Starting phenix.real_space_refine on Fri Sep 27 21:42:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brt_44843/09_2024/9brt_44843.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brt_44843/09_2024/9brt_44843.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brt_44843/09_2024/9brt_44843.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brt_44843/09_2024/9brt_44843.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brt_44843/09_2024/9brt_44843.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9brt_44843/09_2024/9brt_44843.cif" } resolution = 4.3 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= 0.002 sd= 0.062 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: 4 Type Number sf(0) Gaussians S 398 5.16 5 C 42878 2.51 5 N 11309 2.21 5 O 12345 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 89 residue(s): 0.16s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 66930 Number of models: 1 Model: "" Number of chains: 33 Chain: "8" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "R" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "0" Number of atoms: 4551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4551 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 30, 'TRANS': 554} Chain breaks: 3 Chain: "1" Number of atoms: 4627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 596, 4627 Classifications: {'peptide': 596} Link IDs: {'PTRANS': 30, 'TRANS': 565} Chain breaks: 1 Chain: "2" Number of atoms: 4647 Number of conformers: 1 Conformer: "" Number of residues, atoms: 599, 4647 Classifications: {'peptide': 599} Link IDs: {'PTRANS': 30, 'TRANS': 568} Chain: "3" Number of atoms: 3584 Number of conformers: 1 Conformer: "" Number of residues, atoms: 458, 3584 Classifications: {'peptide': 458} Link IDs: {'PTRANS': 27, 'TRANS': 430} Chain breaks: 1 Chain: "4" Number of atoms: 3617 Number of conformers: 1 Conformer: "" Number of residues, atoms: 462, 3617 Classifications: {'peptide': 462} Link IDs: {'PTRANS': 27, 'TRANS': 434} Chain breaks: 1 Chain: "5" Number of atoms: 3575 Number of conformers: 1 Conformer: "" Number of residues, atoms: 457, 3575 Classifications: {'peptide': 457} Link IDs: {'PTRANS': 27, 'TRANS': 429} Chain breaks: 1 Chain: "6" Number of atoms: 2925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 360, 2925 Classifications: {'peptide': 360} Link IDs: {'PTRANS': 9, 'TRANS': 350} Chain breaks: 1 Chain: "7" Number of atoms: 1676 Number of conformers: 1 Conformer: "" Number of residues, atoms: 208, 1676 Classifications: {'peptide': 208} Link IDs: {'PTRANS': 3, 'TRANS': 204} Chain: "U" Number of atoms: 3507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 427, 3507 Classifications: {'peptide': 427} Link IDs: {'PTRANS': 8, 'TRANS': 418} Chain breaks: 1 Chain: "X" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 875 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 4, 'TRANS': 105} Chain: "a" Number of atoms: 6105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 750, 6105 Classifications: {'peptide': 750} Link IDs: {'PTRANS': 31, 'TRANS': 718} Chain breaks: 2 Chain: "b" Number of atoms: 1503 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1503 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 5, 'TRANS': 197} Chain: "d" Number of atoms: 2833 Number of conformers: 1 Conformer: "" Number of residues, atoms: 350, 2833 Classifications: {'peptide': 350} Link IDs: {'PTRANS': 13, 'TRANS': 336} Chain: "g" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "h" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "i" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "j" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "k" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "l" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "m" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "n" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "o" Number of atoms: 1068 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 1068 Classifications: {'peptide': 150} Link IDs: {'PTRANS': 4, 'TRANS': 145} Chain: "p" Number of atoms: 433 Number of conformers: 1 Conformer: "" Number of residues, atoms: 52, 433 Classifications: {'peptide': 52} Link IDs: {'PTRANS': 1, 'TRANS': 50} Chain: "9" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "T" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "Q" Number of atoms: 1823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1823 Classifications: {'peptide': 225} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 219} Chain: "V" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 925 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 2, 'TRANS': 111} Chain: "c" Number of atoms: 1642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1642 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 8, 'TRANS': 194} Chain: "f" Number of atoms: 666 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 666 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 3, 'TRANS': 82} Chain: "s" Number of atoms: 1671 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1671 Classifications: {'peptide': 211} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 203} Chain: "e" Number of atoms: 637 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 637 Classifications: {'peptide': 79} Link IDs: {'PTRANS': 6, 'TRANS': 72} Time building chain proxies: 28.11, per 1000 atoms: 0.42 Number of scatterers: 66930 At special positions: 0 Unit cell: (158.927, 214.496, 298.96, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 398 16.00 O 12345 8.00 N 11309 7.00 C 42878 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 13.08 Conformation dependent library (CDL) restraints added in 6.5 seconds 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15838 Finding SS restraints... Secondary structure from input PDB file: 315 helices and 45 sheets defined 62.1% alpha, 6.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 5.03 Creating SS restraints... Processing helix chain '8' and resid 3 through 107 removed outlier: 3.830A pdb=" N LYS 8 52 " --> pdb=" O THR 8 48 " (cutoff:3.500A) removed outlier: 3.883A pdb=" N LYS 8 107 " --> pdb=" O SER 8 103 " (cutoff:3.500A) Processing helix chain '8' and resid 108 through 128 Processing helix chain '8' and resid 137 through 139 No H-bonds generated for 'chain '8' and resid 137 through 139' Processing helix chain '8' and resid 140 through 160 removed outlier: 3.760A pdb=" N ALA 8 146 " --> pdb=" O PRO 8 142 " (cutoff:3.500A) Proline residue: 8 153 - end of helix Processing helix chain '8' and resid 196 through 217 Proline residue: 8 209 - end of helix Processing helix chain 'R' and resid 4 through 103 removed outlier: 3.988A pdb=" N ILE R 8 " --> pdb=" O GLN R 4 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN R 91 " --> pdb=" O SER R 87 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N ARG R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain '0' and resid 105 through 114 Processing helix chain '0' and resid 231 through 237 Processing helix chain '0' and resid 257 through 267 removed outlier: 3.765A pdb=" N GLN 0 261 " --> pdb=" O THR 0 257 " (cutoff:3.500A) Processing helix chain '0' and resid 280 through 294 Proline residue: 0 292 - end of helix Processing helix chain '0' and resid 304 through 307 Processing helix chain '0' and resid 319 through 340 removed outlier: 3.607A pdb=" N ARG 0 323 " --> pdb=" O PRO 0 319 " (cutoff:3.500A) removed outlier: 4.321A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 4.549A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 351 through 366 Processing helix chain '0' and resid 370 through 374 Processing helix chain '0' and resid 375 through 376 No H-bonds generated for 'chain '0' and resid 375 through 376' Processing helix chain '0' and resid 377 through 386 Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 461 through 469 removed outlier: 3.874A pdb=" N LYS 0 467 " --> pdb=" O GLU 0 463 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N HIS 0 468 " --> pdb=" O TYR 0 464 " (cutoff:3.500A) Processing helix chain '0' and resid 471 through 495 removed outlier: 4.015A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N THR 0 477 " --> pdb=" O VAL 0 473 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N LYS 0 480 " --> pdb=" O ARG 0 476 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N GLU 0 491 " --> pdb=" O GLU 0 487 " (cutoff:3.500A) removed outlier: 4.593A pdb=" N ILE 0 492 " --> pdb=" O ASP 0 488 " (cutoff:3.500A) Processing helix chain '0' and resid 502 through 519 removed outlier: 3.534A pdb=" N LYS 0 506 " --> pdb=" O ALA 0 502 " (cutoff:3.500A) Processing helix chain '0' and resid 526 through 531 removed outlier: 4.336A pdb=" N PHE 0 531 " --> pdb=" O PRO 0 527 " (cutoff:3.500A) Processing helix chain '0' and resid 533 through 550 removed outlier: 4.094A pdb=" N TYR 0 548 " --> pdb=" O MET 0 544 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N MET 0 550 " --> pdb=" O SER 0 546 " (cutoff:3.500A) Processing helix chain '0' and resid 566 through 574 Processing helix chain '0' and resid 574 through 584 Processing helix chain '0' and resid 585 through 587 No H-bonds generated for 'chain '0' and resid 585 through 587' Processing helix chain '0' and resid 593 through 615 Processing helix chain '1' and resid 106 through 111 removed outlier: 3.772A pdb=" N SER 1 111 " --> pdb=" O SER 1 107 " (cutoff:3.500A) Processing helix chain '1' and resid 195 through 198 Processing helix chain '1' and resid 231 through 237 removed outlier: 3.581A pdb=" N ASP 1 235 " --> pdb=" O GLN 1 231 " (cutoff:3.500A) Processing helix chain '1' and resid 255 through 266 removed outlier: 3.552A pdb=" N ILE 1 259 " --> pdb=" O GLY 1 255 " (cutoff:3.500A) Processing helix chain '1' and resid 281 through 291 removed outlier: 3.795A pdb=" N VAL 1 287 " --> pdb=" O GLU 1 283 " (cutoff:3.500A) Processing helix chain '1' and resid 292 through 294 No H-bonds generated for 'chain '1' and resid 292 through 294' Processing helix chain '1' and resid 319 through 340 removed outlier: 4.517A pdb=" N ILE 1 327 " --> pdb=" O ARG 1 323 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N TYR 1 328 " --> pdb=" O GLU 1 324 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 365 removed outlier: 3.566A pdb=" N LEU 1 365 " --> pdb=" O ILE 1 361 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 374 removed outlier: 3.655A pdb=" N TYR 1 374 " --> pdb=" O ASP 1 371 " (cutoff:3.500A) Processing helix chain '1' and resid 377 through 388 Processing helix chain '1' and resid 412 through 416 Processing helix chain '1' and resid 419 through 427 Processing helix chain '1' and resid 436 through 442 removed outlier: 3.855A pdb=" N ALA 1 440 " --> pdb=" O ASP 1 436 " (cutoff:3.500A) Processing helix chain '1' and resid 458 through 460 No H-bonds generated for 'chain '1' and resid 458 through 460' Processing helix chain '1' and resid 461 through 469 Processing helix chain '1' and resid 471 through 496 removed outlier: 4.412A pdb=" N LEU 1 475 " --> pdb=" O GLU 1 471 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ARG 1 476 " --> pdb=" O PHE 1 472 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N THR 1 477 " --> pdb=" O VAL 1 473 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 497 through 501 Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 534 through 552 removed outlier: 3.608A pdb=" N VAL 1 538 " --> pdb=" O PHE 1 534 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N ALA 1 551 " --> pdb=" O PHE 1 547 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N ARG 1 552 " --> pdb=" O TYR 1 548 " (cutoff:3.500A) Processing helix chain '1' and resid 567 through 584 removed outlier: 6.922A pdb=" N GLU 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 6.045A pdb=" N ILE 1 577 " --> pdb=" O HIS 1 573 " (cutoff:3.500A) Processing helix chain '1' and resid 593 through 615 Processing helix chain '2' and resid 105 through 114 Processing helix chain '2' and resid 231 through 238 Processing helix chain '2' and resid 255 through 266 Processing helix chain '2' and resid 280 through 291 removed outlier: 4.004A pdb=" N MET 2 284 " --> pdb=" O ARG 2 280 " (cutoff:3.500A) Processing helix chain '2' and resid 321 through 340 removed outlier: 4.103A pdb=" N ALA 2 325 " --> pdb=" O ALA 2 321 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 366 removed outlier: 4.046A pdb=" N TRP 2 354 " --> pdb=" O SER 2 350 " (cutoff:3.500A) Processing helix chain '2' and resid 370 through 374 Processing helix chain '2' and resid 375 through 376 No H-bonds generated for 'chain '2' and resid 375 through 376' Processing helix chain '2' and resid 377 through 387 Processing helix chain '2' and resid 412 through 416 Processing helix chain '2' and resid 419 through 427 removed outlier: 3.689A pdb=" N GLY 2 427 " --> pdb=" O SER 2 423 " (cutoff:3.500A) Processing helix chain '2' and resid 436 through 442 removed outlier: 3.619A pdb=" N ALA 2 440 " --> pdb=" O ASP 2 436 " (cutoff:3.500A) Processing helix chain '2' and resid 457 through 459 No H-bonds generated for 'chain '2' and resid 457 through 459' Processing helix chain '2' and resid 461 through 468 Processing helix chain '2' and resid 469 through 471 No H-bonds generated for 'chain '2' and resid 469 through 471' Processing helix chain '2' and resid 472 through 496 removed outlier: 3.677A pdb=" N ARG 2 476 " --> pdb=" O PHE 2 472 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N THR 2 477 " --> pdb=" O VAL 2 473 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N GLU 2 491 " --> pdb=" O GLU 2 487 " (cutoff:3.500A) removed outlier: 4.547A pdb=" N ILE 2 492 " --> pdb=" O ASP 2 488 " (cutoff:3.500A) Processing helix chain '2' and resid 502 through 519 Processing helix chain '2' and resid 533 through 558 Processing helix chain '2' and resid 566 through 574 Processing helix chain '2' and resid 574 through 584 Processing helix chain '2' and resid 593 through 615 removed outlier: 3.602A pdb=" N LEU 2 615 " --> pdb=" O ALA 2 611 " (cutoff:3.500A) Processing helix chain '3' and resid 124 through 128 removed outlier: 3.605A pdb=" N LEU 3 128 " --> pdb=" O GLU 3 125 " (cutoff:3.500A) Processing helix chain '3' and resid 159 through 161 No H-bonds generated for 'chain '3' and resid 159 through 161' Processing helix chain '3' and resid 198 through 209 Processing helix chain '3' and resid 237 through 251 removed outlier: 3.616A pdb=" N ALA 3 241 " --> pdb=" O ASN 3 237 " (cutoff:3.500A) Processing helix chain '3' and resid 253 through 255 No H-bonds generated for 'chain '3' and resid 253 through 255' Processing helix chain '3' and resid 267 through 272 removed outlier: 3.932A pdb=" N GLU 3 270 " --> pdb=" O PRO 3 267 " (cutoff:3.500A) Processing helix chain '3' and resid 273 through 288 removed outlier: 3.802A pdb=" N THR 3 281 " --> pdb=" O LEU 3 277 " (cutoff:3.500A) Processing helix chain '3' and resid 299 through 315 removed outlier: 4.091A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) Processing helix chain '3' and resid 326 through 336 Processing helix chain '3' and resid 363 through 371 Processing helix chain '3' and resid 380 through 386 removed outlier: 3.660A pdb=" N HIS 3 384 " --> pdb=" O ASP 3 380 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 437 Processing helix chain '3' and resid 440 through 444 removed outlier: 3.529A pdb=" N ALA 3 443 " --> pdb=" O GLY 3 440 " (cutoff:3.500A) Processing helix chain '3' and resid 445 through 462 Processing helix chain '3' and resid 472 through 487 removed outlier: 3.777A pdb=" N ILE 3 486 " --> pdb=" O GLN 3 482 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N PHE 3 487 " --> pdb=" O LEU 3 483 " (cutoff:3.500A) Processing helix chain '3' and resid 488 through 492 removed outlier: 3.585A pdb=" N LEU 3 492 " --> pdb=" O LYS 3 489 " (cutoff:3.500A) Processing helix chain '3' and resid 496 through 504 Processing helix chain '4' and resid 124 through 128 removed outlier: 3.844A pdb=" N LEU 4 128 " --> pdb=" O GLU 4 125 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 161 No H-bonds generated for 'chain '4' and resid 159 through 161' Processing helix chain '4' and resid 174 through 179 Processing helix chain '4' and resid 199 through 209 Processing helix chain '4' and resid 223 through 225 No H-bonds generated for 'chain '4' and resid 223 through 225' Processing helix chain '4' and resid 241 through 251 removed outlier: 3.807A pdb=" N GLU 4 249 " --> pdb=" O LYS 4 245 " (cutoff:3.500A) Processing helix chain '4' and resid 253 through 255 No H-bonds generated for 'chain '4' and resid 253 through 255' Processing helix chain '4' and resid 267 through 287 Proline residue: 4 275 - end of helix Processing helix chain '4' and resid 299 through 315 removed outlier: 4.010A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 Processing helix chain '4' and resid 324 through 325 No H-bonds generated for 'chain '4' and resid 324 through 325' Processing helix chain '4' and resid 326 through 335 Processing helix chain '4' and resid 357 through 360 removed outlier: 3.524A pdb=" N ASP 4 360 " --> pdb=" O PRO 4 357 " (cutoff:3.500A) No H-bonds generated for 'chain '4' and resid 357 through 360' Processing helix chain '4' and resid 363 through 372 Processing helix chain '4' and resid 380 through 386 Processing helix chain '4' and resid 401 through 406 removed outlier: 3.551A pdb=" N ILE 4 406 " --> pdb=" O MET 4 402 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 440 removed outlier: 3.977A pdb=" N VAL 4 438 " --> pdb=" O ALA 4 434 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY 4 440 " --> pdb=" O LYS 4 436 " (cutoff:3.500A) Processing helix chain '4' and resid 441 through 444 Processing helix chain '4' and resid 445 through 462 Processing helix chain '4' and resid 472 through 485 Processing helix chain '4' and resid 486 through 487 No H-bonds generated for 'chain '4' and resid 486 through 487' Processing helix chain '4' and resid 488 through 492 Processing helix chain '4' and resid 496 through 504 Processing helix chain '5' and resid 124 through 128 