285 GLN S 54 HIS ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Y 285 ASN Z 158 HIS ** Z 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** c 29 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7192 moved from start: 0.1782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 74475 Z= 0.179 Angle : 0.545 12.469 101224 Z= 0.277 Chirality : 0.040 0.212 11172 Planarity : 0.004 0.076 13313 Dihedral : 4.219 57.865 10227 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.39 % Allowed : 14.05 % Favored : 84.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.09), residues: 9336 helix: 2.03 (0.09), residues: 3636 sheet: -0.54 (0.13), residues: 1541 loop : -0.82 (0.10), residues: 4159 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP J 103 HIS 0.007 0.001 HIS b 52 PHE 0.016 0.001 PHE H 348 TYR 0.052 0.001 TYR c 43 ARG 0.008 0.000 ARG E 272 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 642 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 104 poor density : 538 time to evaluate : 6.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 527 GLU cc_start: 0.5820 (OUTLIER) cc_final: 0.5468 (mp0) REVERT: E 279 MET cc_start: 0.6304 (mmp) cc_final: 0.5585 (mmt) REVERT: G 72 VAL cc_start: 0.8680 (OUTLIER) cc_final: 0.8468 (m) REVERT: I 24 LEU cc_start: 0.8205 (OUTLIER) cc_final: 0.7884 (mp) REVERT: K 424 VAL cc_start: 0.7176 (m) cc_final: 0.6958 (m) REVERT: L 407 TRP cc_start: 0.8718 (OUTLIER) cc_final: 0.7936 (m100) REVERT: W 48 CYS cc_start: 0.5173 (m) cc_final: 0.4852 (m) REVERT: Y 304 MET cc_start: 0.8326 (tmm) cc_final: 0.8056 (tmm) REVERT: i 73 ILE cc_start: 0.9184 (OUTLIER) cc_final: 0.8831 (pt) REVERT: j 68 MET cc_start: 0.8311 (tpp) cc_final: 0.8075 (mmt) REVERT: j 73 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8815 (pt) REVERT: k 144 GLU cc_start: 0.3520 (mp0) cc_final: 0.2808 (mp0) REVERT: s 367 ARG cc_start: 0.5729 (OUTLIER) cc_final: 0.5446 (ptt180) REVERT: u 24 MET cc_start: 0.7329 (mtm) cc_final: 0.7109 (mtp) REVERT: u 40 MET cc_start: 0.6519 (tpp) cc_final: 0.6240 (tpp) REVERT: u 62 GLU cc_start: 0.7589 (OUTLIER) cc_final: 0.6542 (mp0) REVERT: v 62 GLU cc_start: 0.7168 (pp20) cc_final: 0.6952 (pp20) REVERT: v 64 GLN cc_start: 0.7403 (tt0) cc_final: 0.7186 (tt0) outliers start: 104 outliers final: 76 residues processed: 619 average time/residue: 0.6912 time to fit residues: 751.8089 Evaluate side-chains 590 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 84 poor density : 506 time to evaluate : 6.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 450 LEU Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 437 GLU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 158 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 116 LEU Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 407 TRP Chi-restraints excluded: chain L residue 444 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 147 ILE Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 60 LEU Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Y residue 285 ASN Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 342 THR Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain j residue 73 ILE Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 367 ARG Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain u residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 549 optimal weight: 2.9990 chunk 885 optimal weight: 3.9990 chunk 540 optimal weight: 3.9990 chunk 419 optimal weight: 0.3980 chunk 615 optimal weight: 3.9990 chunk 928 optimal weight: 1.9990 chunk 854 optimal weight: 2.9990 chunk 739 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 571 optimal weight: 3.9990 chunk 453 optimal weight: 0.0980 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 ASN J 423 ASN ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 372 HIS Y 158 HIS ** Y 236 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** Y 285 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** c 20 GLN d 29 GLN u 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 74475 Z= 0.305 Angle : 0.593 12.045 101224 Z= 0.301 Chirality : 0.042 0.196 11172 Planarity : 0.004 0.074 13313 Dihedral : 4.353 58.793 10227 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.47 % Favored : 96.53 % Rotamer: Outliers : 1.43 % Allowed : 14.14 % Favored : 84.