Processing helix chain '5' and resid 135 through 137 No H-bonds generated for 'chain '5' and resid 135 through 137' Processing helix chain '5' and resid 174 through 179 Processing helix chain '5' and resid 198 through 209 Processing helix chain '5' and resid 237 through 252 removed outlier: 3.540A pdb=" N ALA 5 241 " --> pdb=" O ASN 5 237 " (cutoff:3.500A) Processing helix chain '5' and resid 253 through 255 No H-bonds generated for 'chain '5' and resid 253 through 255' Processing helix chain '5' and resid 269 through 290 removed outlier: 4.194A pdb=" N ILE 5 273 " --> pdb=" O ILE 5 269 " (cutoff:3.500A) Proline residue: 5 275 - end of helix removed outlier: 3.779A pdb=" N ALA 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N GLU 5 290 " --> pdb=" O ALA 5 286 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 314 removed outlier: 4.076A pdb=" N TYR 5 303 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 319 through 323 removed outlier: 3.843A pdb=" N GLY 5 322 " --> pdb=" O GLY 5 319 " (cutoff:3.500A) Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 363 through 373 removed outlier: 3.812A pdb=" N TYR 5 371 " --> pdb=" O ASP 5 367 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N ILE 5 372 " --> pdb=" O LEU 5 368 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N THR 5 373 " --> pdb=" O THR 5 369 " (cutoff:3.500A) Processing helix chain '5' and resid 380 through 386 Processing helix chain '5' and resid 414 through 440 removed outlier: 3.643A pdb=" N VAL 5 418 " --> pdb=" O ASP 5 414 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N VAL 5 438 " --> pdb=" O ALA 5 434 " (cutoff:3.500A) Processing helix chain '5' and resid 445 through 462 Processing helix chain '5' and resid 472 through 485 Processing helix chain '5' and resid 486 through 487 No H-bonds generated for 'chain '5' and resid 486 through 487' Processing helix chain '5' and resid 488 through 492 removed outlier: 3.535A pdb=" N MET 5 491 " --> pdb=" O PRO 5 488 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU 5 492 " --> pdb=" O LYS 5 489 " (cutoff:3.500A) No H-bonds generated for 'chain '5' and resid 488 through 492' Processing helix chain '5' and resid 496 through 504 Processing helix chain '6' and resid 14 through 20 removed outlier: 4.192A pdb=" N THR 6 18 " --> pdb=" O THR 6 14 " (cutoff:3.500A) Processing helix chain '6' and resid 47 through 80 Processing helix chain '6' and resid 98 through 104 Processing helix chain '6' and resid 117 through 157 Processing helix chain '6' and resid 165 through 169 removed outlier: 4.551A pdb=" N GLU 6 168 " --> pdb=" O SER 6 165 " (cutoff:3.500A) removed outlier: 3.715A pdb=" N ILE 6 169 " --> pdb=" O LEU 6 166 " (cutoff:3.500A) No H-bonds generated for 'chain '6' and resid 165 through 169' Processing helix chain '6' and resid 171 through 175 Processing helix chain '6' and resid 193 through 201 Processing helix chain '6' and resid 233 through 244 Processing helix chain '6' and resid 254 through 310 Proline residue: 6 278 - end of helix removed outlier: 4.385A pdb=" N ARG 6 281 " --> pdb=" O GLY 6 277 " (cutoff:3.500A) Processing helix chain '6' and resid 327 through 340 Processing helix chain '7' and resid 12 through 48 Processing helix chain '7' and resid 51 through 77 Processing helix chain '7' and resid 78 through 86 removed outlier: 4.497A pdb=" N THR 7 82 " --> pdb=" O ASP 7 78 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 175 removed outlier: 3.767A pdb=" N THR 7 157 " --> pdb=" O THR 7 153 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N VAL 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 210 removed outlier: 3.594A pdb=" N ARG 7 179 " --> pdb=" O VAL 7 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 50 through 61 Processing helix chain 'U' and resid 75 through 84 removed outlier: 3.760A pdb=" N GLN U 83 " --> pdb=" O CYS U 79 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N ARG U 84 " --> pdb=" O GLU U 80 " (cutoff:3.500A) Processing helix chain 'U' and resid 90 through 99 removed outlier: 4.205A pdb=" N GLU U 96 " --> pdb=" O GLU U 92 " (cutoff:3.500A) removed outlier: 4.620A pdb=" N MET U 97 " --> pdb=" O ASP U 93 " (cutoff:3.500A) removed outlier: 3.971A pdb=" N LEU U 98 " --> pdb=" O LYS U 94 " (cutoff:3.500A) Processing helix chain 'U' and resid 118 through 136 Processing helix chain 'U' and resid 150 through 155 removed outlier: 4.438A pdb=" N TRP U 155 " --> pdb=" O LYS U 151 " (cutoff:3.500A) Processing helix chain 'U' and resid 156 through 159 Processing helix chain 'U' and resid 168 through 177 Processing helix chain 'U' and resid 199 through 204 Processing helix chain 'U' and resid 263 through 278 Processing helix chain 'U' and resid 279 through 289 Processing helix chain 'U' and resid 290 through 301 removed outlier: 3.811A pdb=" N MET U 296 " --> pdb=" O VAL U 292 " (cutoff:3.500A) Processing helix chain 'U' and resid 304 through 319 Processing helix chain 'U' and resid 323 through 329 Processing helix chain 'U' and resid 333 through 344 Processing helix chain 'U' and resid 348 through 364 removed outlier: 4.065A pdb=" N SER U 364 " --> pdb=" O PHE U 360 " (cutoff:3.500A) Processing helix chain 'U' and resid 366 through 371 Processing helix chain 'U' and resid 371 through 380 Processing helix chain 'U' and resid 382 through 392 Processing helix chain 'U' and resid 396 through 418 removed outlier: 3.569A pdb=" N SER U 400 " --> pdb=" O ASP U 396 " (cutoff:3.500A) Processing helix chain 'U' and resid 419 through 430 Processing helix chain 'U' and resid 435 through 440 Processing helix chain 'U' and resid 440 through 446 Processing helix chain 'U' and resid 447 through 452 Processing helix chain 'U' and resid 453 through 455 No H-bonds generated for 'chain 'U' and resid 453 through 455' Processing helix chain 'U' and resid 456 through 469 Processing helix chain 'U' and resid 471 through 489 Processing helix chain 'U' and resid 491 through 540 removed outlier: 4.205A pdb=" N VAL U 495 " --> pdb=" O ARG U 491 " (cutoff:3.500A) Processing helix chain 'U' and resid 540 through 549 Processing helix chain 'U' and resid 553 through 568 Processing helix chain 'X' and resid 14 through 24 Processing helix chain 'X' and resid 44 through 58 removed outlier: 3.990A pdb=" N ILE X 48 " --> pdb=" O THR X 44 " (cutoff:3.500A) Processing helix chain 'X' and resid 68 through 74 Processing helix chain 'X' and resid 74 through 81 Processing helix chain 'X' and resid 103 through 108 Processing helix chain 'a' and resid 19 through 33 Processing helix chain 'a' and resid 51 through 76 Processing helix chain 'a' and resid 93 through 132 Processing helix chain 'a' and resid 179 through 191 Processing helix chain 'a' and resid 226 through 240 Processing helix chain 'a' and resid 251 through 309 removed outlier: 4.286A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.694A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N LYS a 296 " --> pdb=" O VAL a 292 " (cutoff:3.500A) Processing helix chain 'a' and resid 329 through 344 Processing helix chain 'a' and resid 370 through 382 removed outlier: 4.367A pdb=" N PHE a 374 " --> pdb=" O PHE a 370 " (cutoff:3.500A) Processing helix chain 'a' and resid 391 through 406 removed outlier: 4.196A pdb=" N ILE a 397 " --> pdb=" O PRO a 393 " (cutoff:3.500A) Proline residue: a 400 - end of helix Processing helix chain 'a' and resid 409 through 426 removed outlier: 3.523A pdb=" N GLY a 413 " --> pdb=" O ASP a 409 " (cutoff:3.500A) Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 removed outlier: 3.673A pdb=" N GLY a 446 " --> pdb=" O MET a 442 " (cutoff:3.500A) Processing helix chain 'a' and resid 446 through 465 Processing helix chain 'a' and resid 481 through 488 Processing helix chain 'a' and resid 492 through 498 removed outlier: 4.265A pdb=" N LEU a 496 " --> pdb=" O GLU a 492 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 525 removed outlier: 3.782A pdb=" N ASN a 524 " --> pdb=" O ASP a 520 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE a 525 " --> pdb=" O PRO a 521 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 520 through 525' Processing helix chain 'a' and resid 528 through 564 removed outlier: 4.009A pdb=" N SER a 535 " --> pdb=" O THR a 531 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N PHE a 536 " --> pdb=" O PHE a 532 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N LEU a 557 " --> pdb=" O VAL a 553 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 571 Processing helix chain 'a' and resid 572 through 598 removed outlier: 3.868A pdb=" N LEU a 583 " --> pdb=" O PHE a 579 " (cutoff:3.500A) removed outlier: 4.941A pdb=" N TYR a 586 " --> pdb=" O SER a 582 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 619 Processing helix chain 'a' and resid 632 through 647 removed outlier: 3.566A pdb=" N ILE a 636 " --> pdb=" O GLY a 632 " (cutoff:3.500A) Processing helix chain 'a' and resid 647 through 667 removed outlier: 4.306A pdb=" N MET a 651 " --> pdb=" O CYS a 647 " (cutoff:3.500A) removed outlier: 5.497A pdb=" N LYS a 655 " --> pdb=" O MET a 651 " (cutoff:3.500A) Proline residue: a 656 - end of helix Processing helix chain 'a' and resid 713 through 739 Processing helix chain 'a' and resid 740 through 760 Processing helix chain 'a' and resid 769 through 791 removed outlier: 3.625A pdb=" N GLY a 773 " --> pdb=" O SER a 769 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N PHE a 778 " --> pdb=" O LEU a 774 " (cutoff:3.500A) Processing helix chain 'a' and resid 793 through 810 Processing helix chain 'a' and resid 811 through 816 removed outlier: 4.300A pdb=" N PHE a 815 " --> pdb=" O PHE a 811 " (cutoff:3.500A) Processing helix chain 'a' and resid 828 through 832 removed outlier: 3.979A pdb=" N ILE a 831 " --> pdb=" O PHE a 828 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ARG a 832 " --> pdb=" O GLU a 829 " (cutoff:3.500A) No H-bonds generated for 'chain 'a' and resid 828 through 832' Processing helix chain 'b' and resid 3 through 30 Processing helix chain 'b' and resid 36 through 43 removed outlier: 3.731A pdb=" N GLU b 43 " --> pdb=" O TRP b 39 " (cutoff:3.500A) Processing helix chain 'b' and resid 45 through 80 removed outlier: 3.950A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N SER b 61 " --> pdb=" O ALA b 57 " (cutoff:3.500A) Processing helix chain 'b' and resid 81 through 82 No H-bonds generated for 'chain 'b' and resid 81 through 82' Processing helix chain 'b' and resid 83 through 89 Processing helix chain 'b' and resid 90 through 113 removed outlier: 4.255A pdb=" N ILE b 94 " --> pdb=" O ASN b 90 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N GLY b 104 " --> pdb=" O VAL b 100 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N MET b 107 " --> pdb=" O TYR b 103 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 167 removed outlier: 3.783A pdb=" N HIS b 132 " --> pdb=" O HIS b 128 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N TYR b 135 " --> pdb=" O TYR b 131 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 171 No H-bonds generated for 'chain 'b' and resid 169 through 171' Processing helix chain 'b' and resid 172 through 198 removed outlier: 5.241A pdb=" N VAL b 179 " --> pdb=" O LYS b 175 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N GLU b 180 " --> pdb=" O ILE b 176 " (cutoff:3.500A) Processing helix chain 'd' and resid 7 through 26 removed outlier: 4.534A pdb=" N VAL d 11 " --> pdb=" O LEU d 7 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ASP d 12 " --> pdb=" O TYR d 8 " (cutoff:3.500A) removed outlier: 7.172A pdb=" N TYR d 15 " --> pdb=" O VAL d 11 " (cutoff:3.500A) removed outlier: 6.225A pdb=" N LEU d 16 " --> pdb=" O ASP d 12 " (cutoff:3.500A) Processing helix chain 'd' and resid 29 through 38 Processing helix chain 'd' and resid 41 through 51 Processing helix chain 'd' and resid 66 through 88 removed outlier: 3.604A pdb=" N ILE d 70 " --> pdb=" O THR d 66 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N HIS d 88 " --> pdb=" O HIS d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 90 through 113 removed outlier: 3.752A pdb=" N PHE d 96 " --> pdb=" O PRO d 92 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N TYR d 104 " --> pdb=" O ILE d 100 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ASP d 107 " --> pdb=" O SER d 103 " (cutoff:3.500A) Processing helix chain 'd' and resid 121 through 129 removed outlier: 3.865A pdb=" N LEU d 125 " --> pdb=" O SER d 121 " (cutoff:3.500A) Proline residue: d 127 - end of helix Processing helix chain 'd' and resid 146 through 157 Processing helix chain 'd' and resid 158 through 166 removed outlier: 3.991A pdb=" N ALA d 162 " --> pdb=" O PRO d 159 " (cutoff:3.500A) Processing helix chain 'd' and resid 170 through 175 Processing helix chain 'd' and resid 177 through 200 Processing helix chain 'd' and resid 202 through 228 Proline residue: d 210 - end of helix removed outlier: 4.094A pdb=" N PHE d 228 " --> pdb=" O THR d 224 " (cutoff:3.500A) Processing helix chain 'd' and resid 233 through 239 Processing helix chain 'd' and resid 251 through 257 Processing helix chain 'd' and resid 260 through 270 removed outlier: 3.713A pdb=" N TYR d 270 " --> pdb=" O ASN d 266 " (cutoff:3.500A) Processing helix chain 'd' and resid 271 through 281 removed outlier: 4.058A pdb=" N LEU d 277 " --> pdb=" O GLU d 273 " (cutoff:3.500A) Processing helix chain 'd' and resid 289 through 306 removed outlier: 3.571A pdb=" N PHE d 306 " --> pdb=" O ASN d 302 " (cutoff:3.500A) Processing helix chain 'd' and resid 312 through 338 removed outlier: 4.201A pdb=" N TYR d 316 " --> pdb=" O PHE d 312 " (cutoff:3.500A) Processing helix chain 'd' and resid 340 through 344 Processing helix chain 'g' and resid 12 through 45 removed outlier: 3.803A pdb=" N VAL g 16 " --> pdb=" O SER g 12 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N SER g 26 " --> pdb=" O ALA g 22 " (cutoff:3.500A) Processing helix chain 'g' and resid 48 through 52 removed outlier: 3.742A pdb=" N LEU g 51 " --> pdb=" O ARG g 48 " (cutoff:3.500A) removed outlier: 3.935A pdb=" N ILE g 52 " --> pdb=" O PRO g 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'g' and resid 48 through 52' Processing helix chain 'g' and resid 53 through 55 No H-bonds generated for 'chain 'g' and resid 53 through 55' Processing helix chain 'g' and resid 56 through 80 removed outlier: 3.569A pdb=" N MET g 61 " --> pdb=" O ILE g 57 " (cutoff:3.500A) Processing helix chain 'g' and resid 86 through 124 removed outlier: 3.781A pdb=" N PHE g 90 " --> pdb=" O LEU g 86 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 153 removed outlier: 3.653A pdb=" N ALA g 149 " --> pdb=" O GLY g 145 " (cutoff:3.500A) Processing helix chain 'h' and resid 12 through 45 removed outlier: 3.657A pdb=" N VAL h 16 " --> pdb=" O SER h 12 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N SER h 26 " --> pdb=" O ALA h 22 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER h 37 " --> pdb=" O GLY h 33 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 52 removed outlier: 3.589A pdb=" N LEU h 51 " --> pdb=" O ARG h 48 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N ILE h 52 " --> pdb=" O PRO h 49 " (cutoff:3.500A) No H-bonds generated for 'chain 'h' and resid 48 through 52' Processing helix chain 'h' and resid 56 through 79 Processing helix chain 'h' and resid 87 through 124 removed outlier: 3.662A pdb=" N LEU h 91 " --> pdb=" O TYR h 87 " (cutoff:3.500A) Processing helix chain 'h' and resid 127 through 154 Processing helix chain 'i' and resid 12 through 34 removed outlier: 3.689A pdb=" N MET i 17 " --> pdb=" O PHE i 13 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N SER i 20 " --> pdb=" O VAL i 16 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N PHE i 25 " --> pdb=" O SER i 21 " (cutoff:3.500A) removed outlier: 4.192A pdb=" N SER i 26 " --> pdb=" O ALA i 22 " (cutoff:3.500A) Processing helix chain 'i' and resid 35 through 48 Processing helix chain 'i' and resid 49 through 55 removed outlier: 4.761A pdb=" N MET i 53 " --> pdb=" O GLU i 50 " (cutoff:3.500A) Processing helix chain 'i' and resid 56 through 79 removed outlier: 3.818A pdb=" N VAL i 72 " --> pdb=" O TYR i 68 " (cutoff:3.500A) Processing helix chain 'i' and resid 87 through 124 removed outlier: 3.785A pdb=" N ALA i 122 " --> pdb=" O VAL i 118 " (cutoff:3.500A) removed outlier: 4.452A pdb=" N GLN i 123 " --> pdb=" O ARG i 119 " (cutoff:3.500A) Processing helix chain 'i' and resid 126 through 154 removed outlier: 4.568A pdb=" N GLY i 130 " --> pdb=" O ARG i 126 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N THR i 154 " --> pdb=" O LEU i 150 " (cutoff:3.500A) Processing helix chain 'j' and resid 12 through 45 removed outlier: 3.949A pdb=" N MET j 23 " --> pdb=" O ALA j 19 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.382A pdb=" N SER j 26 " --> pdb=" O ALA j 22 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N THR j 39 " --> pdb=" O ALA j 35 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ALA j 43 " --> pdb=" O THR j 39 " (cutoff:3.500A) Processing helix chain 'j' and resid 46 through 47 No H-bonds generated for 'chain 'j' and resid 46 through 47' Processing helix chain 'j' and resid 48 through 55 removed outlier: 4.256A pdb=" N MET j 53 " --> pdb=" O GLU j 50 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N SER j 55 " --> pdb=" O ILE j 52 " (cutoff:3.500A) Processing helix chain 'j' and resid 56 through 80 removed outlier: 3.653A pdb=" N MET j 61 " --> pdb=" O ILE j 57 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ILE j 64 " --> pdb=" O VAL j 60 " (cutoff:3.500A) removed outlier: 4.386A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N VAL j 72 " --> pdb=" O TYR j 68 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N ALA j 73 " --> pdb=" O GLY j 69 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N LEU j 75 " --> pdb=" O VAL j 71 " (cutoff:3.500A) Processing helix chain 'j' and resid 86 through 124 removed outlier: 3.754A pdb=" N PHE j 90 " --> pdb=" O LEU j 86 " (cutoff:3.500A) Processing helix chain 'j' and resid 127 through 155 removed outlier: 4.281A pdb=" N PHE j 137 " --> pdb=" O LEU j 133 " (cutoff:3.500A) removed outlier: 4.293A pdb=" N ALA j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N GLU j 139 " --> pdb=" O LEU j 135 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 45 removed outlier: 3.978A pdb=" N MET k 23 " --> pdb=" O ALA k 19 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N SER k 26 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N SER k 37 " --> pdb=" O GLY k 33 " (cutoff:3.500A) Processing helix chain 'k' and resid 48 through 52 Processing helix chain 'k' and resid 53 through 55 No H-bonds generated for 'chain 'k' and resid 53 through 55' Processing helix chain 'k' and resid 56 through 79 removed outlier: 3.766A pdb=" N GLY k 69 " --> pdb=" O ILE k 65 " (cutoff:3.500A) Processing helix chain 'k' and resid 87 through 124 Processing helix chain 'k' and resid 126 through 155 removed outlier: 4.642A pdb=" N GLY k 130 " --> pdb=" O ARG k 126 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ILE k 132 " --> pdb=" O PHE k 128 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N ALA k 138 " --> pdb=" O ILE k 134 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ALA k 149 " --> pdb=" O GLY k 145 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N THR k 154 " --> pdb=" O LEU k 150 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 46 removed outlier: 3.565A pdb=" N SER l 20 " --> pdb=" O VAL l 16 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N MET l 23 " --> pdb=" O ALA l 19 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N SER l 26 " --> pdb=" O ALA l 22 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N ALA l 35 " --> pdb=" O ALA l 31 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N THR l 39 " --> pdb=" O ALA l 35 " (cutoff:3.500A) Processing helix chain 'l' and resid 48 through 52 removed outlier: 4.007A pdb=" N LEU l 51 " --> pdb=" O ARG l 48 " (cutoff:3.500A) Processing helix chain 'l' and resid 53 through 55 No H-bonds generated for 'chain 'l' and resid 53 through 55' Processing helix chain 'l' and resid 56 through 80 removed outlier: 3.793A pdb=" N GLY l 69 " --> pdb=" O ILE l 65 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N VAL l 72 " --> pdb=" O TYR l 68 " (cutoff:3.500A) Processing helix chain 'l' and resid 87 through 124 removed outlier: 3.742A pdb=" N LEU l 91 " --> pdb=" O TYR l 87 " (cutoff:3.500A) Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.244A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 4.193A pdb=" N ILE l 132 " --> pdb=" O PHE l 128 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N PHE l 137 " --> pdb=" O LEU l 133 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ALA l 138 " --> pdb=" O ILE l 134 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N GLY l 145 " --> pdb=" O LEU l 141 " (cutoff:3.500A) Processing helix chain 'm' and resid 9 through 45 Processing helix chain 'm' and resid 48 through 53 removed outlier: 3.615A pdb=" N LEU m 51 " --> pdb=" O ARG m 48 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ILE m 52 " --> pdb=" O PRO m 49 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N MET m 53 " --> pdb=" O GLU m 50 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 48 through 53' Processing helix chain 'm' and resid 56 through 79 Processing helix chain 'm' and resid 87 through 122 Processing helix chain 'm' and resid 126 through 155 removed outlier: 4.432A pdb=" N GLY m 130 " --> pdb=" O ARG m 126 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N PHE m 137 " --> pdb=" O LEU m 133 " (cutoff:3.500A) removed outlier: 4.078A pdb=" N VAL m 148 " --> pdb=" O TYR m 144 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ALA m 149 " --> pdb=" O GLY m 145 " (cutoff:3.500A) Processing helix chain 'n' and resid 12 through 45 removed outlier: 3.872A pdb=" N VAL n 16 " --> pdb=" O SER n 12 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N MET n 17 " --> pdb=" O PHE n 13 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N SER n 37 " --> pdb=" O GLY n 33 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 53 removed outlier: 3.723A pdb=" N LEU n 51 " --> pdb=" O ARG n 48 " (cutoff:3.500A) removed outlier: 4.534A pdb=" N MET n 53 " --> pdb=" O GLU n 50 " (cutoff:3.500A) Processing helix chain 'n' and resid 56 through 79 Processing helix chain 'n' and resid 87 through 124 removed outlier: 4.001A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 127 through 155 removed outlier: 4.038A pdb=" N ILE n 132 " --> pdb=" O PHE n 128 " (cutoff:3.500A) removed outlier: 4.556A pdb=" N LEU n 133 " --> pdb=" O VAL n 129 " (cutoff:3.500A) removed outlier: 4.147A pdb=" N THR n 154 " --> pdb=" O LEU n 150 " (cutoff:3.500A) Processing helix chain 'o' and resid 12 through 48 removed outlier: 4.344A pdb=" N PHE o 25 " --> pdb=" O SER o 21 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) Processing helix chain 'o' and resid 49 through 55 removed outlier: 4.507A pdb=" N MET o 53 " --> pdb=" O GLU o 50 " (cutoff:3.500A) Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.521A pdb=" N MET o 61 " --> pdb=" O ILE o 57 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N VAL o 72 " --> pdb=" O TYR o 68 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 124 removed outlier: 4.107A pdb=" N LEU o 91 " --> pdb=" O TYR o 87 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N ARG o 119 " --> pdb=" O ASP o 115 " (cutoff:3.500A) Processing helix chain 'o' and resid 127 through 155 removed outlier: 3.581A pdb=" N ALA o 138 " --> pdb=" O ILE o 134 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N VAL o 148 " --> pdb=" O TYR o 144 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N ALA o 149 " --> pdb=" O GLY o 145 " (cutoff:3.500A) Processing helix chain 'p' and resid 600 through 628 removed outlier: 3.663A pdb=" N VAL p 604 " --> pdb=" O GLU p 600 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN p 628 " --> pdb=" O TYR p 624 " (cutoff:3.500A) Processing helix chain 'p' and resid 635 through 641 removed outlier: 3.775A pdb=" N ARG p 639 " --> pdb=" O SER p 635 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 107 removed outlier: 4.036A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 removed outlier: 3.614A pdb=" N VAL 9 114 " --> pdb=" O THR 9 110 " (cutoff:3.500A) Processing helix chain '9' and resid 140 through 160 Proline residue: 9 153 - end of helix Processing helix chain '9' and resid 195 through 207 Processing helix chain '9' and resid 207 through 217 removed outlier: 3.922A pdb=" N VAL 9 211 " --> pdb=" O MET 9 207 " (cutoff:3.500A) Processing helix chain 'T' and resid 4 through 91 Processing helix chain 'T' and resid 92 through 104 Processing helix chain 'Q' and resid 5 through 106 removed outlier: 3.938A pdb=" N ALA Q 17 " --> pdb=" O LYS Q 13 " (cutoff:3.500A) removed outlier: 4.573A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N GLN Q 21 " --> pdb=" O ALA Q 17 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ALA Q 23 " --> pdb=" O ILE Q 19 " (cutoff:3.500A) removed outlier: 4.730A pdb=" N VAL Q 46 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 4.709A pdb=" N GLN Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 128 Processing helix chain 'Q' and resid 137 through 139 No H-bonds generated for 'chain 'Q' and resid 137 through 139' Processing helix chain 'Q' and resid 140 through 160 Proline residue: Q 153 - end of helix Processing helix chain 'Q' and resid 195 through 217 Proline residue: Q 209 - end of helix Processing helix chain 'V' and resid 5 through 88 Processing helix chain 'V' and resid 91 through 105 Processing helix chain 'c' and resid 309 through 313 removed outlier: 3.851A pdb=" N GLY c 312 " --> pdb=" O PRO c 309 " (cutoff:3.500A) Processing helix chain 'c' and resid 416 through 418 No H-bonds generated for 'chain 'c' and resid 416 through 418' Processing helix chain 'c' and resid 419 through 442 removed outlier: 3.718A pdb=" N SER c 442 " --> pdb=" O HIS c 438 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 35 removed outlier: 6.115A pdb=" N CYS f 14 " --> pdb=" O LYS f 10 " (cutoff:3.500A) removed outlier: 4.909A pdb=" N GLY f 15 " --> pdb=" O LEU f 11 " (cutoff:3.500A) Processing helix chain 'f' and resid 55 through 89 removed outlier: 3.871A pdb=" N GLU f 63 " --> pdb=" O TYR f 59 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN f 64 " --> pdb=" O ASN f 60 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N CYS f 69 " --> pdb=" O VAL f 65 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N PHE f 70 " --> pdb=" O SER f 66 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N ILE f 71 " --> pdb=" O TYR f 67 " (cutoff:3.500A) removed outlier: 4.346A pdb=" N ALA f 72 " --> pdb=" O ASN f 68 " (cutoff:3.500A) Processing helix chain 's' and resid 19 through 24 Processing helix chain 's' and resid 24 through 45 removed outlier: 3.836A pdb=" N LYS s 30 " --> pdb=" O LEU s 26 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR s 43 " --> pdb=" O PHE s 39 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N GLY s 45 " --> pdb=" O PHE s 41 " (cutoff:3.500A) Processing helix chain 's' and resid 59 through 63 Processing helix chain 's' and resid 76 through 79 Processing helix chain 's' and resid 101 through 128 removed outlier: 4.483A pdb=" N PHE s 107 " --> pdb=" O SER s 103 " (cutoff:3.500A) Processing helix chain 's' and resid 129 through 135 Processing helix chain 's' and resid 137 through 172 removed outlier: 3.594A pdb=" N MET s 141 " --> pdb=" O ASN s 137 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 181 removed outlier: 4.018A pdb=" N ILE s 177 " --> pdb=" O ASP s 173 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N MET s 181 " --> pdb=" O ILE s 177 " (cutoff:3.500A) Processing helix chain 's' and resid 181 through 186 Processing helix chain 's' and resid 199 through 228 removed outlier: 3.594A pdb=" N ASN s 203 " --> pdb=" O THR s 199 " (cutoff:3.500A) Processing helix chain 'e' and resid 8 through 26 Processing helix chain 'e' and resid 35 through 62 Processing helix chain 'e' and resid 71 through 83 Processing sheet with id=AA1, first strand: chain '8' and resid 131 through 135 WARNING: can't find start of bonding for strands! previous: chain '8' and resid 164 through 167 current: chain '8' and resid 191 through 195 WARNING: can't find start of bonding for strands! previous: chain '8' and resid 191 through 195 current: chain '0' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 28 through 32 current: chain '0' and resid 50 through 58 removed outlier: 6.863A pdb=" N THR 0 63 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 5.358A pdb=" N LEU 0 57 " --> pdb=" O MET 0 61 " (cutoff:3.500A) removed outlier: 7.383A pdb=" N MET 0 61 " --> pdb=" O LEU 0 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '0' and resid 61 through 66 current: chain '1' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 28 through 32 current: chain '1' and resid 50 through 58 removed outlier: 6.769A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.253A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N MET 1 61 " --> pdb=" O LEU 1 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '1' and resid 61 through 66 current: chain '2' and resid 28 through 32 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 28 through 32 current: chain '2' and resid 50 through 58 removed outlier: 6.818A pdb=" N THR 2 63 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) removed outlier: 4.959A pdb=" N LEU 2 57 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 7.132A pdb=" N MET 2 61 " --> pdb=" O LEU 2 57 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '2' and resid 61 through 66 current: chain '3' and resid 57 through 61 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 61 current: chain '3' and resid 81 through 90 removed outlier: 5.994A pdb=" N VAL 3 86 " --> pdb=" O GLN 3 97 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N GLN 3 97 " --> pdb=" O VAL 3 86 " (cutoff:3.500A) removed outlier: 3.987A pdb=" N GLU 3 88 " --> pdb=" O VAL 3 95 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '3' and resid 93 through 98 current: chain '4' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '4' and resid 57 through 60 current: chain '4' and resid 81 through 90 removed outlier: 7.193A pdb=" N VAL 4 95 " --> pdb=" O LEU 4 87 " (cutoff:3.500A) removed outlier: 5.305A pdb=" N VAL 4 89 " --> pdb=" O LYS 4 93 " (cutoff:3.500A) removed outlier: 7.427A pdb=" N LYS 4 93 " --> pdb=" O VAL 4 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '4' and resid 93 through 98 current: chain '5' and resid 57 through 60 WARNING: can't find start of bonding for strands! previous: chain '5' and resid 57 through 60 current: chain '5' and resid 81 through 90 removed outlier: 7.120A pdb=" N VAL 5 95 " --> pdb=" O LEU 5 87 " (cutoff:3.500A) removed outlier: 5.138A pdb=" N VAL 5 89 " --> pdb=" O LYS 5 93 " (cutoff:3.500A) removed outlier: 7.178A pdb=" N LYS 5 93 " --> pdb=" O VAL 5 89 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain '5' and resid 93 through 98 current: chain 'Q' and resid 164 through 167 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 164 through 167 current: chain 'Q' and resid 191 through 193 Processing sheet with id=AA2, first strand: chain '0' and resid 87 through 90 Processing sheet with id=AA3, first strand: chain '0' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 98 through 99 current: chain '0' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 309 through 315 current: chain '0' and resid 401 through 410 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain '0' and resid 165 through 166 removed outlier: 4.117A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain '0' and resid 178 through 179 removed outlier: 3.546A pdb=" N TYR 0 178 " --> pdb=" O GLU 0 193 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '1' and resid 87 through 89 Processing sheet with id=AA7, first strand: chain '1' and resid 98 through 99 removed outlier: 6.792A pdb=" N ILE 1 272 " --> pdb=" O ALA 1 310 " (cutoff:3.500A) removed outlier: 8.159A pdb=" N VAL 1 312 " --> pdb=" O ILE 1 272 " (cutoff:3.500A) removed outlier: 6.326A pdb=" N TYR 1 274 " --> pdb=" O VAL 1 312 " (cutoff:3.500A) removed outlier: 6.620A pdb=" N VAL 1 271 " --> pdb=" O SER 1 345 " (cutoff:3.500A) removed outlier: 8.497A pdb=" N MET 1 347 " --> pdb=" O VAL 1 271 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N ILE 1 273 " --> pdb=" O MET 1 347 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N GLU 1 219 " --> pdb=" O LYS 1 393 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 136 through 137 removed outlier: 6.809A pdb=" N ILE 1 166 " --> pdb=" O TYR 1 153 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain '1' and resid 146 through 147 removed outlier: 6.655A pdb=" N LEU 1 192 " --> pdb=" O THR 1 177 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N ILE 1 179 " --> pdb=" O VAL 1 190 " (cutoff:3.500A) removed outlier: 8.250A pdb=" N VAL 1 190 " --> pdb=" O ILE 1 179 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain '1' and resid 406 through 410 removed outlier: 6.601A pdb=" N THR 1 246 " --> pdb=" O GLY 1 408 " (cutoff:3.500A) removed outlier: 7.837A pdb=" N VAL 1 410 " --> pdb=" O THR 1 246 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ILE 1 248 " --> pdb=" O VAL 1 410 " (cutoff:3.500A) removed outlier: 6.769A pdb=" N THR 1 245 " --> pdb=" O VAL 1 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain '2' and resid 87 through 90 Processing sheet with id=AB3, first strand: chain '2' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 98 through 99 current: chain '2' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 309 through 315 current: chain '2' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 401 through 410 current: chain '2' and resid 454 through 455 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain '2' and resid 154 through 156 Processing sheet with id=AB5, first strand: chain '2' and resid 151 through 152 removed outlier: 3.523A pdb=" N ASP 2 151 " --> pdb=" O LEU 2 168 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain '2' and resid 175 through 179 removed outlier: 6.738A pdb=" N GLU 2 193 " --> pdb=" O THR 2 177 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N LEU 2 192 " --> pdb=" O PHE 2 203 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain '2' and resid 226 through 227 removed outlier: 4.654A pdb=" N CYS 2 240 " --> pdb=" O LEU 2 227 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 295 through 298 Processing sheet with id=AB9, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AC1, first strand: chain '3' and resid 131 through 133 removed outlier: 6.693A pdb=" N ILE 3 229 " --> pdb=" O CYS 3 258 " (cutoff:3.500A) removed outlier: 7.964A pdb=" N PHE 3 260 " --> pdb=" O ILE 3 229 " (cutoff:3.500A) removed outlier: 6.770A pdb=" N PHE 3 231 " --> pdb=" O PHE 3 260 " (cutoff:3.500A) removed outlier: 8.112A pdb=" N ASN 3 262 " --> pdb=" O PHE 3 231 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N ALA 3 233 " --> pdb=" O ASN 3 262 " (cutoff:3.500A) removed outlier: 6.039A pdb=" N ALA 3 228 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) removed outlier: 7.331A pdb=" N ILE 3 296 " --> pdb=" O ALA 3 228 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N VAL 3 230 " --> pdb=" O ILE 3 296 " (cutoff:3.500A) removed outlier: 7.103A pdb=" N VAL 3 293 " --> pdb=" O THR 3 349 " (cutoff:3.500A) removed outlier: 7.987A pdb=" N ILE 3 351 " --> pdb=" O VAL 3 293 " (cutoff:3.500A) removed outlier: 6.608A pdb=" N VAL 3 295 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain '3' and resid 163 through 164 removed outlier: 3.711A pdb=" N ARG 3 340 " --> pdb=" O ILE 3 164 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 169 through 170 removed outlier: 4.681A pdb=" N ILE 3 183 " --> pdb=" O ILE 3 170 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '3' and resid 353 through 355 Processing sheet with