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.01 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.09), residues: 9336 helix: 1.94 (0.09), residues: 3633 sheet: -0.61 (0.13), residues: 1565 loop : -0.85 (0.10), residues: 4138 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP J 103 HIS 0.008 0.001 HIS b 52 PHE 0.035 0.002 PHE B 550 TYR 0.069 0.002 TYR a 34 ARG 0.011 0.000 ARG E 272 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 18672 Ramachandran restraints generated. 9336 Oldfield, 0 Emsley, 9336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 613 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 107 poor density : 506 time to evaluate : 6.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 716 MET cc_start: 0.8172 (mtt) cc_final: 0.7827 (mtt) REVERT: C 527 GLU cc_start: 0.5831 (OUTLIER) cc_final: 0.5483 (mp0) REVERT: E 279 MET cc_start: 0.6246 (mmp) cc_final: 0.5969 (mmt) REVERT: G 72 VAL cc_start: 0.8696 (OUTLIER) cc_final: 0.8476 (m) REVERT: I 24 LEU cc_start: 0.8238 (OUTLIER) cc_final: 0.7915 (mp) REVERT: J 185 TRP cc_start: 0.9278 (OUTLIER) cc_final: 0.8955 (t-100) REVERT: L 407 TRP cc_start: 0.8660 (OUTLIER) cc_final: 0.8192 (m100) REVERT: W 48 CYS cc_start: 0.5255 (m) cc_final: 0.4958 (m) REVERT: Y 304 MET cc_start: 0.8336 (tmm) cc_final: 0.8060 (tmm) REVERT: i 73 ILE cc_start: 0.9201 (OUTLIER) cc_final: 0.8863 (pt) REVERT: j 73 ILE cc_start: 0.9146 (OUTLIER) cc_final: 0.8858 (pt) REVERT: k 144 GLU cc_start: 0.3463 (mp0) cc_final: 0.2805 (mp0) REVERT: s 367 ARG cc_start: 0.5966 (OUTLIER) cc_final: 0.5612 (ptt180) REVERT: u 24 MET cc_start: 0.7365 (mtm) cc_final: 0.7153 (mtp) REVERT: u 40 MET cc_start: 0.6527 (tpp) cc_final: 0.6198 (tpp) REVERT: u 62 GLU cc_start: 0.7627 (OUTLIER) cc_final: 0.6558 (mp0) outliers start: 107 outliers final: 84 residues processed: 590 average time/residue: 0.6699 time to fit residues: 695.5910 Evaluate side-chains 591 residues out of total 7562 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 93 poor density : 498 time to evaluate : 6.470 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 CYS Chi-restraints excluded: chain A residue 176 SER Chi-restraints excluded: chain A residue 199 LEU Chi-restraints excluded: chain A residue 344 VAL Chi-restraints excluded: chain A residue 362 LEU Chi-restraints excluded: chain A residue 445 THR Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 740 ILE Chi-restraints excluded: chain B residue 76 VAL Chi-restraints excluded: chain B residue 82 ILE Chi-restraints excluded: chain B residue 199 LEU Chi-restraints excluded: chain B residue 708 LEU Chi-restraints excluded: chain B residue 709 THR Chi-restraints excluded: chain B residue 740 ILE Chi-restraints excluded: chain B residue 800 ILE Chi-restraints excluded: chain C residue 502 HIS Chi-restraints excluded: chain C residue 527 GLU Chi-restraints excluded: chain C residue 587 VAL Chi-restraints excluded: chain D residue 53 VAL Chi-restraints excluded: chain D residue 573 LEU Chi-restraints excluded: chain E residue 343 LEU Chi-restraints excluded: chain E residue 368 SER Chi-restraints excluded: chain F residue 158 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 278 PHE Chi-restraints excluded: chain G residue 70 ILE Chi-restraints excluded: chain G residue 72 VAL Chi-restraints excluded: chain G residue 448 LEU Chi-restraints excluded: chain H residue 93 ILE Chi-restraints excluded: chain I residue 24 LEU Chi-restraints excluded: chain I residue 280 VAL Chi-restraints excluded: chain I residue 290 VAL Chi-restraints excluded: chain I residue 406 VAL Chi-restraints excluded: chain I residue 462 CYS Chi-restraints excluded: chain I residue 495 VAL Chi-restraints excluded: chain J residue 185 TRP Chi-restraints excluded: chain J residue 290 VAL Chi-restraints excluded: chain J residue 495 VAL Chi-restraints excluded: chain K residue 89 LEU Chi-restraints excluded: chain K residue 403 MET Chi-restraints excluded: chain K residue 405 VAL Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 405 VAL Chi-restraints excluded: chain L residue 407 TRP Chi-restraints excluded: chain L residue 418 CYS Chi-restraints excluded: chain L residue 444 CYS Chi-restraints excluded: chain M residue 10 THR Chi-restraints excluded: chain O residue 7 ASN Chi-restraints excluded: chain O residue 147 ILE Chi-restraints excluded: chain O residue 166 VAL Chi-restraints excluded: chain P