id=AC5, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AC6, first strand: chain '4' and resid 131 through 132 removed outlier: 6.879A pdb=" N ALA 4 228 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE 4 296 " --> pdb=" O ALA 4 228 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N VAL 4 230 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) removed outlier: 8.262A pdb=" N THR 4 298 " --> pdb=" O VAL 4 230 " (cutoff:3.500A) removed outlier: 7.621A pdb=" N ALA 4 232 " --> pdb=" O THR 4 298 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N LEU 4 297 " --> pdb=" O ILE 4 351 " (cutoff:3.500A) removed outlier: 6.759A pdb=" N ILE 4 191 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain '4' and resid 163 through 164 removed outlier: 3.943A pdb=" N ARG 4 340 " --> pdb=" O ILE 4 164 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AC9, first strand: chain '4' and resid 375 through 379 removed outlier: 6.448A pdb=" N TYR 4 378 " --> pdb=" O PRO 4 396 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 120 through 123 Processing sheet with id=AD2, first strand: chain '5' and resid 130 through 133 removed outlier: 6.768A pdb=" N ARG 5 130 " --> pdb=" O LEU 5 259 " (cutoff:3.500A) removed outlier: 8.233A pdb=" N LEU 5 261 " --> pdb=" O ARG 5 130 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N PHE 5 132 " --> pdb=" O LEU 5 261 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N ILE 5 229 " --> pdb=" O CYS 5 258 " (cutoff:3.500A) removed outlier: 8.259A pdb=" N PHE 5 260 " --> pdb=" O ILE 5 229 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N PHE 5 231 " --> pdb=" O PHE 5 260 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE 5 191 " --> pdb=" O LEU 5 354 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '5' and resid 163 through 164 removed outlier: 4.090A pdb=" N ARG 5 340 " --> pdb=" O ILE 5 164 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '5' and resid 170 through 171 Processing sheet with id=AD5, first strand: chain '6' and resid 34 through 37 removed outlier: 3.740A pdb=" N VAL 6 34 " --> pdb=" O GLN 6 322 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain '6' and resid 92 through 93 Processing sheet with id=AD7, first strand: chain '6' and resid 214 through 218 removed outlier: 5.661A pdb=" N VAL 6 215 " --> pdb=" O ASN 6 226 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ASN 6 226 " --> pdb=" O VAL 6 215 " (cutoff:3.500A) Processing sheet with id=AD8, first strand: chain '7' and resid 93 through 99 Processing sheet with id=AD9, first strand: chain 'X' and resid 36 through 39 removed outlier: 8.426A pdb=" N ASP X 13 " --> pdb=" O ASN X 67 " (cutoff:3.500A) removed outlier: 7.336A pdb=" N ILE X 64 " --> pdb=" O LEU X 89 " (cutoff:3.500A) removed outlier: 7.930A pdb=" N ILE X 91 " --> pdb=" O ILE X 64 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N ILE X 66 " --> pdb=" O ILE X 91 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'a' and resid 13 through 18 WARNING: can't find start of bonding for strands! previous: chain 'a' and resid 13 through 18 current: chain 'a' and resid 318 through 324 No H-bonds generated for sheet with id=AE1 Processing sheet with id=AE2, first strand: chain 'a' and resid 174 through 175 Processing sheet with id=AE3, first strand: chain 'a' and resid 197 through 202 removed outlier: 4.067A pdb=" N LYS a 217 " --> pdb=" O ILE a 202 " (cutoff:3.500A) Processing sheet with id=AE4, first strand: chain '9' and resid 164 through 167 removed outlier: 3.682A pdb=" N ILE 9 183 " --> pdb=" O VAL 9 192 " (cutoff:3.500A) Processing sheet with id=AE5, first strand: chain 'c' and resid 252 through 253 Processing sheet with id=AE6, first strand: chain 'c' and resid 276 through 278 removed outlier: 3.524A pdb=" N SER c 269 " --> pdb=" O THR c 389 " (cutoff:3.500A) Processing sheet with id=AE7, first strand: chain 'c' and resid 301 through 306 removed outlier: 3.607A pdb=" N PHE c 319 " --> pdb=" O LEU c 303 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N ILE c 320 " --> pdb=" O ARG c 338 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N ARG c 338 " --> pdb=" O ILE c 320 " (cutoff:3.500A) removed outlier: 8.662A pdb=" N ALA c 322 " --> pdb=" O MET c 336 " (cutoff:3.500A) removed outlier: 5.830A pdb=" N MET c 336 " --> pdb=" O ALA c 322 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N ARG c 324 " --> pdb=" O PHE c 334 " (cutoff:3.500A) removed outlier: 5.570A pdb=" N PHE c 334 " --> pdb=" O ARG c 324 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N TYR c 326 " --> pdb=" O TYR c 332 " (cutoff:3.500A) removed outlier: 5.739A pdb=" N TYR c 332 " --> pdb=" O TYR c 326 " (cutoff:3.500A) removed outlier: 4.739A pdb=" N VAL c 355 " --> pdb=" O MET c 336 " (cutoff:3.500A) removed outlier: 7.318A pdb=" N ARG c 338 " --> pdb=" O SER c 353 " (cutoff:3.500A) removed outlier: 8.857A pdb=" N SER c 353 " --> pdb=" O ARG c 338 " (cutoff:3.500A) removed outlier: 9.096A pdb=" N GLU c 340 " --> pdb=" O ASN c 351 " (cutoff:3.500A) removed outlier: 9.898A pdb=" N ASN c 351 " --> pdb=" O GLU c 340 " (cutoff:3.500A) removed outlier: 9.896A pdb=" N HIS c 342 " --> pdb=" O HIS c 349 " (cutoff:3.500A) removed outlier: 10.403A pdb=" N HIS c 349 " --> pdb=" O HIS c 342 " (cutoff:3.500A) Processing sheet with id=AE8, first strand: chain 's' and resid 64 through 72 removed outlier: 4.961A pdb=" N LEU s 65 " --> pdb=" O VAL s 55 " (cutoff:3.500A) removed outlier: 5.462A pdb=" N VAL s 55 " --> pdb=" O LEU s 65 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N SER s 54 " --> pdb=" O GLU s 193 " (cutoff:3.500A) removed outlier: 5.241A pdb=" N GLU s 193 " --> pdb=" O SER s 54 " (cutoff:3.500A) removed outlier: 6.898A pdb=" N GLU s 56 " --> pdb=" O CYS s 191 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N CYS s 191 " --> pdb=" O GLU s 56 " (cutoff:3.500A) Processing sheet with id=AE9, first strand: chain 's' and resid 81 through 85 4034 hydrogen bonds defined for protein. 11820 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: 23.52 Time building geometry restraints manager: 15.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.34: 21097 1.34 - 1.46: 12214 1.46 - 1.58: 34179 1.58 - 1.70: 0 1.70 - 1.82: 703 Bond restraints: 68193 Sorted by residual: bond pdb=" N MET a 406 " pdb=" CA MET a 406 " ideal model delta sigma weight residual 1.456 1.489 -0.032 1.31e-02 5.83e+03 5.99e+00 bond pdb=" N PHE l 90 " pdb=" CA PHE l 90 " ideal model delta sigma weight residual 1.459 1.486 -0.027 1.19e-02 7.06e+03 5.07e+00 bond pdb=" C SER 6 8 " pdb=" N ALA 6 9 " ideal model delta sigma weight residual 1.323 1.359 -0.036 1.64e-02 3.72e+03 4.81e+00 bond pdb=" N TYR b 135 " pdb=" CA TYR b 135 " ideal model delta sigma weight residual 1.459 1.484 -0.025 1.19e-02 7.06e+03 4.25e+00 bond pdb=" CA TYR b 135 " pdb=" C TYR b 135 " ideal model delta sigma weight residual 1.524 1.498 0.026 1.27e-02 6.20e+03 4.17e+00 ... (remaining 68188 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.37: 90632 2.37 - 4.74: 1359 4.74 - 7.12: 150 7.12 - 9.49: 18 9.49 - 11.86: 5 Bond angle restraints: 92164 Sorted by residual: angle pdb=" C TYR b 135 " pdb=" CA TYR b 135 " pdb=" CB TYR b 135 " ideal model delta sigma weight residual 110.88 102.52 8.36 1.57e+00 4.06e-01 2.84e+01 angle pdb=" N TYR b 70 " pdb=" CA TYR b 70 " pdb=" CB TYR b 70 " ideal model delta sigma weight residual 110.28 117.61 -7.33 1.55e+00 4.16e-01 2.24e+01 angle pdb=" C ILE b 69 " pdb=" N TYR b 70 " pdb=" CA TYR b 70 " ideal model delta sigma weight residual 120.31 113.92 6.39 1.52e+00 4.33e-01 1.77e+01 angle pdb=" CB MET c 439 " pdb=" CG MET c 439 " pdb=" SD MET c 439 " ideal model delta sigma weight residual 112.70 124.56 -11.86 3.00e+00 1.11e-01 1.56e+01 angle pdb=" N GLU R 38 " pdb=" CA GLU R 38 " pdb=" CB GLU R 38 " ideal model delta sigma weight residual 110.16 115.97 -5.81 1.48e+00 4.57e-01 1.54e+01 ... (remaining 92159 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.52: 38251 17.52 - 35.05: 2379 35.05 - 52.57: 400 52.57 - 70.09: 71 70.09 - 87.62: 38 Dihedral angle restraints: 41139 sinusoidal: 16465 harmonic: 24674 Sorted by residual: dihedral pdb=" CA LYS 7 50 " pdb=" C LYS 7 50 " pdb=" N ILE 7 51 " pdb=" CA ILE 7 51 " ideal model delta harmonic sigma weight residual 180.00 152.21 27.79 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA GLU 0 158 " pdb=" C GLU 0 158 " pdb=" N ASN 0 159 " pdb=" CA ASN 0 159 " ideal model delta harmonic sigma weight residual 180.00 154.49 25.51 0 5.00e+00 4.00e-02 2.60e+01 dihedral pdb=" CA HIS 2 444 " pdb=" C HIS 2 444 " pdb=" N PHE 2 445 " pdb=" CA PHE 2 445 " ideal model delta harmonic sigma weight residual 180.00 -155.03 -24.97 0 5.00e+00 4.00e-02 2.49e+01 ... (remaining 41136 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.056: 8686 0.056 - 0.112: 1543 0.112 - 0.169: 214 0.169 - 0.225: 9 0.225 - 0.281: 1 Chirality restraints: 10453 Sorted by residual: chirality pdb=" CB THR e 17 " pdb=" CA THR e 17 " pdb=" OG1 THR e 17 " pdb=" CG2 THR e 17 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CA GLU d 6 " pdb=" N GLU d 6 " pdb=" C GLU d 6 " pdb=" CB GLU d 6 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CA TYR b 135 " pdb=" N TYR b 135 " pdb=" C TYR b 135 " pdb=" CB TYR b 135 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 8.90e-01 ... (remaining 10450 not shown) Planarity restraints: 11796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE k 14 " -0.016 2.00e-02 2.50e+03 3.21e-02 1.03e+01 pdb=" C PHE k 14 " 0.056 2.00e-02 2.50e+03 pdb=" O PHE k 14 " -0.021 2.00e-02 2.50e+03 pdb=" N GLY k 15 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG k 119 " -0.264 9.50e-02 1.11e+02 1.19e-01 1.02e+01 pdb=" NE ARG k 119 " 0.023 2.00e-02 2.50e+03 pdb=" CZ ARG k 119 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG k 119 " 0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG k 119 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP U 155 " -0.047 5.00e-02 4.00e+02 7.11e-02 8.09e+00 pdb=" N PRO U 156 " 0.123 5.00e-02 4.00e+02 pdb=" CA PRO U 156 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO U 156 " -0.040 5.00e-02 4.00e+02 ... (remaining 11793 not shown) Histogram of nonbonded interaction distances: 2.37 - 2.88: 24210 2.88 - 3.38: 74111 3.38 - 3.89: 112364 3.89 - 4.39: 130423 4.39 - 4.90: 206481 Nonbonded interactions: 547589 Sorted by model distance: nonbonded pdb=" O GLU 4 239 " pdb=" OG1 THR 4 240 " model vdw 2.370 3.040 nonbonded pdb=" O LYS R 34 " pdb=" OE1 GLU R 38 " model vdw 2.373 3.040 nonbonded pdb=" O LEU 4 455 " pdb=" OE1 GLU 4 459 " model vdw 2.395 3.040 nonbonded pdb=" O LEU 3 452 " pdb=" OE1 GLN 3 456 " model vdw 2.425 3.040 nonbonded pdb=" O ASN 7 86 " pdb=" OD1 ASN 7 86 " model vdw 2.438 3.040 ... (remaining 547584 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 '0' and (resid 17 through 558 or resid 565 through 615)) selection = (chain '1' and (resid 17 through 251 or resid 256 through 495 or resid 501 throu \ gh 558 or resid 565 through 615)) selection = (chain '2' and (resid 17 through 251 or resid 256 through 495 or resid 501 throu \ gh 558 or resid 565 through 615)) } ncs_group { reference = (chain '3' and (resid 39 through 224 or resid 226 through 505)) selection = (chain '4' and (resid 39 through 214 or resid 224 or resid 226 through 505)) selection = chain '5' } ncs_group { reference = chain '8' selection = chain '9' selection = chain 'Q' } ncs_group { reference = chain 'R' selection = chain 'T' selection = chain 'V' } ncs_group { reference = chain 'g' selection = chain 'h' selection = chain 'i' selection = chain 'j' selection = chain 'k' selection = chain 'l' selection = chain 'm' selection = chain 'n' selection = chain 'o' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 10.590 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.050 Extract box with map and model: 2.030 Check model and map are aligned: 0.400 Set scattering table: 0.460 Process input model: 113.500 Find NCS groups from input model: 1.990 Set up NCS constraints: 0.370 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.020 Load rotamer database and sin/cos tables:2.310 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 131.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.077 68193 Z= 0.254 Angle : 0.734 11.861 92164 Z= 0.401 Chirality : 0.043 0.281 10453 Planarity : 0.005 0.119 11796 Dihedral : 12.084 87.618 25301 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.02 % Allowed : 4.90 % Favored : 95.08 % Rotamer: Outliers : 0.01 % Allowed : 0.18 % Favored : 99.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: -0.02 (0.09), residues: 8475 helix: 0.96 (0.07), residues: 4821 sheet: -1.35 (0.18), residues: 724 loop : -1.23 (0.12), residues: 2930 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.002 TRP e 83 HIS 0.009 0.001 HIS U 171 PHE 0.037 0.002 PHE k 14 TYR 0.045 0.002 TYR j 32 ARG 0.022 0.001 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 882 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 881 time to evaluate : 5.976 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 MET cc_start: 0.9021 (mmp) cc_final: 0.8568 (ppp) REVERT: 0 34 MET cc_start: 0.9280 (mmp) cc_final: 0.8862 (mmm) REVERT: 0 284 MET cc_start: 0.9446 (tpp) cc_final: 0.9048 (tpt) REVERT: 0 340 MET cc_start: 0.9002 (mtp) cc_final: 0.8699 (ttm) REVERT: 0 368 MET cc_start: 0.8770 (ttp) cc_final: 0.8503 (ttp) REVERT: 0 608 MET cc_start: 0.9010 (mtp) cc_final: 0.8795 (mtt) REVERT: 1 34 MET cc_start: 0.9402 (mmm) cc_final: 0.9151 (mmm) REVERT: 1 167 MET cc_start: 0.9078 (ptp) cc_final: 0.8852 (ptm) REVERT: 1 235 ASP cc_start: 0.9127 (t70) cc_final: 0.8919 (t0) REVERT: 1 318 MET cc_start: 0.9337 (mmm) cc_final: 0.8986 (mmm) REVERT: 1 340 MET cc_start: 0.9065 (tpp) cc_final: 0.8663 (tpp) REVERT: 1 419 ASP cc_start: 0.9167 (t0) cc_final: 0.8895 (t0) REVERT: 1 519 PHE cc_start: 0.9260 (t80) cc_final: 0.9032 (t80) REVERT: 1 574 MET cc_start: 0.9118 (pmm) cc_final: 0.8696 (pmm) REVERT: 2 306 MET cc_start: 0.8991 (tmm) cc_final: 0.8573 (tmm) REVERT: 2 318 MET cc_start: 0.9315 (mtt) cc_final: 0.8978 (mtp) REVERT: 2 324 GLU cc_start: 0.8011 (tt0) cc_final: 0.7616 (tm-30) REVERT: 2 485 GLU cc_start: 0.9242 (mt-10) cc_final: 0.8914 (mm-30) REVERT: 2 540 MET cc_start: 0.9064 (mtt) cc_final: 0.8548 (mmm) REVERT: 2 550 MET cc_start: 0.9399 (mtm) cc_final: 0.9144 (mtp) REVERT: 2 608 MET cc_start: 0.9215 (mtp) cc_final: 0.8960 (mtp) REVERT: 3 127 MET cc_start: 0.9202 (mtp) cc_final: 0.9001 (mtt) REVERT: 3 169 MET cc_start: 0.8676 (tmm) cc_final: 0.8410 (tmm) REVERT: 3 356 MET cc_start: 0.9090 (mmm) cc_final: 0.8725 (tmm) REVERT: 3 431 ASP cc_start: 0.9150 (m-30) cc_final: 0.8936 (m-30) REVERT: 3 435 MET cc_start: 0.9443 (tmm) cc_final: 0.9240 (tmm) REVERT: 4 162 CYS cc_start: 0.9375 (m) cc_final: 0.8480 (t) REVERT: 4 180 MET cc_start: 0.8779 (tpp) cc_final: 0.8078 (tpp) REVERT: 4 334 ILE cc_start: 0.9354 (mm) cc_final: 0.9129 (tt) REVERT: 4 435 MET cc_start: 0.9244 (mmp) cc_final: 0.8774 (tpp) REVERT: 5 127 MET cc_start: 0.8866 (mtt) cc_final: 0.8539 (mtt) REVERT: 5 234 MET cc_start: 0.8630 (mmt) cc_final: 0.8151 (mmm) REVERT: 5 402 MET cc_start: 0.8803 (mmm) cc_final: 0.8531 (mmm) REVERT: 5 410 MET cc_start: 0.8482 (mpp) cc_final: 0.7978 (mpp) REVERT: 5 494 ARG cc_start: 0.8864 (tpp-160) cc_final: 0.8350 (tpp-160) REVERT: U 73 MET cc_start: -0.2900 (mtm) cc_final: -0.4374 (mmm) REVERT: X 103 ASP cc_start: 0.7938 (t0) cc_final: 0.7729 (t0) REVERT: a 293 TRP cc_start: 0.7441 (t-100) cc_final: 0.7231 (t-100) REVERT: a 304 TYR cc_start: 0.8225 (m-10) cc_final: 0.7909 (m-10) REVERT: a 331 ASP cc_start: 0.8813 (m-30) cc_final: 0.8324 (p0) REVERT: a 423 MET cc_start: 0.8580 (mmm) cc_final: 0.8266 (mmm) REVERT: a 651 MET cc_start: 0.7880 (mpp) cc_final: 0.7520 (mpp) REVERT: a 745 LEU cc_start: 0.8783 (mm) cc_final: 0.8337 (mp) REVERT: a 791 LEU cc_start: 0.9022 (mt) cc_final: 0.7980 (mp) REVERT: b 4 LEU cc_start: 0.9094 (mt) cc_final: 0.8379 (pp) REVERT: b 18 CYS cc_start: 0.8969 (m) cc_final: 0.8595 (p) REVERT: b 192 ILE cc_start: 0.8853 (mm) cc_final: 0.8612 (pt) REVERT: d 84 HIS cc_start: 0.8714 (t70) cc_final: 0.8461 (t-170) REVERT: d 262 GLU cc_start: 0.9006 (mm-30) cc_final: 0.8247 (pp20) REVERT: g 21 SER cc_start: 0.9231 (m) cc_final: 0.8973 (p) REVERT: g 64 ILE cc_start: 0.6618 (mm) cc_final: 0.6261 (mm) REVERT: g 134 ILE cc_start: 0.8217 (mp) cc_final: 0.7612 (tt) REVERT: h 14 PHE cc_start: 0.8805 (m-80) cc_final: 0.8425 (m-80) REVERT: h 41 ILE cc_start: 0.8111 (mm) cc_final: 0.7834 (mm) REVERT: h 123 GLN cc_start: 0.6157 (mm-40) cc_final: 0.5822 (mm-40) REVERT: i 32 TYR cc_start: 0.7523 (t80) cc_final: 0.7231 (t80) REVERT: i 61 MET cc_start: 0.5772 (mmp) cc_final: 0.5152 (mmt) REVERT: i 112 ILE cc_start: 0.9219 (mt) cc_final: 0.8375 (mt) REVERT: j 136 ILE cc_start: 0.8192 (mt) cc_final: 0.7950 (mt) REVERT: k 90 PHE cc_start: 0.5642 (m-80) cc_final: 0.5338 (m-80) REVERT: l 39 THR cc_start: 0.7088 (m) cc_final: 0.6846 (p) REVERT: l 64 ILE cc_start: 0.7662 (mt) cc_final: 0.7426 (mt) REVERT: m 39 THR cc_start: 0.8416 (m) cc_final: 0.8115 (m) REVERT: m 64 ILE cc_start: 0.6302 (mt) cc_final: 0.5642 (mt) REVERT: m 143 LEU cc_start: 0.9209 (tp) cc_final: 0.8854 (mp) REVERT: n 53 MET cc_start: 0.6473 (mmp) cc_final: 0.6022 (tpp) REVERT: n 131 MET cc_start: 0.8158 (ptm) cc_final: 0.7808 (ptm) REVERT: o 92 GLN cc_start: 0.6588 (mm-40) cc_final: 0.6175 (mm110) REVERT: p 630 ASP cc_start: 0.8264 (p0) cc_final: 0.7685 (p0) REVERT: 9 54 MET cc_start: 0.8930 (mmm) cc_final: 0.8578 (mmm) REVERT: 9 58 GLU cc_start: 0.9453 (tp30) cc_final: 0.9191 (tp30) REVERT: 9 208 MET cc_start: 0.9181 (mmm) cc_final: 0.8917 (tpp) REVERT: T 11 LEU cc_start: 0.7742 (mm) cc_final: 0.7052 (tt) REVERT: Q 15 MET cc_start: -0.0755 (tmm) cc_final: -0.1332 (tmm) REVERT: Q 16 MET cc_start: -0.2546 (mmm) cc_final: -0.2833 (mmt) REVERT: f 77 LEU cc_start: 0.8907 (mt) cc_final: 0.8503 (mt) REVERT: s 20 ARG cc_start: 0.5059 (tpt90) cc_final: 0.4028 (mmp80) REVERT: s 100 ASP cc_start: 0.8252 (t0) cc_final: 0.8033 (t0) outliers start: 1 outliers final: 0 residues processed: 882 average time/residue: 0.6207 time to fit residues: 947.7884 Evaluate side-chains 685 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 685 time to evaluate : 6.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 714 optimal weight: 0.5980 chunk 641 optimal weight: 40.0000 chunk 355 optimal weight: 20.0000 chunk 219 optimal weight: 6.9990 chunk 432 optimal weight: 8.9990 chunk 342 optimal weight: 10.0000 chunk 663 optimal weight: 20.0000 chunk 256 optimal weight: 0.0040 chunk 403 optimal weight: 30.0000 chunk 493 optimal weight: 20.0000 chunk 768 optimal weight: 10.0000 overall best weight: 5.3200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 66 GLN R 111 HIS R 113 ASN 0 573 HIS 1 444 HIS 2 444 HIS 2 573 HIS 3 345 ASN 3 415 HIS 4 171 GLN 4 345 ASN 4 358 ASN 7 174 HIS a 41 ASN a 204 ASN a 365 ASN a 749 HIS b 51 ASN ** b 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** h 92 GLN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 98 GLN ** Q 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 21 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.061 68193 Z= 0.306 Angle : 0.647 9.477 92164 Z= 0.341 Chirality : 0.042 0.226 10453 Planarity : 0.005 0.058 11796 Dihedral : 4.650 29.754 9269 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 10.12 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 0.17 % Allowed : 3.10 % Favored : 96.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.53 (0.09), residues: 8475 helix: 1.35 (0.07), residues: 4866 sheet: -0.75 (0.19), residues: 752 loop : -1.02 (0.12), residues: 2857 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 0 567 HIS 0.008 0.001 HIS 7 174 PHE 0.037 0.002 PHE m 14 TYR 0.031 0.002 TYR h 144 ARG 0.016 0.001 ARG e 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 797 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 785 time to evaluate : 5.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 MET cc_start: 0.8933 (mmp) cc_final: 0.8502 (ppp) REVERT: 0 34 MET cc_start: 0.9374 (mmp) cc_final: 0.8958 (mmm) REVERT: 0 61 MET cc_start: 0.9120 (mmm) cc_final: 0.8864 (tpp) REVERT: 0 284 MET cc_start: 0.9432 (tpp) cc_final: 0.9029 (tpt) REVERT: 0 360 GLU cc_start: 0.8845 (tm-30) cc_final: 0.8486 (tm-30) REVERT: 0 509 LEU cc_start: 0.7751 (pp) cc_final: 0.7438 (mp) REVERT: 0 540 MET cc_start: 0.7681 (ppp) cc_final: 0.7410 (ppp) REVERT: 0 608 MET cc_start: 0.9160 (mtp) cc_final: 0.8908 (mtt) REVERT: 1 34 MET cc_start: 0.9528 (mmm) cc_final: 0.9322 (mmm) REVERT: 1 39 MET cc_start: 0.9334 (tpp) cc_final: 0.9100 (tpp) REVERT: 1 108 ASP cc_start: 0.8959 (p0) cc_final: 0.8732 (p0) REVERT: 1 235 ASP cc_start: 0.9152 (t70) cc_final: 0.8895 (t0) REVERT: 1 318 MET cc_start: 0.9220 (mmm) cc_final: 0.8875 (mmm) REVERT: 1 340 MET cc_start: 0.9046 (tpp) cc_final: 0.8611 (tpp) REVERT: 1 419 ASP cc_start: 0.8860 (t0) cc_final: 0.8467 (t0) REVERT: 1 540 MET cc_start: 0.9355 (mtm) cc_final: 0.9037 (mtp) REVERT: 1 574 MET cc_start: 0.9027 (pmm) cc_final: 0.8733 (pmm) REVERT: 2 34 MET cc_start: 0.9266 (mmm) cc_final: 0.8979 (mmm) REVERT: 2 205 MET cc_start: 0.9030 (ptp) cc_final: 0.8653 (ptp) REVERT: 2 306 MET cc_start: 0.9011 (tmm) cc_final: 0.8578 (tmm) REVERT: 2 318 MET cc_start: 0.9347 (mtt) cc_final: 0.8928 (mtp) REVERT: 2 324 GLU cc_start: 0.7917 (tt0) cc_final: 0.7504 (tm-30) REVERT: 2 485 GLU cc_start: 0.9300 (mt-10) cc_final: 0.8955 (mm-30) REVERT: 2 540 MET cc_start: 0.9091 (mtt) cc_final: 0.8019 (mtp) REVERT: 2 550 MET cc_start: 0.9384 (mtm) cc_final: 0.8978 (mtp) REVERT: 2 608 MET cc_start: 0.9234 (mtp) cc_final: 0.8993 (mtp) REVERT: 3 127 MET cc_start: 0.9358 (mtp) cc_final: 0.9021 (mtt) REVERT: 3 169 MET cc_start: 0.8815 (tmm) cc_final: 0.8496 (tmm) REVERT: 3 410 MET cc_start: 0.9009 (mpp) cc_final: 0.8738 (mpp) REVERT: 3 431 ASP cc_start: 0.9221 (m-30) cc_final: 0.9001 (m-30) REVERT: 4 162 CYS cc_start: 0.9537 (m) cc_final: 0.8531 (t) REVERT: 4 180 MET cc_start: 0.8795 (tpp) cc_final: 0.8045 (tpp) REVERT: 4 334 ILE cc_start: 0.9419 (mm) cc_final: 0.9181 (tt) REVERT: 5 127 MET cc_start: 0.9076 (mtt) cc_final: 0.8713 (mtt) REVERT: 5 356 MET cc_start: 0.9174 (mpp) cc_final: 0.8611 (mmp) REVERT: 5 410 MET cc_start: 0.8461 (mpp) cc_final: 0.7949 (mpp) REVERT: 5 494 ARG cc_start: 0.8878 (tpp-160) cc_final: 0.8262 (tpp-160) REVERT: 6 319 MET cc_start: 0.4009 (mmt) cc_final: 0.3036 (mmt) REVERT: 7 58 MET cc_start: 0.6736 (tmm) cc_final: 0.6493 (tmm) REVERT: 7 78 ASP cc_start: 0.8354 (t0) cc_final: 0.7874 (t0) REVERT: 7 112 TYR cc_start: 0.8933 (t80) cc_final: 0.8648 (t80) REVERT: U 73 MET cc_start: -0.2914 (mtm) cc_final: -0.4277 (mmm) REVERT: U 276 MET cc_start: 0.7270 (tpp) cc_final: 0.6929 (mmm) REVERT: X 103 ASP cc_start: 0.7859 (t0) cc_final: 0.7522 (t70) REVERT: a 300 MET cc_start: 0.8599 (mmp) cc_final: 0.8363 (mmm) REVERT: a 304 TYR cc_start: 0.8358 (m-10) cc_final: 0.8002 (m-10) REVERT: a 331 ASP cc_start: 0.8836 (m-30) cc_final: 0.8370 (p0) REVERT: a 423 MET cc_start: 0.8754 (mmm) cc_final: 0.8548 (mmm) REVERT: a 651 MET cc_start: 0.8110 (mpp) cc_final: 0.7769 (mpp) REVERT: a 718 MET cc_start: 0.8125 (tpt) cc_final: 0.7746 (tpt) REVERT: a 745 LEU cc_start: 0.8914 (mm) cc_final: 0.8425 (mm) REVERT: a 791 LEU cc_start: 0.8895 (mt) cc_final: 0.8404 (mp) REVERT: a 806 LEU cc_start: 0.9550 (tt) cc_final: 0.9012 (tp) REVERT: b 4 LEU cc_start: 0.9160 (mt) cc_final: 0.8675 (pp) REVERT: b 18 CYS cc_start: 0.8993 (m) cc_final: 0.8637 (p) REVERT: b 192 ILE cc_start: 0.8814 (mm) cc_final: 0.8551 (pt) REVERT: d 84 HIS cc_start: 0.8746 (t70) cc_final: 0.8370 (t70) REVERT: d 215 GLU cc_start: 0.8585 (tm-30) cc_final: 0.8338 (tm-30) REVERT: d 262 GLU cc_start: 0.9019 (mm-30) cc_final: 0.8086 (pp20) REVERT: d 334 GLU cc_start: 0.9423 (mm-30) cc_final: 0.9117 (mm-30) REVERT: g 21 SER cc_start: 0.9291 (m) cc_final: 0.8896 (p) REVERT: g 64 ILE cc_start: 0.6825 (mm) cc_final: 0.6521 (mm) REVERT: g 134 ILE cc_start: 0.8372 (mp) cc_final: 0.7753 (tt) REVERT: g 144 TYR cc_start: 0.7467 (m-10) cc_final: 0.7252 (m-80) REVERT: h 14 PHE cc_start: 0.8810 (m-80) cc_final: 0.8401 (m-80) REVERT: h 41 ILE cc_start: 0.7990 (mm) cc_final: 0.7722 (mm) REVERT: h 123 GLN cc_start: 0.6448 (mm-40) cc_final: 0.6097 (mm-40) REVERT: i 61 MET cc_start: 0.6331 (mmp) cc_final: 0.5113 (mmt) REVERT: j 136 ILE cc_start: 0.8195 (mt) cc_final: 0.7931 (mt) REVERT: k 23 MET cc_start: 0.2787 (ptm) cc_final: 0.2220 (ttp) REVERT: k 131 MET cc_start: 0.7866 (ppp) cc_final: 0.7239 (ptt) REVERT: l 23 MET cc_start: 0.7122 (pmm) cc_final: 0.6843 (pmm) REVERT: l 39 THR cc_start: 0.7019 (m) cc_final: 0.6769 (p) REVERT: m 64 ILE cc_start: 0.6234 (mt) cc_final: 0.5679 (mt) REVERT: n 131 MET cc_start: 0.7763 (ptm) cc_final: 0.7474 (ptm) REVERT: o 61 MET cc_start: 0.6114 (ptp) cc_final: 0.5879 (ptp) REVERT: o 92 GLN cc_start: 0.6795 (mm-40) cc_final: 0.6484 (mm110) REVERT: p 630 ASP cc_start: 0.8171 (p0) cc_final: 0.7794 (p0) REVERT: p 634 ASP cc_start: 0.7720 (p0) cc_final: 0.7391 (p0) REVERT: 9 54 MET cc_start: 0.8829 (mmm) cc_final: 0.8462 (mmm) REVERT: 9 58 GLU cc_start: 0.9453 (tp30) cc_final: 0.9246 (tp30) REVERT: 9 208 MET cc_start: 0.9165 (mmm) cc_final: 0.8849 (tpp) REVERT: T 11 LEU cc_start: 0.7984 (mm) cc_final: 0.7642 (tt) REVERT: T 84 MET cc_start: 0.8867 (mtp) cc_final: 0.8598 (mtp) REVERT: Q 15 MET cc_start: -0.0497 (tmm) cc_final: -0.1036 (tmm) REVERT: Q 16 MET cc_start: -0.2032 (mmm) cc_final: -0.2336 (mmt) REVERT: c 445 THR cc_start: 0.8211 (t) cc_final: 0.7981 (t) REVERT: f 77 LEU cc_start: 0.8918 (mt) cc_final: 0.8521 (mt) REVERT: s 20 ARG cc_start: 0.5067 (tpt90) cc_final: 0.3896 (mmt-90) REVERT: s 100 ASP cc_start: 0.8479 (t0) cc_final: 0.8252 (t0) REVERT: e 56 ILE cc_start: 0.8702 (pt) cc_final: 0.8480 (pt) outliers start: 12 outliers final: 2 residues processed: 794 average time/residue: 0.6059 time to fit residues: 840.9320 Evaluate side-chains 642 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 640 time to evaluate : 5.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 426 optimal weight: 5.9990 chunk 238 optimal weight: 9.9990 chunk 639 optimal weight: 5.9990 chunk 523 optimal weight: 8.9990 chunk 211 optimal weight: 4.9990 chunk 769 optimal weight: 3.9990 chunk 831 optimal weight: 10.0000 chunk 685 optimal weight: 5.9990 chunk 763 optimal weight: 9.9990 chunk 262 optimal weight: 0.7980 chunk 617 optimal weight: 20.0000 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 0 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 358 ASN a 749 HIS a 751 GLN a 802 HIS ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7483 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 68193 Z= 0.256 Angle : 0.599 12.044 92164 Z= 0.316 Chirality : 0.042 0.193 10453 Planarity : 0.004 0.054 11796 Dihedral : 4.577 26.949 9269 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.55 % Favored : 95.43 % Rotamer: Outliers : 0.11 % Allowed : 2.76 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.71 (0.09), residues: 8475 helix: 1.48 (0.07), residues: 4877 sheet: -0.37 (0.20), residues: 728 loop : -1.04 (0.12), residues: 2870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.001 TRP e 83 HIS 0.009 0.001 HIS 8 14 PHE 0.057 0.002 PHE m 14 TYR 0.032 0.002 TYR n 32 ARG 0.006 0.000 ARG n 126 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 803 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 795 time to evaluate : 5.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 MET cc_start: 0.8968 (mmp) cc_final: 0.8551 (ppp) REVERT: 0 34 MET cc_start: 0.9372 (mmp) cc_final: 0.8930 (mmm) REVERT: 0 61 MET cc_start: 0.9059 (mmm) cc_final: 0.8747 (mmm) REVERT: 0 284 MET cc_start: 0.9493 (tpp) cc_final: 0.9143 (tpt) REVERT: 0 318 MET cc_start: 0.8795 (mpp) cc_final: 0.8426 (mpp) REVERT: 0 360 GLU cc_start: 0.8893 (tm-30) cc_final: 0.8673 (tm-30) REVERT: 1 34 MET cc_start: 0.9559 (mmm) cc_final: 0.9341 (mmm) REVERT: 1 39 MET cc_start: 0.9375 (tpp) cc_final: 0.9138 (tpp) REVERT: 1 61 MET cc_start: 0.8855 (mmm) cc_final: 0.8642 (mmt) REVERT: 1 108 ASP cc_start: 0.8974 (p0) cc_final: 0.8730 (p0) REVERT: 1 235 ASP cc_start: 0.9105 (t70) cc_final: 0.8851 (t0) REVERT: 1 306 MET cc_start: 0.7429 (mmp) cc_final: 0.6755 (mmp) REVERT: 1 340 MET cc_start: 0.9028 (tpp) cc_final: 0.8615 (tpp) REVERT: 1 419 ASP cc_start: 0.8861 (t0) cc_final: 0.8553 (t0) REVERT: 1 540 MET cc_start: 0.9412 (mtm) cc_final: 0.8947 (mtp) REVERT: 2 34 MET cc_start: 0.9268 (mmm) cc_final: 0.8991 (mmm) REVERT: 2 205 MET cc_start: 0.9001 (ptp) cc_final: 0.8651 (ptp) REVERT: 2 306 MET cc_start: 0.8999 (tmm) cc_final: 0.8565 (tmm) REVERT: 2 318 MET cc_start: 0.9336 (mtt) cc_final: 0.8905 (mtp) REVERT: 2 324 GLU cc_start: 0.8033 (tt0) cc_final: 0.7621 (tm-30) REVERT: 2 485 GLU cc_start: 0.9295 (mt-10) cc_final: 0.8929 (mm-30) REVERT: 2 550 MET cc_start: 0.9394 (mtm) cc_final: 0.8975 (mtp) REVERT: 2 608 MET cc_start: 0.9179 (mtp) cc_final: 0.8975 (mtp) REVERT: 3 127 MET cc_start: 0.9379 (mtp) cc_final: 0.9100 (mtt) REVERT: 3 169 MET cc_start: 0.8842 (tmm) cc_final: 0.8505 (tmm) REVERT: 3 316 GLU cc_start: 0.8959 (mt-10) cc_final: 0.8340 (mp0) REVERT: 3 327 MET cc_start: 0.9601 (ppp) cc_final: 0.9335 (tmm) REVERT: 4 162 CYS cc_start: 0.9537 (m) cc_final: 0.8519 (t) REVERT: 4 180 MET cc_start: 0.8783 (tpp) cc_final: 0.8058 (tpp) REVERT: 4 334 ILE cc_start: 0.9373 (mm) cc_final: 0.9148 (tt) REVERT: 5 127 MET cc_start: 0.9133 (mtt) cc_final: 0.8802 (mtt) REVERT: 5 154 MET cc_start: 0.9491 (mmm) cc_final: 0.9253 (mmm) REVERT: 5 356 MET cc_start: 0.9186 (mpp) cc_final: 0.8586 (mmp) REVERT: 5 410 MET cc_start: 0.8448 (mpp) cc_final: 0.7926 (mpp) REVERT: 5 494 ARG cc_start: 0.8874 (tpp-160) cc_final: 0.8236 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8441 (t0) cc_final: 0.8149 (t0) REVERT: 7 112 TYR cc_start: 0.9006 (t80) cc_final: 0.8708 (t80) REVERT: U 73 MET cc_start: -0.2965 (mtm) cc_final: -0.4242 (mmm) REVERT: U 276 MET cc_start: 0.7399 (tpp) cc_final: 0.7038 (mmm) REVERT: X 59 ASP cc_start: 0.8973 (p0) cc_final: 0.8771 (p0) REVERT: a 293 TRP cc_start: 0.7509 (t-100) cc_final: 0.7126 (t-100) REVERT: a 300 MET cc_start: 0.8598 (mmp) cc_final: 0.8321 (mmm) REVERT: a 304 TYR cc_start: 0.8336 (m-10) cc_final: 0.7995 (m-10) REVERT: a 331 ASP cc_start: 0.8903 (m-30) cc_final: 0.8480 (p0) REVERT: a 423 MET cc_start: 0.8700 (mmm) cc_final: 0.8494 (mmm) REVERT: a 536 PHE cc_start: 0.8290 (p90) cc_final: 0.8058 (p90) REVERT: a 651 MET cc_start: 0.8130 (mpp) cc_final: 0.7792 (mpp) REVERT: a 718 MET cc_start: 0.8163 (tpt) cc_final: 0.7828 (tpt) REVERT: a 745 LEU cc_start: 0.8862 (mm) cc_final: 0.8343 (mm) REVERT: a 791 LEU cc_start: 0.8568 (mt) cc_final: 0.8205 (mp) REVERT: b 4 LEU cc_start: 0.9122 (mt) cc_final: 0.8547 (pt) REVERT: b 18 CYS cc_start: 0.8985 (m) cc_final: 0.8623 (p) REVERT: d 84 HIS cc_start: 0.8664 (t70) cc_final: 0.8346 (t70) REVERT: d 215 GLU cc_start: 0.8498 (tm-30) cc_final: 0.8226 (tm-30) REVERT: d 262 GLU cc_start: 0.9009 (mm-30) cc_final: 0.8189 (pp20) REVERT: d 334 GLU cc_start: 0.9412 (mm-30) cc_final: 0.9118 (mm-30) REVERT: g 21 SER cc_start: 0.9305 (m) cc_final: 0.8893 (p) REVERT: g 44 MET cc_start: 0.1421 (mmt) cc_final: 0.0361 (mmt) REVERT: g 64 ILE cc_start: 0.6817 (mm) cc_final: 0.6556 (mm) REVERT: g 134 ILE cc_start: 0.8311 (mp) cc_final: 0.7777 (tt) REVERT: h 14 PHE cc_start: 0.8841 (m-80) cc_final: 0.8421 (m-80) REVERT: h 41 ILE cc_start: 0.8058 (mm) cc_final: 0.7772 (mm) REVERT: h 68 TYR cc_start: 0.6233 (m-80) cc_final: 0.5868 (m-80) REVERT: h 123 GLN cc_start: 0.6610 (mm-40) cc_final: 0.6232 (mm-40) REVERT: i 61 MET cc_start: 0.6344 (mmp) cc_final: 0.5340 (mmt) REVERT: i 64 ILE cc_start: 0.7432 (mt) cc_final: 0.6801 (mt) REVERT: i 112 ILE cc_start: 0.9376 (OUTLIER) cc_final: 0.9004 (mt) REVERT: j 136 ILE cc_start: 0.8170 (mt) cc_final: 0.7903 (mt) REVERT: k 23 MET cc_start: 0.3012 (ptm) cc_final: 0.2495 (ttp) REVERT: k 131 MET cc_start: 0.7934 (ppp) cc_final: 0.7136 (ptt) REVERT: l 39 THR cc_start: 0.6858 (m) cc_final: 0.6599 (p) REVERT: l 67 ILE cc_start: 0.8497 (OUTLIER) cc_final: 0.8235 (mp) REVERT: m 64 ILE cc_start: 0.6297 (mt) cc_final: 0.5636 (mt) REVERT: m 143 LEU cc_start: 0.9279 (tp) cc_final: 0.8984 (mp) REVERT: n 131 MET cc_start: 0.7581 (ptm) cc_final: 0.7242 (ptm) REVERT: o 44 MET cc_start: 0.6560 (mmp) cc_final: 0.6089 (mmt) REVERT: o 92 GLN cc_start: 0.6725 (mm-40) cc_final: 0.6416 (mm110) REVERT: o 140 VAL cc_start: 0.8933 (t) cc_final: 0.8693 (t) REVERT: p 630 ASP cc_start: 0.8067 (p0) cc_final: 0.7733 (p0) REVERT: p 638 TYR cc_start: 0.9170 (m-80) cc_final: 0.8892 (m-80) REVERT: 9 54 MET cc_start: 0.8836 (mmm) cc_final: 0.8480 (mmm) REVERT: 9 58 GLU cc_start: 0.9462 (tp30) cc_final: 0.9241 (tp30) REVERT: 9 208 MET cc_start: 0.9248 (mmm) cc_final: 0.8937 (tpp) REVERT: T 11 LEU cc_start: 0.7974 (mm) cc_final: 0.7619 (tt) REVERT: T 84 MET cc_start: 0.8890 (mtp) cc_final: 0.8590 (mtp) REVERT: f 77 LEU cc_start: 0.8934 (mt) cc_final: 0.8523 (mt) REVERT: s 20 ARG cc_start: 0.5132 (tpt90) cc_final: 0.3917 (mmt-90) outliers start: 8 outliers final: 0 residues processed: 798 average time/residue: 0.6187 time to fit residues: 863.7421 Evaluate side-chains 647 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 645 time to evaluate : 5.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 760 optimal weight: 5.9990 chunk 578 optimal weight: 10.0000 chunk 399 optimal weight: 0.7980 chunk 85 optimal weight: 8.9990 chunk 367 optimal weight: 40.0000 chunk 516 optimal weight: 20.0000 chunk 772 optimal weight: 3.9990 chunk 817 optimal weight: 10.0000 chunk 403 optimal weight: 9.9990 chunk 732 optimal weight: 6.9990 chunk 220 optimal weight: 2.9990 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** R 53 GLN ** 0 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 358 ASN 5 209 GLN X 33 HIS ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 340 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 68193 Z= 0.250 Angle : 0.599 10.882 92164 Z= 0.315 Chirality : 0.042 0.260 10453 Planarity : 0.004 0.072 11796 Dihedral : 4.566 28.410 9269 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.64 % Favored : 95.35 % Rotamer: Outliers : 0.07 % Allowed : 2.80 % Favored : 97.