residue 112 LEU Chi-restraints excluded: chain Q residue 2 VAL Chi-restraints excluded: chain Q residue 180 VAL Chi-restraints excluded: chain R residue 144 VAL Chi-restraints excluded: chain R residue 185 LEU Chi-restraints excluded: chain S residue 52 MET Chi-restraints excluded: chain S residue 152 THR Chi-restraints excluded: chain T residue 165 MET Chi-restraints excluded: chain V residue 3 VAL Chi-restraints excluded: chain V residue 13 VAL Chi-restraints excluded: chain V residue 35 THR Chi-restraints excluded: chain W residue 80 ASP Chi-restraints excluded: chain W residue 176 ILE Chi-restraints excluded: chain X residue 7 ILE Chi-restraints excluded: chain X residue 32 THR Chi-restraints excluded: chain X residue 212 VAL Chi-restraints excluded: chain X residue 307 VAL Chi-restraints excluded: chain X residue 370 PHE Chi-restraints excluded: chain X residue 371 LYS Chi-restraints excluded: chain Y residue 142 GLU Chi-restraints excluded: chain Y residue 178 VAL Chi-restraints excluded: chain Y residue 180 VAL Chi-restraints excluded: chain Z residue 145 LEU Chi-restraints excluded: chain Z residue 162 VAL Chi-restraints excluded: chain Z residue 180 VAL Chi-restraints excluded: chain Z residue 220 VAL Chi-restraints excluded: chain Z residue 342 THR Chi-restraints excluded: chain a residue 9 VAL Chi-restraints excluded: chain b residue 36 ILE Chi-restraints excluded: chain b residue 48 PHE Chi-restraints excluded: chain d residue 55 THR Chi-restraints excluded: chain i residue 73 ILE Chi-restraints excluded: chain i residue 91 MET Chi-restraints excluded: chain j residue 65 VAL Chi-restraints excluded: chain j residue 73 ILE Chi-restraints excluded: chain k residue 75 ILE Chi-restraints excluded: chain k residue 92 ILE Chi-restraints excluded: chain k residue 162 ASN Chi-restraints excluded: chain k residue 166 LYS Chi-restraints excluded: chain k residue 225 ASP Chi-restraints excluded: chain s residue 367 ARG Chi-restraints excluded: chain u residue 35 GLU Chi-restraints excluded: chain u residue 62 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 932 random chunks: chunk 587 optimal weight: 0.0970 chunk 787 optimal weight: 0.0770 chunk 226 optimal weight: 2.9990 chunk 681 optimal weight: 3.9990 chunk 109 optimal weight: 40.0000 chunk 205 optimal weight: 2.9990 chunk 740 optimal weight: 3.9990 chunk 309 optimal weight: 0.1980 chunk 760 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 136 optimal weight: 0.9980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 49 HIS ** S 134 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 141 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 191 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** X 372 HIS Y 158 HIS Y 285 ASN Z 158 HIS Z 236 HIS ** b 53 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** u 64 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3592 r_free = 0.3592 target = 0.072711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.059329 restraints weight = 250514.734| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.76 r_work: 0.3137 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3148 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.53 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3148 r_free = 0.3148 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 1 | |-----------------------------------------------------------------------------| r_final: 0.3148 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8218 moved from start: 0.1933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.051 74475 Z= 0.163 Angle : 0.542 11.787 101224 Z= 0.274 Chirality : 0.040 0.230 11172 Planarity : 0.004 0.076 13313 Dihedral : 4.117 57.029 10227 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 1.02 % Allowed : 14.48 % Favored : 84.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.96 % 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: 0.65 (0.09), residues: 9336 helix: 2.14 (0.09), residues: 3630 sheet: -0.45 (0.13), residues: 1527 loop : -0.76 (0.10), residues: 4179 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.001 TRP J 103 HIS 0.005 0.001 HIS b 52 PHE 0.016 0.001 PHE D 521 TYR 0.042 0.001 TYR a 34 ARG 0.009 0.000 ARG E 187 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 16779.79 seconds wall clock time: 291 minutes 4.42 seconds (17464.42 seconds total)