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.80 (0.09), residues: 8475 helix: 1.57 (0.07), residues: 4845 sheet: -0.22 (0.20), residues: 732 loop : -1.05 (0.12), residues: 2898 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP f 21 HIS 0.010 0.001 HIS a 802 PHE 0.028 0.002 PHE j 13 TYR 0.025 0.002 TYR n 32 ARG 0.011 0.000 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 793 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 788 time to evaluate : 5.890 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: R 42 MET cc_start: 0.8925 (mmp) cc_final: 0.8520 (ppp) REVERT: 0 34 MET cc_start: 0.9402 (mmp) cc_final: 0.9017 (mmm) REVERT: 0 61 MET cc_start: 0.8998 (mmm) cc_final: 0.8625 (mmm) REVERT: 0 284 MET cc_start: 0.9514 (tpp) cc_final: 0.9231 (tpt) REVERT: 0 360 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8730 (tm-30) REVERT: 0 540 MET cc_start: 0.7703 (ppp) cc_final: 0.7301 (ppp) REVERT: 0 608 MET cc_start: 0.9020 (mtp) cc_final: 0.8812 (mtm) REVERT: 1 39 MET cc_start: 0.9398 (tpp) cc_final: 0.9164 (tpp) REVERT: 1 340 MET cc_start: 0.9025 (tpp) cc_final: 0.8616 (tpp) REVERT: 1 419 ASP cc_start: 0.8841 (t0) cc_final: 0.8422 (t0) REVERT: 1 540 MET cc_start: 0.9410 (mtm) cc_final: 0.8928 (mtp) REVERT: 1 571 ARG cc_start: 0.9087 (tpp80) cc_final: 0.8762 (ttm110) REVERT: 1 574 MET cc_start: 0.8895 (pmm) cc_final: 0.8528 (pmm) REVERT: 2 34 MET cc_start: 0.9269 (mmm) cc_final: 0.8998 (mmm) REVERT: 2 205 MET cc_start: 0.9005 (ptp) cc_final: 0.8672 (ptp) REVERT: 2 306 MET cc_start: 0.8940 (tmm) cc_final: 0.8544 (tmm) REVERT: 2 318 MET cc_start: 0.9314 (mtt) cc_final: 0.8880 (mtp) REVERT: 2 324 GLU cc_start: 0.7976 (tt0) cc_final: 0.7531 (tm-30) REVERT: 2 485 GLU cc_start: 0.9282 (mt-10) cc_final: 0.8914 (mm-30) REVERT: 2 540 MET cc_start: 0.9101 (mtp) cc_final: 0.7138 (mmt) REVERT: 2 550 MET cc_start: 0.9390 (mtm) cc_final: 0.8966 (mtp) REVERT: 3 127 MET cc_start: 0.9400 (mtp) cc_final: 0.9109 (mtt) REVERT: 3 169 MET cc_start: 0.8883 (tmm) cc_final: 0.8530 (tmm) REVERT: 3 316 GLU cc_start: 0.8911 (mt-10) cc_final: 0.8297 (mp0) REVERT: 3 327 MET cc_start: 0.9582 (ppp) cc_final: 0.9365 (tmm) REVERT: 3 410 MET cc_start: 0.9019 (mpp) cc_final: 0.8615 (mpp) REVERT: 4 162 CYS cc_start: 0.9542 (m) cc_final: 0.8543 (t) REVERT: 4 180 MET cc_start: 0.8760 (tpp) cc_final: 0.8008 (tpp) REVERT: 4 309 GLU cc_start: 0.8959 (tp30) cc_final: 0.8675 (tp30) REVERT: 4 327 MET cc_start: 0.9382 (ppp) cc_final: 0.9105 (ppp) REVERT: 5 127 MET cc_start: 0.9062 (mtt) cc_final: 0.8714 (mtt) REVERT: 5 356 MET cc_start: 0.9187 (mpp) cc_final: 0.8630 (mmp) REVERT: 5 410 MET cc_start: 0.8495 (mpp) cc_final: 0.8025 (mpp) REVERT: 5 494 ARG cc_start: 0.8815 (mmt180) cc_final: 0.8290 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8453 (t0) cc_final: 0.8100 (t0) REVERT: 7 112 TYR cc_start: 0.9037 (t80) cc_final: 0.8731 (t80) REVERT: U 73 MET cc_start: -0.2947 (mtm) cc_final: -0.4257 (mmm) REVERT: U 97 MET cc_start: 0.6494 (ptt) cc_final: 0.6103 (ppp) REVERT: U 276 MET cc_start: 0.7320 (tpp) cc_final: 0.6950 (mmm) REVERT: X 59 ASP cc_start: 0.8981 (p0) cc_final: 0.8773 (p0) REVERT: X 112 MET cc_start: 0.4495 (mmt) cc_final: 0.4197 (mmt) REVERT: a 293 TRP cc_start: 0.7514 (t-100) cc_final: 0.7213 (t-100) REVERT: a 300 MET cc_start: 0.8712 (mmp) cc_final: 0.8331 (mmm) REVERT: a 304 TYR cc_start: 0.8340 (m-10) cc_final: 0.8001 (m-10) REVERT: a 331 ASP cc_start: 0.8862 (m-30) cc_final: 0.8484 (p0) REVERT: a 401 PHE cc_start: 0.8248 (t80) cc_final: 0.7959 (t80) REVERT: a 423 MET cc_start: 0.8742 (mmm) cc_final: 0.8320 (mmm) REVERT: a 651 MET cc_start: 0.8161 (mpp) cc_final: 0.7807 (mpp) REVERT: a 718 MET cc_start: 0.8264 (tpt) cc_final: 0.7911 (tpt) REVERT: a 745 LEU cc_start: 0.8878 (mm) cc_final: 0.8403 (mm) REVERT: b 4 LEU cc_start: 0.8894 (mt) cc_final: 0.8317 (pt) REVERT: b 8 TYR cc_start: 0.8787 (m-80) cc_final: 0.8502 (m-80) REVERT: b 18 CYS cc_start: 0.9017 (m) cc_final: 0.8655 (p) REVERT: d 84 HIS cc_start: 0.8693 (t70) cc_final: 0.8398 (t70) REVERT: d 105 MET cc_start: 0.8544 (mmp) cc_final: 0.8310 (mmp) REVERT: d 215 GLU cc_start: 0.8312 (tm-30) cc_final: 0.7574 (tm-30) REVERT: d 219 ARG cc_start: 0.8666 (mtt-85) cc_final: 0.8463 (mtt90) REVERT: d 262 GLU cc_start: 0.8980 (mm-30) cc_final: 0.8172 (pp20) REVERT: g 21 SER cc_start: 0.9325 (m) cc_final: 0.8927 (p) REVERT: g 64 ILE cc_start: 0.6719 (mm) cc_final: 0.6464 (mm) REVERT: g 134 ILE cc_start: 0.8119 (mp) cc_final: 0.7543 (tt) REVERT: h 14 PHE cc_start: 0.8846 (m-80) cc_final: 0.8437 (m-80) REVERT: h 41 ILE cc_start: 0.7988 (mm) cc_final: 0.7712 (mm) REVERT: h 123 GLN cc_start: 0.6748 (mm-40) cc_final: 0.6363 (mm-40) REVERT: h 131 MET cc_start: 0.7387 (ptt) cc_final: 0.7129 (ppp) REVERT: h 147 ILE cc_start: 0.8949 (mt) cc_final: 0.8696 (mt) REVERT: i 61 MET cc_start: 0.6247 (mmp) cc_final: 0.5107 (mmt) REVERT: i 64 ILE cc_start: 0.7306 (mt) cc_final: 0.6869 (mt) REVERT: i 112 ILE cc_start: 0.9384 (mt) cc_final: 0.8842 (mt) REVERT: j 67 ILE cc_start: 0.8697 (mm) cc_final: 0.8488 (mt) REVERT: j 136 ILE cc_start: 0.8185 (mt) cc_final: 0.7904 (mt) REVERT: k 23 MET cc_start: 0.3527 (ptm) cc_final: 0.2408 (ttp) REVERT: k 131 MET cc_start: 0.7999 (ppp) cc_final: 0.7143 (ptt) REVERT: l 23 MET cc_start: 0.7158 (pmm) cc_final: 0.6285 (pmm) REVERT: l 39 THR cc_start: 0.6886 (m) cc_final: 0.6673 (p) REVERT: l 67 ILE cc_start: 0.8528 (OUTLIER) cc_final: 0.8197 (mp) REVERT: m 64 ILE cc_start: 0.6366 (mt) cc_final: 0.5634 (mt) REVERT: m 143 LEU cc_start: 0.9295 (tp) cc_final: 0.9017 (mp) REVERT: n 131 MET cc_start: 0.7560 (ptm) cc_final: 0.7217 (ptm) REVERT: o 92 GLN cc_start: 0.6777 (mm-40) cc_final: 0.6536 (mm110) REVERT: p 630 ASP cc_start: 0.8012 (p0) cc_final: 0.7677 (p0) REVERT: p 638 TYR cc_start: 0.9194 (m-80) cc_final: 0.8923 (m-80) REVERT: 9 54 MET cc_start: 0.8891 (mmm) cc_final: 0.8518 (mmm) REVERT: 9 58 GLU cc_start: 0.9460 (tp30) cc_final: 0.9239 (tp30) REVERT: 9 208 MET cc_start: 0.9257 (mmm) cc_final: 0.8967 (tpp) REVERT: T 11 LEU cc_start: 0.8004 (mm) cc_final: 0.7659 (tt) REVERT: T 84 MET cc_start: 0.8929 (mtp) cc_final: 0.8692 (mtp) REVERT: Q 15 MET cc_start: 0.0439 (tmm) cc_final: -0.0368 (tmm) REVERT: Q 16 MET cc_start: 0.0490 (mpp) cc_final: 0.0161 (mpp) REVERT: f 77 LEU cc_start: 0.8930 (mt) cc_final: 0.8516 (mt) REVERT: s 20 ARG cc_start: 0.4851 (tpt90) cc_final: 0.4041 (mmt-90) REVERT: e 12 VAL cc_start: 0.9164 (t) cc_final: 0.8956 (t) outliers start: 5 outliers final: 0 residues processed: 788 average time/residue: 0.6090 time to fit residues: 837.4417 Evaluate side-chains 650 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 649 time to evaluate : 5.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 681 optimal weight: 8.9990 chunk 464 optimal weight: 5.9990 chunk 11 optimal weight: 8.9990 chunk 608 optimal weight: 6.9990 chunk 337 optimal weight: 1.9990 chunk 697 optimal weight: 6.9990 chunk 565 optimal weight: 9.9990 chunk 0 optimal weight: 30.0000 chunk 417 optimal weight: 20.0000 chunk 733 optimal weight: 9.9990 chunk 206 optimal weight: 4.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 0 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 65 GLN 2 317 ASN ** 4 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 216 HIS a 316 GLN ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 243 HIS k 7 ASN l 7 ASN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 77 ASN V 113 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 68193 Z= 0.302 Angle : 0.635 9.117 92164 Z= 0.335 Chirality : 0.042 0.217 10453 Planarity : 0.004 0.059 11796 Dihedral : 4.671 28.146 9269 Min Nonbonded Distance : 2.370 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.01 % Allowed : 5.30 % Favored : 94.69 % Rotamer: Outliers : 0.08 % Allowed : 2.21 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.09), residues: 8475 helix: 1.45 (0.07), residues: 4863 sheet: -0.37 (0.20), residues: 749 loop : -1.12 (0.12), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP e 83 HIS 0.010 0.001 HIS a 802 PHE 0.035 0.002 PHE m 14 TYR 0.035 0.002 TYR h 68 ARG 0.006 0.001 ARG k 119 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 778 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 772 time to evaluate : 5.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 76 MET cc_start: 0.9414 (mmp) cc_final: 0.9135 (mmm) REVERT: 8 132 MET cc_start: 0.7710 (mmp) cc_final: 0.7493 (mmm) REVERT: R 42 MET cc_start: 0.8946 (mmp) cc_final: 0.8544 (ppp) REVERT: 0 34 MET cc_start: 0.9389 (mmp) cc_final: 0.9084 (mmm) REVERT: 0 61 MET cc_start: 0.9008 (mmm) cc_final: 0.8635 (mmm) REVERT: 0 284 MET cc_start: 0.9480 (tpp) cc_final: 0.9248 (tpt) REVERT: 0 318 MET cc_start: 0.8620 (mpp) cc_final: 0.8351 (mpp) REVERT: 0 360 GLU cc_start: 0.9014 (tm-30) cc_final: 0.8660 (tm-30) REVERT: 0 540 MET cc_start: 0.7830 (ppp) cc_final: 0.7485 (ppp) REVERT: 1 39 MET cc_start: 0.9398 (tpp) cc_final: 0.9179 (tpp) REVERT: 1 61 MET cc_start: 0.8984 (mmm) cc_final: 0.8642 (mmm) REVERT: 1 108 ASP cc_start: 0.9030 (p0) cc_final: 0.8758 (p0) REVERT: 1 340 MET cc_start: 0.9013 (tpp) cc_final: 0.8612 (tpp) REVERT: 1 419 ASP cc_start: 0.8926 (t0) cc_final: 0.8542 (t0) REVERT: 1 540 MET cc_start: 0.9439 (mtm) cc_final: 0.8939 (mtp) REVERT: 1 571 ARG cc_start: 0.9164 (tpp80) cc_final: 0.8784 (ttp-110) REVERT: 1 574 MET cc_start: 0.9192 (pmm) cc_final: 0.8976 (pmm) REVERT: 2 34 MET cc_start: 0.9278 (mmm) cc_final: 0.8998 (mmm) REVERT: 2 205 MET cc_start: 0.8984 (ptp) cc_final: 0.8647 (ptp) REVERT: 2 306 MET cc_start: 0.9086 (tmm) cc_final: 0.8623 (tmm) REVERT: 2 318 MET cc_start: 0.9335 (mtt) cc_final: 0.8933 (mtp) REVERT: 2 485 GLU cc_start: 0.9306 (mt-10) cc_final: 0.8961 (mm-30) REVERT: 2 550 MET cc_start: 0.9373 (mtm) cc_final: 0.9057 (mtp) REVERT: 2 608 MET cc_start: 0.9445 (mtm) cc_final: 0.9190 (mpp) REVERT: 3 127 MET cc_start: 0.9410 (mtp) cc_final: 0.9089 (mtt) REVERT: 3 169 MET cc_start: 0.8922 (tmm) cc_final: 0.8610 (tmm) REVERT: 3 316 GLU cc_start: 0.8893 (mt-10) cc_final: 0.8303 (mp0) REVERT: 3 327 MET cc_start: 0.9563 (ppp) cc_final: 0.9318 (tmm) REVERT: 3 410 MET cc_start: 0.9010 (mpp) cc_final: 0.8548 (mpp) REVERT: 4 162 CYS cc_start: 0.9566 (m) cc_final: 0.8592 (t) REVERT: 4 180 MET cc_start: 0.8753 (tpp) cc_final: 0.8021 (tpp) REVERT: 4 309 GLU cc_start: 0.8923 (tp30) cc_final: 0.8664 (tp30) REVERT: 4 435 MET cc_start: 0.9169 (mmp) cc_final: 0.8966 (mmp) REVERT: 5 127 MET cc_start: 0.9071 (mtt) cc_final: 0.8715 (mtt) REVERT: 5 356 MET cc_start: 0.9207 (mpp) cc_final: 0.8639 (mmp) REVERT: 5 410 MET cc_start: 0.8430 (mpp) cc_final: 0.7946 (mpp) REVERT: 5 494 ARG cc_start: 0.8836 (mmt180) cc_final: 0.8052 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8510 (t0) cc_final: 0.8164 (t0) REVERT: 7 112 TYR cc_start: 0.9070 (t80) cc_final: 0.8741 (t80) REVERT: U 73 MET cc_start: -0.2879 (mtm) cc_final: -0.4216 (mmm) REVERT: U 276 MET cc_start: 0.7308 (tpp) cc_final: 0.6931 (mmm) REVERT: X 22 LEU cc_start: 0.9283 (mt) cc_final: 0.8867 (tp) REVERT: a 293 TRP cc_start: 0.7562 (t-100) cc_final: 0.7247 (t-100) REVERT: a 300 MET cc_start: 0.8882 (mmp) cc_final: 0.8599 (mmm) REVERT: a 304 TYR cc_start: 0.8433 (m-10) cc_final: 0.8082 (m-10) REVERT: a 331 ASP cc_start: 0.8861 (m-30) cc_final: 0.8482 (p0) REVERT: a 401 PHE cc_start: 0.8323 (t80) cc_final: 0.7917 (t80) REVERT: a 423 MET cc_start: 0.8740 (mmm) cc_final: 0.8321 (mmm) REVERT: a 536 PHE cc_start: 0.8264 (p90) cc_final: 0.7990 (p90) REVERT: a 651 MET cc_start: 0.8204 (mpp) cc_final: 0.7830 (mpp) REVERT: a 745 LEU cc_start: 0.8832 (mm) cc_final: 0.8287 (mm) REVERT: a 806 LEU cc_start: 0.9518 (tt) cc_final: 0.8996 (tp) REVERT: b 4 LEU cc_start: 0.8937 (mt) cc_final: 0.8282 (pt) REVERT: b 8 TYR cc_start: 0.8827 (m-80) cc_final: 0.8539 (m-80) REVERT: b 18 CYS cc_start: 0.9022 (m) cc_final: 0.8662 (p) REVERT: d 84 HIS cc_start: 0.8704 (t70) cc_final: 0.8425 (t70) REVERT: d 215 GLU cc_start: 0.8414 (tm-30) cc_final: 0.7691 (tm-30) REVERT: d 262 GLU cc_start: 0.8996 (mm-30) cc_final: 0.8200 (pp20) REVERT: g 21 SER cc_start: 0.9308 (m) cc_final: 0.8791 (p) REVERT: g 64 ILE cc_start: 0.6830 (mm) cc_final: 0.6601 (mm) REVERT: g 134 ILE cc_start: 0.8154 (mp) cc_final: 0.7542 (tt) REVERT: h 14 PHE cc_start: 0.8845 (m-80) cc_final: 0.8380 (m-80) REVERT: h 41 ILE cc_start: 0.7940 (mm) cc_final: 0.7652 (mm) REVERT: h 64 ILE cc_start: 0.7181 (mt) cc_final: 0.6937 (mt) REVERT: h 123 GLN cc_start: 0.6778 (mm-40) cc_final: 0.6403 (mm-40) REVERT: i 61 MET cc_start: 0.6286 (mmp) cc_final: 0.5021 (mmt) REVERT: i 64 ILE cc_start: 0.7314 (mt) cc_final: 0.6581 (mt) REVERT: i 65 ILE cc_start: 0.7397 (mm) cc_final: 0.6955 (mm) REVERT: j 13 PHE cc_start: 0.6808 (p90) cc_final: 0.6556 (p90) REVERT: j 67 ILE cc_start: 0.8709 (mm) cc_final: 0.8340 (mt) REVERT: j 136 ILE cc_start: 0.8197 (mt) cc_final: 0.7946 (mt) REVERT: k 23 MET cc_start: 0.2956 (ptm) cc_final: 0.2430 (ttp) REVERT: l 39 THR cc_start: 0.7148 (m) cc_final: 0.6930 (p) REVERT: l 67 ILE cc_start: 0.8530 (mp) cc_final: 0.8115 (mp) REVERT: m 64 ILE cc_start: 0.6465 (mt) cc_final: 0.5729 (mt) REVERT: n 28 MET cc_start: 0.8952 (mtp) cc_final: 0.8747 (mmt) REVERT: n 131 MET cc_start: 0.7719 (ptm) cc_final: 0.7487 (ptm) REVERT: o 44 MET cc_start: 0.6785 (mmp) cc_final: 0.6214 (mmt) REVERT: o 92 GLN cc_start: 0.6880 (mm-40) cc_final: 0.6635 (mm110) REVERT: p 629 MET cc_start: 0.7352 (mmp) cc_final: 0.6964 (mmm) REVERT: p 638 TYR cc_start: 0.9268 (m-80) cc_final: 0.8969 (m-80) REVERT: 9 54 MET cc_start: 0.8883 (mmm) cc_final: 0.8517 (mmm) REVERT: 9 208 MET cc_start: 0.9288 (mmm) cc_final: 0.9023 (tpp) REVERT: T 11 LEU cc_start: 0.8105 (mm) cc_final: 0.7713 (tt) REVERT: T 84 MET cc_start: 0.8948 (mtp) cc_final: 0.8701 (mtp) REVERT: Q 15 MET cc_start: 0.0801 (tmm) cc_final: 0.0363 (tmm) REVERT: f 77 LEU cc_start: 0.8950 (mt) cc_final: 0.8547 (mt) REVERT: s 20 ARG cc_start: 0.4714 (tpt90) cc_final: 0.3717 (mmt-90) outliers start: 6 outliers final: 0 residues processed: 774 average time/residue: 0.6671 time to fit residues: 908.9532 Evaluate side-chains 640 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 640 time to evaluate : 5.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 275 optimal weight: 6.9990 chunk 736 optimal weight: 8.9990 chunk 161 optimal weight: 8.9990 chunk 480 optimal weight: 5.9990 chunk 201 optimal weight: 0.9990 chunk 818 optimal weight: 10.0000 chunk 679 optimal weight: 5.9990 chunk 378 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 270 optimal weight: 0.9980 chunk 429 optimal weight: 10.0000 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 0 164 HIS ** 4 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** a 802 HIS ** d 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7485 moved from start: 0.2323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 68193 Z= 0.220 Angle : 0.593 11.237 92164 Z= 0.309 Chirality : 0.042 0.268 10453 Planarity : 0.004 0.059 11796 Dihedral : 4.574 27.473 9269 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.52 % Favored : 95.47 % Rotamer: Outliers : 0.00 % Allowed : 1.53 % Favored : 98.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.82 (0.09), residues: 8475 helix: 1.61 (0.07), residues: 4856 sheet: -0.27 (0.20), residues: 752 loop : -1.07 (0.12), residues: 2867 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP e 83 HIS 0.011 0.001 HIS a 802 PHE 0.040 0.002 PHE f 33 TYR 0.032 0.002 TYR h 144 ARG 0.007 0.000 ARG l 119 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 771 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 771 time to evaluate : 5.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 76 MET cc_start: 0.9373 (mmp) cc_final: 0.9121 (mmm) REVERT: R 16 LYS cc_start: 0.8801 (ptpt) cc_final: 0.8601 (tppt) REVERT: R 42 MET cc_start: 0.8946 (mmp) cc_final: 0.8554 (ppp) REVERT: 0 34 MET cc_start: 0.9406 (mmp) cc_final: 0.9159 (mmm) REVERT: 0 61 MET cc_start: 0.9065 (mmm) cc_final: 0.8680 (mmm) REVERT: 0 65 GLN cc_start: 0.9084 (tm-30) cc_final: 0.8834 (tm-30) REVERT: 0 284 MET cc_start: 0.9455 (tpp) cc_final: 0.9176 (tpt) REVERT: 0 291 PHE cc_start: 0.8770 (t80) cc_final: 0.8386 (t80) REVERT: 0 340 MET cc_start: 0.8599 (tpp) cc_final: 0.8321 (tpp) REVERT: 0 360 GLU cc_start: 0.9016 (tm-30) cc_final: 0.8586 (tm-30) REVERT: 0 540 MET cc_start: 0.7849 (ppp) cc_final: 0.7500 (ppp) REVERT: 1 39 MET cc_start: 0.9421 (tpp) cc_final: 0.9206 (tpp) REVERT: 1 61 MET cc_start: 0.8996 (mmm) cc_final: 0.8660 (mmm) REVERT: 1 108 ASP cc_start: 0.9005 (p0) cc_final: 0.8745 (p0) REVERT: 1 306 MET cc_start: 0.7481 (mmp) cc_final: 0.7215 (mmp) REVERT: 1 340 MET cc_start: 0.9078 (tpp) cc_final: 0.8578 (tpp) REVERT: 1 419 ASP cc_start: 0.8800 (t0) cc_final: 0.8372 (t0) REVERT: 1 540 MET cc_start: 0.9441 (mtm) cc_final: 0.8916 (mtp) REVERT: 1 571 ARG cc_start: 0.9170 (tpp80) cc_final: 0.8794 (ttm110) REVERT: 2 34 MET cc_start: 0.9275 (mmm) cc_final: 0.9009 (mmm) REVERT: 2 205 MET cc_start: 0.9000 (ptp) cc_final: 0.8700 (ptp) REVERT: 2 306 MET cc_start: 0.9034 (tmm) cc_final: 0.8547 (tmm) REVERT: 2 318 MET cc_start: 0.9335 (mtt) cc_final: 0.8907 (mtp) REVERT: 2 485 GLU cc_start: 0.9262 (mt-10) cc_final: 0.8909 (mm-30) REVERT: 2 540 MET cc_start: 0.9111 (mtp) cc_final: 0.7538 (mmt) REVERT: 2 550 MET cc_start: 0.9381 (mtm) cc_final: 0.9058 (mtp) REVERT: 2 608 MET cc_start: 0.9438 (mtm) cc_final: 0.9229 (mpp) REVERT: 3 127 MET cc_start: 0.9387 (mtp) cc_final: 0.9077 (mtt) REVERT: 3 169 MET cc_start: 0.8915 (tmm) cc_final: 0.8611 (tmm) REVERT: 3 316 GLU cc_start: 0.8872 (mt-10) cc_final: 0.8279 (mp0) REVERT: 3 327 MET cc_start: 0.9566 (ppp) cc_final: 0.9233 (tmm) REVERT: 3 410 MET cc_start: 0.8981 (mpp) cc_final: 0.8614 (mpp) REVERT: 3 431 ASP cc_start: 0.9249 (m-30) cc_final: 0.9039 (m-30) REVERT: 4 127 MET cc_start: 0.9523 (mtp) cc_final: 0.9082 (mtt) REVERT: 4 162 CYS cc_start: 0.9567 (m) cc_final: 0.8548 (t) REVERT: 4 180 MET cc_start: 0.8743 (tpp) cc_final: 0.8030 (tpp) REVERT: 4 309 GLU cc_start: 0.8960 (tp30) cc_final: 0.8671 (tp30) REVERT: 5 127 MET cc_start: 0.9135 (mtt) cc_final: 0.8776 (mtt) REVERT: 5 356 MET cc_start: 0.9210 (mpp) cc_final: 0.8635 (mmp) REVERT: 5 410 MET cc_start: 0.8460 (mpp) cc_final: 0.7997 (mpp) REVERT: 5 494 ARG cc_start: 0.8834 (mmt180) cc_final: 0.8020 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8455 (t0) cc_final: 0.8087 (t0) REVERT: 7 112 TYR cc_start: 0.9053 (t80) cc_final: 0.8741 (t80) REVERT: U 73 MET cc_start: -0.2938 (mtm) cc_final: -0.4216 (mmm) REVERT: U 276 MET cc_start: 0.7226 (tpp) cc_final: 0.6848 (mmm) REVERT: X 59 ASP cc_start: 0.8992 (p0) cc_final: 0.8772 (p0) REVERT: a 293 TRP cc_start: 0.7568 (t-100) cc_final: 0.7320 (t-100) REVERT: a 300 MET cc_start: 0.8921 (mmp) cc_final: 0.8591 (mmm) REVERT: a 304 TYR cc_start: 0.8399 (m-10) cc_final: 0.8037 (m-10) REVERT: a 331 ASP cc_start: 0.8826 (m-30) cc_final: 0.8462 (p0) REVERT: a 401 PHE cc_start: 0.8189 (t80) cc_final: 0.7922 (t80) REVERT: a 423 MET cc_start: 0.8686 (mmm) cc_final: 0.8350 (mmm) REVERT: a 645 MET cc_start: 0.8980 (tmm) cc_final: 0.8711 (tmm) REVERT: a 651 MET cc_start: 0.8306 (mpp) cc_final: 0.7888 (mpp) REVERT: a 718 MET cc_start: 0.8150 (tpt) cc_final: 0.7796 (tpt) REVERT: a 745 LEU cc_start: 0.8926 (mm) cc_final: 0.8419 (mm) REVERT: b 4 LEU cc_start: 0.8841 (mt) cc_final: 0.8559 (pt) REVERT: b 18 CYS cc_start: 0.9073 (m) cc_final: 0.8688 (p) REVERT: b 135 TYR cc_start: 0.2643 (t80) cc_final: 0.2335 (t80) REVERT: b 192 ILE cc_start: 0.8827 (mm) cc_final: 0.8581 (pt) REVERT: d 84 HIS cc_start: 0.8567 (t70) cc_final: 0.8339 (t-170) REVERT: d 105 MET cc_start: 0.8604 (mmp) cc_final: 0.8199 (mmp) REVERT: d 209 CYS cc_start: 0.9076 (m) cc_final: 0.8803 (m) REVERT: d 215 GLU cc_start: 0.8629 (tm-30) cc_final: 0.8328 (tm-30) REVERT: d 262 GLU cc_start: 0.8961 (mm-30) cc_final: 0.8188 (pp20) REVERT: g 21 SER cc_start: 0.9336 (m) cc_final: 0.8889 (p) REVERT: g 64 ILE cc_start: 0.6743 (mm) cc_final: 0.6517 (mm) REVERT: g 134 ILE cc_start: 0.8021 (mp) cc_final: 0.7477 (tt) REVERT: h 14 PHE cc_start: 0.8833 (m-80) cc_final: 0.8361 (m-80) REVERT: h 41 ILE cc_start: 0.7925 (mm) cc_final: 0.7622 (mm) REVERT: h 64 ILE cc_start: 0.7264 (mt) cc_final: 0.7023 (mt) REVERT: h 123 GLN cc_start: 0.6842 (mm-40) cc_final: 0.6445 (mm-40) REVERT: h 131 MET cc_start: 0.7275 (ptt) cc_final: 0.6967 (ppp) REVERT: i 61 MET cc_start: 0.6514 (mmp) cc_final: 0.5372 (mtt) REVERT: i 64 ILE cc_start: 0.7490 (mt) cc_final: 0.6813 (mt) REVERT: i 65 ILE cc_start: 0.7452 (mm) cc_final: 0.7104 (mm) REVERT: j 136 ILE cc_start: 0.8226 (mt) cc_final: 0.7950 (mt) REVERT: k 23 MET cc_start: 0.2694 (ptm) cc_final: 0.2159 (mtp) REVERT: k 131 MET cc_start: 0.7895 (ppp) cc_final: 0.6987 (ptt) REVERT: l 67 ILE cc_start: 0.8551 (mp) cc_final: 0.8079 (mp) REVERT: m 64 ILE cc_start: 0.6409 (mt) cc_final: 0.5631 (mt) REVERT: m 143 LEU cc_start: 0.9364 (tp) cc_final: 0.9050 (mp) REVERT: n 44 MET cc_start: 0.2030 (ttp) cc_final: 0.1460 (tmm) REVERT: o 44 MET cc_start: 0.6645 (mmp) cc_final: 0.6056 (mmt) REVERT: o 92 GLN cc_start: 0.6970 (mm-40) cc_final: 0.6719 (mm110) REVERT: p 629 MET cc_start: 0.7085 (mmp) cc_final: 0.6791 (mmm) REVERT: p 638 TYR cc_start: 0.9261 (m-80) cc_final: 0.8996 (m-80) REVERT: 9 54 MET cc_start: 0.8879 (mmm) cc_final: 0.8499 (mmm) REVERT: 9 208 MET cc_start: 0.9188 (mmm) cc_final: 0.8810 (tpp) REVERT: T 11 LEU cc_start: 0.8023 (mm) cc_final: 0.7682 (tt) REVERT: T 84 MET cc_start: 0.8942 (mtp) cc_final: 0.8711 (mtp) REVERT: f 77 LEU cc_start: 0.8940 (mt) cc_final: 0.8530 (mt) REVERT: s 153 MET cc_start: 0.4525 (ppp) cc_final: 0.4029 (tmm) outliers start: 0 outliers final: 0 residues processed: 771 average time/residue: 0.6439 time to fit residues: 875.0136 Evaluate side-chains 643 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 643 time to evaluate : 5.934 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 789 optimal weight: 0.2980 chunk 92 optimal weight: 0.7980 chunk 466 optimal weight: 5.9990 chunk 597 optimal weight: 5.9990 chunk 463 optimal weight: 6.9990 chunk 689 optimal weight: 9.9990 chunk 457 optimal weight: 5.9990 chunk 815 optimal weight: 7.9990 chunk 510 optimal weight: 20.0000 chunk 497 optimal weight: 20.0000 chunk 376 optimal weight: 30.0000 overall best weight: 3.8186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 8 122 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 288 GLN ** 7 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 802 HIS d 119 GLN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 68193 Z= 0.240 Angle : 0.604 9.691 92164 Z= 0.315 Chirality : 0.042 0.269 10453 Planarity : 0.004 0.054 11796 Dihedral : 4.567 26.905 9269 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.88 % Favored : 95.10 % Rotamer: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.81 (0.09), residues: 8475 helix: 1.60 (0.07), residues: 4864 sheet: -0.22 (0.20), residues: 747 loop : -1.09 (0.12), residues: 2864 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP e 83 HIS 0.010 0.001 HIS a 802 PHE 0.035 0.002 PHE m 14 TYR 0.036 0.002 TYR h 144 ARG 0.006 0.000 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 764 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 764 time to evaluate : 5.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 76 MET cc_start: 0.9366 (mmp) cc_final: 0.9106 (mmm) REVERT: 8 132 MET cc_start: 0.7669 (mmp) cc_final: 0.7453 (mmm) REVERT: R 42 MET cc_start: 0.8949 (mmp) cc_final: 0.8555 (ppp) REVERT: 0 34 MET cc_start: 0.9414 (mmp) cc_final: 0.9163 (mmm) REVERT: 0 61 MET cc_start: 0.9047 (mmm) cc_final: 0.8663 (mmm) REVERT: 0 65 GLN cc_start: 0.9088 (tm-30) cc_final: 0.8822 (tm-30) REVERT: 0 284 MET cc_start: 0.9457 (tpp) cc_final: 0.9179 (tpt) REVERT: 0 291 PHE cc_start: 0.8859 (t80) cc_final: 0.8430 (t80) REVERT: 0 318 MET cc_start: 0.8513 (mpp) cc_final: 0.8236 (mpp) REVERT: 0 360 GLU cc_start: 0.9013 (tm-30) cc_final: 0.8582 (tm-30) REVERT: 0 540 MET cc_start: 0.7951 (ppp) cc_final: 0.7568 (ppp) REVERT: 1 39 MET cc_start: 0.9430 (tpp) cc_final: 0.9222 (tpp) REVERT: 1 61 MET cc_start: 0.9006 (mmm) cc_final: 0.8693 (mmm) REVERT: 1 108 ASP cc_start: 0.9012 (p0) cc_final: 0.8740 (p0) REVERT: 1 306 MET cc_start: 0.7451 (mmp) cc_final: 0.7190 (mmp) REVERT: 1 340 MET cc_start: 0.9068 (tpp) cc_final: 0.8554 (tpp) REVERT: 1 346 MET cc_start: 0.9265 (ttp) cc_final: 0.8616 (tmm) REVERT: 1 419 ASP cc_start: 0.8801 (t0) cc_final: 0.8372 (t0) REVERT: 1 540 MET cc_start: 0.9442 (mtm) cc_final: 0.8892 (mtp) REVERT: 1 571 ARG cc_start: 0.9176 (tpp80) cc_final: 0.8797 (ttm110) REVERT: 2 34 MET cc_start: 0.9277 (mmm) cc_final: 0.9011 (mmm) REVERT: 2 205 MET cc_start: 0.8975 (ptp) cc_final: 0.8657 (ptp) REVERT: 2 306 MET cc_start: 0.9021 (tmm) cc_final: 0.8531 (tmm) REVERT: 2 318 MET cc_start: 0.9313 (mtt) cc_final: 0.8917 (mtp) REVERT: 2 485 GLU cc_start: 0.9281 (mt-10) cc_final: 0.8935 (mm-30) REVERT: 2 540 MET cc_start: 0.9168 (mtp) cc_final: 0.7154 (mmt) REVERT: 2 550 MET cc_start: 0.9374 (mtm) cc_final: 0.9053 (mtp) REVERT: 2 608 MET cc_start: 0.9442 (mtm) cc_final: 0.9235 (mpp) REVERT: 3 127 MET cc_start: 0.9396 (mtp) cc_final: 0.9139 (mtt) REVERT: 3 169 MET cc_start: 0.8960 (tmm) cc_final: 0.8609 (tmm) REVERT: 3 316 GLU cc_start: 0.8867 (mt-10) cc_final: 0.8279 (mp0) REVERT: 3 327 MET cc_start: 0.9563 (ppp) cc_final: 0.9254 (tmm) REVERT: 3 356 MET cc_start: 0.8862 (mmm) cc_final: 0.8577 (mmm) REVERT: 3 410 MET cc_start: 0.8950 (mpp) cc_final: 0.8565 (mpp) REVERT: 3 431 ASP cc_start: 0.9248 (m-30) cc_final: 0.9039 (m-30) REVERT: 4 162 CYS cc_start: 0.9553 (m) cc_final: 0.8567 (t) REVERT: 4 169 MET cc_start: 0.9161 (tmm) cc_final: 0.8915 (tmm) REVERT: 4 180 MET cc_start: 0.8738 (tpp) cc_final: 0.8038 (tpp) REVERT: 4 309 GLU cc_start: 0.8953 (tp30) cc_final: 0.8656 (tp30) REVERT: 5 127 MET cc_start: 0.9123 (mtt) cc_final: 0.8760 (mtt) REVERT: 5 356 MET cc_start: 0.9223 (mpp) cc_final: 0.8642 (mmp) REVERT: 5 410 MET cc_start: 0.8371 (mpp) cc_final: 0.7900 (mpp) REVERT: 5 494 ARG cc_start: 0.8820 (mmt180) cc_final: 0.7998 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8478 (t0) cc_final: 0.8096 (t0) REVERT: 7 112 TYR cc_start: 0.9046 (t80) cc_final: 0.8738 (t80) REVERT: U 73 MET cc_start: -0.2969 (mtm) cc_final: -0.4235 (mmm) REVERT: U 276 MET cc_start: 0.7189 (tpp) cc_final: 0.6798 (mmm) REVERT: U 389 LEU cc_start: 0.9015 (mt) cc_final: 0.8755 (mt) REVERT: X 59 ASP cc_start: 0.9007 (p0) cc_final: 0.8769 (p0) REVERT: a 293 TRP cc_start: 0.7568 (t-100) cc_final: 0.7319 (t-100) REVERT: a 300 MET cc_start: 0.8965 (mmp) cc_final: 0.8624 (mmm) REVERT: a 304 TYR cc_start: 0.8400 (m-10) cc_final: 0.8038 (m-10) REVERT: a 331 ASP cc_start: 0.8798 (m-30) cc_final: 0.8390 (p0) REVERT: a 401 PHE cc_start: 0.8201 (t80) cc_final: 0.7971 (t80) REVERT: a 423 MET cc_start: 0.8687 (mmm) cc_final: 0.8436 (mmm) REVERT: a 536 PHE cc_start: 0.8171 (p90) cc_final: 0.7924 (p90) REVERT: a 645 MET cc_start: 0.9032 (tmm) cc_final: 0.8825 (tmm) REVERT: a 651 MET cc_start: 0.8273 (mpp) cc_final: 0.7856 (mpp) REVERT: a 718 MET cc_start: 0.8179 (tpt) cc_final: 0.7799 (tpt) REVERT: a 745 LEU cc_start: 0.8925 (mm) cc_final: 0.8210 (mm) REVERT: b 4 LEU cc_start: 0.8940 (mt) cc_final: 0.8327 (pt) REVERT: b 8 TYR cc_start: 0.8876 (m-80) cc_final: 0.8620 (m-80) REVERT: b 18 CYS cc_start: 0.9076 (m) cc_final: 0.8694 (p) REVERT: b 135 TYR cc_start: 0.2412 (t80) cc_final: 0.2149 (t80) REVERT: b 192 ILE cc_start: 0.8786 (mm) cc_final: 0.8541 (pt) REVERT: d 209 CYS cc_start: 0.9110 (m) cc_final: 0.8828 (m) REVERT: d 215 GLU cc_start: 0.8589 (tm-30) cc_final: 0.8302 (tm-30) REVERT: d 262 GLU cc_start: 0.8950 (mm-30) cc_final: 0.8164 (pp20) REVERT: g 21 SER cc_start: 0.9327 (m) cc_final: 0.8851 (p) REVERT: g 64 ILE cc_start: 0.6702 (mm) cc_final: 0.6313 (mm) REVERT: g 134 ILE cc_start: 0.7974 (mp) cc_final: 0.7377 (tt) REVERT: h 14 PHE cc_start: 0.8836 (m-80) cc_final: 0.8358 (m-80) REVERT: h 41 ILE cc_start: 0.7916 (mm) cc_final: 0.7612 (mm) REVERT: h 64 ILE cc_start: 0.7282 (mt) cc_final: 0.7042 (mt) REVERT: h 123 GLN cc_start: 0.6721 (mm-40) cc_final: 0.6345 (mm-40) REVERT: h 131 MET cc_start: 0.7207 (ptt) cc_final: 0.6907 (ppp) REVERT: i 61 MET cc_start: 0.6431 (mmp) cc_final: 0.5317 (mtt) REVERT: i 64 ILE cc_start: 0.7509 (mt) cc_final: 0.6796 (mt) REVERT: i 65 ILE cc_start: 0.7464 (mm) cc_final: 0.7106 (mm) REVERT: j 136 ILE cc_start: 0.8194 (mt) cc_final: 0.7982 (mt) REVERT: k 23 MET cc_start: 0.2701 (ptm) cc_final: 0.2257 (mtp) REVERT: k 131 MET cc_start: 0.7917 (ppp) cc_final: 0.7007 (ptt) REVERT: l 23 MET cc_start: 0.7206 (pmm) cc_final: 0.6913 (pmm) REVERT: l 39 THR cc_start: 0.6388 (p) cc_final: 0.6125 (p) REVERT: l 67 ILE cc_start: 0.8424 (mp) cc_final: 0.7887 (mp) REVERT: m 64 ILE cc_start: 0.6438 (mt) cc_final: 0.5633 (mt) REVERT: n 25 PHE cc_start: 0.9333 (m-10) cc_final: 0.9094 (m-10) REVERT: o 44 MET cc_start: 0.6680 (mmp) cc_final: 0.6082 (mmt) REVERT: o 92 GLN cc_start: 0.6999 (mm-40) cc_final: 0.6650 (mm110) REVERT: p 634 ASP cc_start: 0.7839 (p0) cc_final: 0.7611 (p0) REVERT: 9 54 MET cc_start: 0.8882 (mmm) cc_final: 0.8498 (mmm) REVERT: 9 208 MET cc_start: 0.9218 (mmm) cc_final: 0.8924 (tpp) REVERT: T 11 LEU cc_start: 0.8024 (mm) cc_final: 0.7652 (tt) REVERT: T 84 MET cc_start: 0.8944 (mtp) cc_final: 0.8721 (mtp) REVERT: f 77 LEU cc_start: 0.8953 (mt) cc_final: 0.8537 (mt) REVERT: s 153 MET cc_start: 0.4363 (ppp) cc_final: 0.3697 (tmm) outliers start: 0 outliers final: 0 residues processed: 764 average time/residue: 0.6242 time to fit residues: 837.7001 Evaluate side-chains 644 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 5.880 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 504 optimal weight: 0.9990 chunk 325 optimal weight: 7.9990 chunk 487 optimal weight: 0.9980 chunk 245 optimal weight: 20.0000 chunk 160 optimal weight: 5.9990 chunk 157 optimal weight: 7.9990 chunk 518 optimal weight: 6.9990 chunk 555 optimal weight: 8.9990 chunk 403 optimal weight: 0.5980 chunk 75 optimal weight: 20.0000 chunk 640 optimal weight: 9.9990 overall best weight: 3.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 8 122 GLN 0 573 HIS ** 7 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 176 ASN a 534 ASN a 802 HIS d 84 HIS d 88 HIS ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2526 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 68193 Z= 0.215 Angle : 0.599 9.925 92164 Z= 0.311 Chirality : 0.042 0.292 10453 Planarity : 0.004 0.054 11796 Dihedral : 4.527 25.826 9269 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.63 % Favored : 95.36 % Rotamer: Outliers : 0.00 % Allowed : 0.72 % Favored : 99.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.09), residues: 8475 helix: 1.64 (0.07), residues: 4864 sheet: -0.18 (0.20), residues: 748 loop : -1.07 (0.12), residues: 2863 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.065 0.002 TRP 6 294 HIS 0.011 0.001 HIS a 802 PHE 0.059 0.002 PHE j 13 TYR 0.037 0.001 TYR h 144 ARG 0.009 0.000 ARG 2 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 779 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 779 time to evaluate : 5.904 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 76 MET cc_start: 0.9367 (mmp) cc_final: 0.9116 (mmm) REVERT: R 42 MET cc_start: 0.8949 (mmp) cc_final: 0.8554 (ppp) REVERT: 0 34 MET cc_start: 0.9423 (mmp) cc_final: 0.9201 (mmm) REVERT: 0 61 MET cc_start: 0.9062 (mmm) cc_final: 0.8668 (mmm) REVERT: 0 65 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8807 (tm-30) REVERT: 0 284 MET cc_start: 0.9460 (tpp) cc_final: 0.9227 (tpt) REVERT: 0 291 PHE cc_start: 0.8887 (t80) cc_final: 0.8392 (t80) REVERT: 0 318 MET cc_start: 0.8501 (mpp) cc_final: 0.8193 (mpp) REVERT: 0 540 MET cc_start: 0.7915 (ppp) cc_final: 0.7533 (ppp) REVERT: 1 39 MET cc_start: 0.9440 (tpp) cc_final: 0.9234 (tpp) REVERT: 1 61 MET cc_start: 0.8972 (mmm) cc_final: 0.8681 (mmm) REVERT: 1 108 ASP cc_start: 0.9012 (p0) cc_final: 0.8801 (p0) REVERT: 1 306 MET cc_start: 0.7293 (mmp) cc_final: 0.7032 (mmp) REVERT: 1 340 MET cc_start: 0.9092 (tpp) cc_final: 0.8564 (tpp) REVERT: 1 346 MET cc_start: 0.9193 (ttp) cc_final: 0.8630 (tmm) REVERT: 1 419 ASP cc_start: 0.8757 (t0) cc_final: 0.8336 (t0) REVERT: 1 540 MET cc_start: 0.9447 (mtm) cc_final: 0.8853 (mtp) REVERT: 1 571 ARG cc_start: 0.9197 (tpp80) cc_final: 0.8812 (ttm110) REVERT: 2 34 MET cc_start: 0.9291 (mmm) cc_final: 0.9023 (mmm) REVERT: 2 205 MET cc_start: 0.8973 (ptp) cc_final: 0.8666 (ptp) REVERT: 2 306 MET cc_start: 0.9011 (tmm) cc_final: 0.8514 (tmm) REVERT: 2 318 MET cc_start: 0.9314 (mtt) cc_final: 0.8955 (mtp) REVERT: 2 485 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8921 (mm-30) REVERT: 2 540 MET cc_start: 0.8769 (mtp) cc_final: 0.7862 (mmt) REVERT: 2 550 MET cc_start: 0.9374 (mtm) cc_final: 0.9041 (mtp) REVERT: 2 584 MET cc_start: 0.8924 (ptp) cc_final: 0.8052 (ptp) REVERT: 2 608 MET cc_start: 0.9422 (mtm) cc_final: 0.9187 (mpp) REVERT: 3 127 MET cc_start: 0.9386 (mtp) cc_final: 0.9093 (mtt) REVERT: 3 169 MET cc_start: 0.8947 (tmm) cc_final: 0.8608 (tmm) REVERT: 3 316 GLU cc_start: 0.8849 (mt-10) cc_final: 0.8302 (mp0) REVERT: 3 327 MET cc_start: 0.9570 (ppp) cc_final: 0.9267 (tmm) REVERT: 3 356 MET cc_start: 0.8969 (mmm) cc_final: 0.8627 (tmm) REVERT: 3 410 MET cc_start: 0.8881 (mpp) cc_final: 0.8515 (mpp) REVERT: 3 431 ASP cc_start: 0.9242 (m-30) cc_final: 0.9031 (m-30) REVERT: 4 127 MET cc_start: 0.9531 (mtp) cc_final: 0.9002 (mtt) REVERT: 4 162 CYS cc_start: 0.9548 (m) cc_final: 0.8550 (t) REVERT: 4 169 MET cc_start: 0.9138 (tmm) cc_final: 0.8911 (tmm) REVERT: 4 180 MET cc_start: 0.8769 (tpp) cc_final: 0.8044 (tpp) REVERT: 4 309 GLU cc_start: 0.8958 (tp30) cc_final: 0.8677 (tp30) REVERT: 5 127 MET cc_start: 0.9151 (mtt) cc_final: 0.8825 (mtt) REVERT: 5 356 MET cc_start: 0.9202 (mpp) cc_final: 0.8629 (mmp) REVERT: 5 410 MET cc_start: 0.8440 (mpp) cc_final: 0.8000 (mpp) REVERT: 5 494 ARG cc_start: 0.8796 (mmt180) cc_final: 0.7974 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8431 (t0) cc_final: 0.8073 (t0) REVERT: 7 112 TYR cc_start: 0.9027 (t80) cc_final: 0.8732 (t80) REVERT: U 73 MET cc_start: -0.2972 (mtm) cc_final: -0.4234 (mmm) REVERT: U 97 MET cc_start: 0.6328 (ptt) cc_final: 0.5877 (ppp) REVERT: U 276 MET cc_start: 0.7179 (tpp) cc_final: 0.6789 (mmm) REVERT: U 389 LEU cc_start: 0.9021 (mt) cc_final: 0.8746 (mt) REVERT: X 59 ASP cc_start: 0.9038 (p0) cc_final: 0.8820 (p0) REVERT: a 293 TRP cc_start: 0.7543 (t-100) cc_final: 0.7296 (t-100) REVERT: a 300 MET cc_start: 0.8867 (mmp) cc_final: 0.8588 (mmm) REVERT: a 304 TYR cc_start: 0.8332 (m-10) cc_final: 0.7971 (m-10) REVERT: a 331 ASP cc_start: 0.8822 (m-30) cc_final: 0.8442 (p0) REVERT: a 401 PHE cc_start: 0.8223 (t80) cc_final: 0.8012 (t80) REVERT: a 423 MET cc_start: 0.8672 (mmm) cc_final: 0.8438 (mmm) REVERT: a 536 PHE cc_start: 0.8176 (p90) cc_final: 0.7957 (p90) REVERT: a 651 MET cc_start: 0.8277 (mpp) cc_final: 0.7853 (mpp) REVERT: a 718 MET cc_start: 0.8155 (tpt) cc_final: 0.7781 (tpt) REVERT: a 745 LEU cc_start: 0.8850 (mm) cc_final: 0.8159 (mm) REVERT: b 4 LEU cc_start: 0.8944 (mt) cc_final: 0.8319 (pt) REVERT: b 8 TYR cc_start: 0.8871 (m-80) cc_final: 0.8606 (m-80) REVERT: b 18 CYS cc_start: 0.9098 (m) cc_final: 0.8726 (p) REVERT: b 192 ILE cc_start: 0.8758 (mm) cc_final: 0.8500 (pt) REVERT: b 203 MET cc_start: 0.4632 (tpt) cc_final: 0.4214 (tpt) REVERT: d 105 MET cc_start: 0.8560 (mmp) cc_final: 0.8202 (mmp) REVERT: d 209 CYS cc_start: 0.9115 (m) cc_final: 0.8808 (m) REVERT: d 215 GLU cc_start: 0.8531 (tm-30) cc_final: 0.8257 (tm-30) REVERT: d 262 GLU cc_start: 0.8915 (mm-30) cc_final: 0.8150 (pp20) REVERT: d 334 GLU cc_start: 0.9449 (mm-30) cc_final: 0.9205 (mm-30) REVERT: g 21 SER cc_start: 0.9296 (m) cc_final: 0.8770 (p) REVERT: g 44 MET cc_start: 0.0095 (mtm) cc_final: -0.0109 (mtm) REVERT: g 64 ILE cc_start: 0.6655 (mm) cc_final: 0.6430 (mm) REVERT: g 108 PHE cc_start: 0.7503 (t80) cc_final: 0.7299 (t80) REVERT: g 134 ILE cc_start: 0.7976 (mp) cc_final: 0.7362 (tt) REVERT: h 14 PHE cc_start: 0.8796 (m-80) cc_final: 0.8382 (m-80) REVERT: h 41 ILE cc_start: 0.7890 (mm) cc_final: 0.7575 (mm) REVERT: h 53 MET cc_start: 0.7444 (mmp) cc_final: 0.6106 (tpt) REVERT: h 64 ILE cc_start: 0.7279 (mt) cc_final: 0.7039 (mt) REVERT: h 123 GLN cc_start: 0.6692 (mm-40) cc_final: 0.6316 (mm-40) REVERT: h 131 MET cc_start: 0.7547 (ptt) cc_final: 0.7237 (ppp) REVERT: i 61 MET cc_start: 0.6577 (mmp) cc_final: 0.5495 (mtt) REVERT: i 64 ILE cc_start: 0.7576 (mt) cc_final: 0.6874 (mt) REVERT: i 65 ILE cc_start: 0.7434 (mm) cc_final: 0.7066 (mm) REVERT: j 136 ILE cc_start: 0.8223 (mt) cc_final: 0.7968 (mt) REVERT: k 23 MET cc_start: 0.2776 (ptm) cc_final: 0.2452 (mtp) REVERT: k 131 MET cc_start: 0.7916 (ppp) cc_final: 0.7019 (ptt) REVERT: l 39 THR cc_start: 0.6242 (p) cc_final: 0.5971 (p) REVERT: m 64 ILE cc_start: 0.6495 (mt) cc_final: 0.5908 (mt) REVERT: n 28 MET cc_start: 0.8943 (mtp) cc_final: 0.8738 (mmp) REVERT: o 44 MET cc_start: 0.6600 (mmp) cc_final: 0.5985 (mmt) REVERT: o 92 GLN cc_start: 0.6971 (mm-40) cc_final: 0.6472 (mm110) REVERT: p 634 ASP cc_start: 0.7789 (p0) cc_final: 0.7573 (p0) REVERT: 9 54 MET cc_start: 0.8893 (mmm) cc_final: 0.8510 (mmm) REVERT: 9 208 MET cc_start: 0.9203 (mmm) cc_final: 0.8792 (tpp) REVERT: T 11 LEU cc_start: 0.7799 (mm) cc_final: 0.7391 (tt) REVERT: T 84 MET cc_start: 0.8941 (mtp) cc_final: 0.8733 (mtp) REVERT: f 77 LEU cc_start: 0.8951 (mt) cc_final: 0.8531 (mt) outliers start: 0 outliers final: 0 residues processed: 779 average time/residue: 0.5893 time to fit residues: 806.8802 Evaluate side-chains 647 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 647 time to evaluate : 5.904 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 741 optimal weight: 4.9990 chunk 781 optimal weight: 8.9990 chunk 712 optimal weight: 6.9990 chunk 759 optimal weight: 8.9990 chunk 780 optimal weight: 5.9990 chunk 457 optimal weight: 1.9990 chunk 331 optimal weight: 0.9980 chunk 596 optimal weight: 6.9990 chunk 233 optimal weight: 3.9990 chunk 686 optimal weight: 5.9990 chunk 718 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 7 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 171 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 176 ASN a 802 HIS ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 9 205 GLN V 113 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7487 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 68193 Z= 0.233 Angle : 0.612 12.110 92164 Z= 0.318 Chirality : 0.042 0.417 10453 Planarity : 0.004 0.054 11796 Dihedral : 4.541 25.572 9269 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 12.85 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.96 % Favored : 95.03 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.88 (0.09), residues: 8475 helix: 1.67 (0.07), residues: 4846 sheet: -0.18 (0.20), residues: 743 loop : -1.09 (0.12), residues: 2886 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.082 0.002 TRP e 83 HIS 0.011 0.001 HIS a 802 PHE 0.044 0.002 PHE j 14 TYR 0.037 0.002 TYR h 144 ARG 0.007 0.000 ARG n 119 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 767 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 767 time to evaluate : 5.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 76 MET cc_start: 0.9359 (mmp) cc_final: 0.9103 (mmm) REVERT: R 42 MET cc_start: 0.8946 (mmp) cc_final: 0.8562 (ppp) REVERT: 0 60 ASP cc_start: 0.8268 (p0) cc_final: 0.7809 (p0) REVERT: 0 61 MET cc_start: 0.9119 (mmm) cc_final: 0.8674 (mmm) REVERT: 0 65 GLN cc_start: 0.9078 (tm-30) cc_final: 0.8790 (tm-30) REVERT: 0 284 MET cc_start: 0.9460 (tpp) cc_final: 0.9238 (tpt) REVERT: 0 296 MET cc_start: 0.8596 (mmm) cc_final: 0.8344 (mmm) REVERT: 0 318 MET cc_start: 0.8543 (mpp) cc_final: 0.8232 (mpp) REVERT: 0 340 MET cc_start: 0.8416 (tpp) cc_final: 0.8108 (tpt) REVERT: 0 540 MET cc_start: 0.7860 (ppp) cc_final: 0.7515 (ppp) REVERT: 1 39 MET cc_start: 0.9431 (tpp) cc_final: 0.9227 (tpp) REVERT: 1 61 MET cc_start: 0.8951 (mmm) cc_final: 0.8682 (mmm) REVERT: 1 108 ASP cc_start: 0.9034 (p0) cc_final: 0.8763 (p0) REVERT: 1 235 ASP cc_start: 0.9227 (t70) cc_final: 0.8923 (t0) REVERT: 1 340 MET cc_start: 0.9096 (tpp) cc_final: 0.8546 (tpp) REVERT: 1 346 MET cc_start: 0.9153 (ttp) cc_final: 0.8595 (tmm) REVERT: 1 419 ASP cc_start: 0.8814 (t0) cc_final: 0.8400 (t0) REVERT: 1 540 MET cc_start: 0.9424 (mtm) cc_final: 0.8819 (mtp) REVERT: 1 571 ARG cc_start: 0.9202 (tpp80) cc_final: 0.8889 (ttp-110) REVERT: 2 34 MET cc_start: 0.9260 (mmm) cc_final: 0.9008 (mmm) REVERT: 2 205 MET cc_start: 0.8982 (ptp) cc_final: 0.8675 (ptp) REVERT: 2 306 MET cc_start: 0.8985 (tmm) cc_final: 0.8682 (tmm) REVERT: 2 318 MET cc_start: 0.9302 (mtt) cc_final: 0.8915 (mtp) REVERT: 2 485 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8898 (mm-30) REVERT: 2 540 MET cc_start: 0.9178 (mtp) cc_final: 0.7512 (mmt) REVERT: 2 550 MET cc_start: 0.9375 (mtm) cc_final: 0.9073 (mtp) REVERT: 2 608 MET cc_start: 0.9406 (mtm) cc_final: 0.9168 (mpp) REVERT: 3 127 MET cc_start: 0.9383 (mtp) cc_final: 0.8970 (mtt) REVERT: 3 169 MET cc_start: 0.8958 (tmm) cc_final: 0.8621 (tmm) REVERT: 3 300 MET cc_start: 0.9415 (mmp) cc_final: 0.9130 (mmp) REVERT: 3 316 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8286 (mp0) REVERT: 3 327 MET cc_start: 0.9578 (ppp) cc_final: 0.8987 (ppp) REVERT: 3 356 MET cc_start: 0.8973 (mmm) cc_final: 0.8572 (tmm) REVERT: 3 410 MET cc_start: 0.8969 (mpp) cc_final: 0.8571 (mpp) REVERT: 3 431 ASP cc_start: 0.9243 (m-30) cc_final: 0.9031 (m-30) REVERT: 4 127 MET cc_start: 0.9540 (mtp) cc_final: 0.8996 (mtt) REVERT: 4 162 CYS cc_start: 0.9553 (m) cc_final: 0.8561 (t) REVERT: 4 169 MET cc_start: 0.9150 (tmm) cc_final: 0.8902 (tmm) REVERT: 4 180 MET cc_start: 0.8768 (tpp) cc_final: 0.8042 (tpp) REVERT: 4 309 GLU cc_start: 0.8940 (tp30) cc_final: 0.8642 (tp30) REVERT: 5 127 MET cc_start: 0.9142 (mtt) cc_final: 0.8798 (mtt) REVERT: 5 356 MET cc_start: 0.9223 (mpp) cc_final: 0.8688 (mmp) REVERT: 5 410 MET cc_start: 0.8384 (mpp) cc_final: 0.7979 (mpp) REVERT: 5 494 ARG cc_start: 0.8833 (mmt180) cc_final: 0.8256 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8448 (t0) cc_final: 0.8080 (t0) REVERT: 7 112 TYR cc_start: 0.9009 (t80) cc_final: 0.8721 (t80) REVERT: U 73 MET cc_start: -0.2974 (mtm) cc_final: -0.4240 (mmm) REVERT: U 97 MET cc_start: 0.6346 (ptt) cc_final: 0.5871 (ppp) REVERT: U 276 MET cc_start: 0.7121 (tpp) cc_final: 0.6720 (mmm) REVERT: U 324 MET cc_start: 0.5635 (mmm) cc_final: 0.5346 (mmm) REVERT: U 389 LEU cc_start: 0.9044 (mt) cc_final: 0.8763 (mt) REVERT: X 59 ASP cc_start: 0.9040 (p0) cc_final: 0.8820 (p0) REVERT: X 69 TYR cc_start: 0.7816 (p90) cc_final: 0.7526 (p90) REVERT: a 293 TRP cc_start: 0.7560 (t-100) cc_final: 0.7332 (t-100) REVERT: a 300 MET cc_start: 0.8796 (mmp) cc_final: 0.8250 (mmm) REVERT: a 304 TYR cc_start: 0.8411 (m-10) cc_final: 0.7748 (m-10) REVERT: a 331 ASP cc_start: 0.8849 (m-30) cc_final: 0.8498 (p0) REVERT: a 401 PHE cc_start: 0.8261 (t80) cc_final: 0.8037 (t80) REVERT: a 423 MET cc_start: 0.8673 (mmm) cc_final: 0.8448 (mmm) REVERT: a 536 PHE cc_start: 0.8186 (p90) cc_final: 0.7957 (p90) REVERT: a 651 MET cc_start: 0.8294 (mpp) cc_final: 0.7859 (mpp) REVERT: a 718 MET cc_start: 0.8109 (tpt) cc_final: 0.7736 (tpt) REVERT: a 745 LEU cc_start: 0.8910 (mm) cc_final: 0.8625 (mm) REVERT: b 4 LEU cc_start: 0.8926 (mt) cc_final: 0.8300 (pt) REVERT: b 8 TYR cc_start: 0.8915 (m-80) cc_final: 0.8644 (m-80) REVERT: b 18 CYS cc_start: 0.9084 (m) cc_final: 0.8700 (p) REVERT: b 82 LYS cc_start: 0.8391 (pptt) cc_final: 0.7439 (mmmt) REVERT: b 192 ILE cc_start: 0.8793 (mm) cc_final: 0.8531 (pt) REVERT: b 203 MET cc_start: 0.4761 (tpt) cc_final: 0.4387 (tpt) REVERT: d 105 MET cc_start: 0.8707 (mmp) cc_final: 0.8473 (mmp) REVERT: d 209 CYS cc_start: 0.9114 (m) cc_final: 0.8850 (m) REVERT: d 215 GLU cc_start: 0.8530 (tm-30) cc_final: 0.8257 (tm-30) REVERT: d 262 GLU cc_start: 0.8920 (mm-30) cc_final: 0.8161 (pp20) REVERT: d 334 GLU cc_start: 0.9535 (mm-30) cc_final: 0.9171 (mm-30) REVERT: g 21 SER cc_start: 0.9310 (m) cc_final: 0.8717 (p) REVERT: g 64 ILE cc_start: 0.6768 (mm) cc_final: 0.6530 (mm) REVERT: g 134 ILE cc_start: 0.7999 (mp) cc_final: 0.7351 (tt) REVERT: h 14 PHE cc_start: 0.8804 (m-80) cc_final: 0.8386 (m-80) REVERT: h 41 ILE cc_start: 0.7876 (mm) cc_final: 0.7561 (mm) REVERT: h 53 MET cc_start: 0.7379 (mmp) cc_final: 0.6022 (tpt) REVERT: h 64 ILE cc_start: 0.7282 (mt) cc_final: 0.7027 (mt) REVERT: h 123 GLN cc_start: 0.6702 (mm-40) cc_final: 0.6271 (mm-40) REVERT: i 61 MET cc_start: 0.6596 (mmp) cc_final: 0.5497 (mtt) REVERT: i 64 ILE cc_start: 0.7505 (mt) cc_final: 0.6811 (mt) REVERT: i 65 ILE cc_start: 0.7506 (mm) cc_final: 0.7169 (mm) REVERT: j 136 ILE cc_start: 0.8230 (mt) cc_final: 0.7974 (mt) REVERT: k 23 MET cc_start: 0.2766 (ptm) cc_final: 0.2462 (mtp) REVERT: k 131 MET cc_start: 0.7948 (ppp) cc_final: 0.6742 (ptm) REVERT: m 13 PHE cc_start: 0.7567 (t80) cc_final: 0.7354 (t80) REVERT: m 64 ILE cc_start: 0.6315 (mt) cc_final: 0.5416 (mt) REVERT: n 47 MET cc_start: 0.7689 (ppp) cc_final: 0.7433 (ppp) REVERT: o 14 PHE cc_start: 0.7552 (m-10) cc_final: 0.7159 (m-10) REVERT: o 44 MET cc_start: 0.6557 (mmp) cc_final: 0.5934 (mmt) REVERT: 9 54 MET cc_start: 0.8924 (mmm) cc_final: 0.8534 (mmm) REVERT: 9 208 MET cc_start: 0.9256 (mmm) cc_final: 0.8897 (tpp) REVERT: T 11 LEU cc_start: 0.7988 (mm) cc_final: 0.7566 (tt) REVERT: T 84 MET cc_start: 0.8952 (mtp) cc_final: 0.8738 (mtp) REVERT: c 388 MET cc_start: 0.8250 (ppp) cc_final: 0.8029 (ppp) REVERT: f 77 LEU cc_start: 0.8953 (mt) cc_final: 0.8533 (mt) REVERT: s 153 MET cc_start: 0.5042 (ppp) cc_final: 0.4752 (tmm) outliers start: 0 outliers final: 0 residues processed: 767 average time/residue: 0.6336 time to fit residues: 859.2629 Evaluate side-chains 644 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 644 time to evaluate : 6.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 757 optimal weight: 5.9990 chunk 498 optimal weight: 7.9990 chunk 803 optimal weight: 0.0970 chunk 490 optimal weight: 8.9990 chunk 381 optimal weight: 6.9990 chunk 558 optimal weight: 3.9990 chunk 842 optimal weight: 6.9990 chunk 775 optimal weight: 10.0000 chunk 671 optimal weight: 0.0670 chunk 69 optimal weight: 5.9990 chunk 518 optimal weight: 5.9990 overall best weight: 3.2322 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 2 521 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 3 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 4 350 GLN ** 7 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** X 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 802 HIS ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** V 113 ASN ** s 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7477 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 68193 Z= 0.219 Angle : 0.612 11.339 92164 Z= 0.317 Chirality : 0.042 0.361 10453 Planarity : 0.004 0.062 11796 Dihedral : 4.530 25.209 9269 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 12.63 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.57 % Favored : 95.42 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % 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: 0.91 (0.09), residues: 8475 helix: 1.71 (0.07), residues: 4838 sheet: -0.17 (0.20), residues: 733 loop : -1.10 (0.12), residues: 2904 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP e 83 HIS 0.011 0.001 HIS a 802 PHE 0.037 0.002 PHE i 108 TYR 0.036 0.002 TYR h 144 ARG 0.012 0.000 ARG 5 308 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16950 Ramachandran restraints generated. 8475 Oldfield, 0 Emsley, 8475 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 773 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 773 time to evaluate : 5.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: 8 76 MET cc_start: 0.9349 (mmp) cc_final: 0.9126 (mmm) REVERT: R 42 MET cc_start: 0.8946 (mmp) cc_final: 0.8567 (ppp) REVERT: 0 60 ASP cc_start: 0.8230 (p0) cc_final: 0.7878 (p0) REVERT: 0 61 MET cc_start: 0.9150 (mmm) cc_final: 0.8934 (mmm) REVERT: 0 65 GLN cc_start: 0.9082 (tm-30) cc_final: 0.8806 (tm-30) REVERT: 0 284 MET cc_start: 0.9454 (tpp) cc_final: 0.9228 (tpt) REVERT: 0 318 MET cc_start: 0.8533 (mpp) cc_final: 0.8210 (mpp) REVERT: 0 340 MET cc_start: 0.8448 (tpp) cc_final: 0.8120 (tpt) REVERT: 0 540 MET cc_start: 0.7866 (ppp) cc_final: 0.7511 (ppp) REVERT: 1 61 MET cc_start: 0.8944 (mmm) cc_final: 0.8684 (mmm) REVERT: 1 67 TYR cc_start: 0.9129 (p90) cc_final: 0.8877 (p90) REVERT: 1 108 ASP cc_start: 0.9019 (p0) cc_final: 0.8766 (p0) REVERT: 1 235 ASP cc_start: 0.9201 (t70) cc_final: 0.8879 (t0) REVERT: 1 340 MET cc_start: 0.9112 (tpp) cc_final: 0.8572 (tpp) REVERT: 1 346 MET cc_start: 0.9133 (ttp) cc_final: 0.8582 (tmm) REVERT: 1 419 ASP cc_start: 0.8802 (t0) cc_final: 0.8384 (t0) REVERT: 1 540 MET cc_start: 0.9427 (mtm) cc_final: 0.8791 (mtp) REVERT: 2 34 MET cc_start: 0.9284 (mmm) cc_final: 0.9018 (mmm) REVERT: 2 205 MET cc_start: 0.8983 (ptp) cc_final: 0.8686 (ptp) REVERT: 2 306 MET cc_start: 0.9010 (tmm) cc_final: 0.8722 (tmm) REVERT: 2 318 MET cc_start: 0.9322 (mtt) cc_final: 0.8974 (mtp) REVERT: 2 485 GLU cc_start: 0.9257 (mt-10) cc_final: 0.8914 (mm-30) REVERT: 2 540 MET cc_start: 0.9182 (mtp) cc_final: 0.7529 (mmt) REVERT: 2 550 MET cc_start: 0.9377 (mtm) cc_final: 0.9071 (mtp) REVERT: 2 608 MET cc_start: 0.9411 (mtm) cc_final: 0.9160 (mpp) REVERT: 3 127 MET cc_start: 0.9373 (mtp) cc_final: 0.8961 (mtt) REVERT: 3 169 MET cc_start: 0.8948 (tmm) cc_final: 0.8604 (tmm) REVERT: 3 316 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8314 (mp0) REVERT: 3 327 MET cc_start: 0.9620 (ppp) cc_final: 0.9119 (ppp) REVERT: 3 410 MET cc_start: 0.8875 (mpp) cc_final: 0.8527 (mpp) REVERT: 3 431 ASP cc_start: 0.9243 (m-30) cc_final: 0.9029 (m-30) REVERT: 4 127 MET cc_start: 0.9555 (mtp) cc_final: 0.9040 (mtt) REVERT: 4 162 CYS cc_start: 0.9553 (m) cc_final: 0.8555 (t) REVERT: 4 169 MET cc_start: 0.9134 (tmm) cc_final: 0.8923 (tmm) REVERT: 4 180 MET cc_start: 0.8762 (tpp) cc_final: 0.8045 (tpp) REVERT: 4 309 GLU cc_start: 0.8951 (tp30) cc_final: 0.8669 (tp30) REVERT: 5 127 MET cc_start: 0.9165 (mtt) cc_final: 0.8835 (mtt) REVERT: 5 238 MET cc_start: 0.9219 (ppp) cc_final: 0.9000 (ppp) REVERT: 5 356 MET cc_start: 0.9218 (mpp) cc_final: 0.8660 (mmp) REVERT: 5 410 MET cc_start: 0.8434 (mpp) cc_final: 0.8013 (mpp) REVERT: 5 423 TYR cc_start: 0.9319 (m-80) cc_final: 0.8772 (m-80) REVERT: 5 494 ARG cc_start: 0.8847 (mmt180) cc_final: 0.8271 (tpp-160) REVERT: 7 78 ASP cc_start: 0.8413 (t0) cc_final: 0.8025 (t0) REVERT: 7 112 TYR cc_start: 0.9012 (t80) cc_final: 0.8712 (t80) REVERT: U 73 MET cc_start: -0.2933 (mtm) cc_final: -0.4180 (mmm) REVERT: U 97 MET cc_start: 0.6263 (ptt) cc_final: 0.5819 (ppp) REVERT: U 276 MET cc_start: 0.7118 (tpp) cc_final: 0.6722 (mmm) REVERT: U 324 MET cc_start: 0.5561 (mmm) cc_final: 0.5284 (mmm) REVERT: U 389 LEU cc_start: 0.9084 (mt) cc_final: 0.8836 (mt) REVERT: X 22 LEU cc_start: 0.9121 (mt) cc_final: 0.8865 (tp) REVERT: X 59 ASP cc_start: 0.9035 (p0) cc_final: 0.8811 (p0) REVERT: X 69 TYR cc_start: 0.7799 (p90) cc_final: 0.7514 (p90) REVERT: a 293 TRP cc_start: 0.7596 (t-100) cc_final: 0.7366 (t-100) REVERT: a 300 MET cc_start: 0.8809 (mmp) cc_final: 0.8246 (mmm) REVERT: a 304 TYR cc_start: 0.8399 (m-10) cc_final: 0.7744 (m-10) REVERT: a 331 ASP cc_start: 0.8875 (m-30) cc_final: 0.8517 (p0) REVERT: a 401 PHE cc_start: 0.8282 (t80) cc_final: 0.8080 (t80) REVERT: a 423 MET cc_start: 0.8670 (mmm) cc_final: 0.8453 (mmm) REVERT: a 651 MET cc_start: 0.8297 (mpp) cc_final: 0.7856 (mpp) REVERT: a 718 MET cc_start: 0.8118 (tpt) cc_final: 0.7749 (tpt) REVERT: b 4 LEU cc_start: 0.8923 (mt) cc_final: 0.8240 (pt) REVERT: b 8 TYR cc_start: 0.8922 (m-80) cc_final: 0.8640 (m-80) REVERT: b 18 CYS cc_start: 0.9070 (m) cc_final: 0.8679 (p) REVERT: b 82 LYS cc_start: 0.8380 (pptt) cc_final: 0.7477 (mmmt) REVERT: b 192 ILE cc_start: 0.8777 (mm) cc_final: 0.8533 (pt) REVERT: b 203 MET cc_start: 0.4629 (tpt) cc_final: 0.4255 (tpt) REVERT: d 105 MET cc_start: 0.8752 (mmp) cc_final: 0.8528 (mmp) REVERT: d 209 CYS cc_start: 0.9108 (m) cc_final: 0.8814 (m) REVERT: d 262 GLU cc_start: 0.8919 (mm-30) cc_final: 0.8223 (pp20) REVERT: d 330 VAL cc_start: 0.8996 (t) cc_final: 0.8464 (t) REVERT: d 334 GLU cc_start: 0.9548 (mm-30) cc_final: 0.9139 (mm-30) REVERT: g 21 SER cc_start: 0.9294 (m) cc_final: 0.8736 (p) REVERT: g 64 ILE cc_start: 0.6822 (mm) cc_final: 0.6459 (mm) REVERT: g 134 ILE cc_start: 0.8029 (mp) cc_final: 0.7401 (tt) REVERT: h 14 PHE cc_start: 0.8794 (m-80) cc_final: 0.8349 (m-80) REVERT: h 41 ILE cc_start: 0.7860 (mm) cc_final: 0.7542 (mm) REVERT: h 53 MET cc_start: 0.7313 (mmp) cc_final: 0.5867 (tpt) REVERT: h 64 ILE cc_start: 0.7238 (mt) cc_final: 0.7001 (mt) REVERT: h 123 GLN cc_start: 0.6693 (mm-40) cc_final: 0.6283 (mm-40) REVERT: h 131 MET cc_start: 0.8209 (ppp) cc_final: 0.7563 (ptt) REVERT: i 61 MET cc_start: 0.6640 (mmp) cc_final: 0.5557 (mtt) REVERT: i 64 ILE cc_start: 0.7507 (mt) cc_final: 0.6706 (mt) REVERT: i 65 ILE cc_start: 0.7621 (mm) cc_final: 0.7305 (mm) REVERT: j 136 ILE cc_start: 0.8224 (mt) cc_final: 0.7985 (mt) REVERT: k 23 MET cc_start: 0.2792 (ptm) cc_final: 0.2322 (mtp) REVERT: k 36 LYS cc_start: 0.8144 (mptt) cc_final: 0.7816 (mmmt) REVERT: k 131 MET cc_start: 0.7953 (ppp) cc_final: 0.7114 (ptt) REVERT: l 68 TYR cc_start: 0.4039 (m-10) cc_final: 0.3668 (m-10) REVERT: m 143 LEU cc_start: 0.9316 (tp) cc_final: 0.8906 (mp) REVERT: n 25 PHE cc_start: 0.9330 (m-10) cc_final: 0.9040 (m-10) REVERT: n 32 TYR cc_start: 0.7482 (t80) cc_final: 0.7280 (t80) REVERT: n 46 VAL cc_start: 0.7745 (m) cc_final: 0.6778 (m) REVERT: n 47 MET cc_start: 0.7673 (ppp) cc_final: 0.7459 (pmm) REVERT: p 634 ASP cc_start: 0.7851 (p0) cc_final: 0.7592 (p0) REVERT: 9 54 MET cc_start: 0.8908 (mmm) cc_final: 0.8516 (mmm) REVERT: 9 208 MET cc_start: 0.9188 (mmm) cc_final: 0.8806 (tpp) REVERT: T 11 LEU cc_start: 0.7984 (mm) cc_final: 0.7460 (tt) REVERT: T 84 MET cc_start: 0.8947 (mtp) cc_final: 0.8735 (mtp) REVERT: Q 15 MET cc_start: 0.2536 (tmm) cc_final: 0.0928 (tpp) REVERT: Q 16 MET cc_start: -0.2699 (mpp) cc_final: -0.3407 (mpp) REVERT: c 388 MET cc_start: 0.8253 (ppp) cc_final: 0.7939 (ppp) REVERT: f 70 PHE cc_start: 0.7780 (m-10) cc_final: 0.7460 (m-80) REVERT: f 77 LEU cc_start: 0.8932 (mt) cc_final: 0.8499 (mt) REVERT: s 153 MET cc_start: 0.5096 (ppp) cc_final: 0.4366 (tmm) outliers start: 0 outliers final: 0 residues processed: 773 average time/residue: 0.6045 time to fit residues: 820.9883 Evaluate side-chains 652 residues out of total 7202 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 652 time to evaluate : 5.874 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 846 random chunks: chunk 411 optimal weight: 9.9990 chunk 533 optimal weight: 5.9990 chunk 714 optimal weight: 5.9990 chunk 205 optimal weight: 0.0670 chunk 618 optimal weight: 0.0570 chunk 99 optimal weight: 4.9990 chunk 186 optimal weight: 1.9990 chunk 672 optimal weight: 7.9990 chunk 281 optimal weight: 0.9980 chunk 690 optimal weight: 10.0000 chunk 85 optimal weight: 3.9990 overall best weight: 1.4240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 8 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** R 10 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 261 GLN 2 521 GLN ** 7 91 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 267 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 310 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 749 HIS a 802 HIS ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** T 4 GLN Q 11 GLN V 113 ASN ** s 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.072432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.051948 restraints weight = 478739.265| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.053044 restraints weight = 252297.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3214 r_free = 0.3214 target = 0.053850 restraints weight = 160914.871| |-----------------------------------------------------------------------------| r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 68193 Z= 0.168 Angle : 0.591 11.720 92164 Z= 0.303 Chirality : 0.042 0.340 10453 Planarity : 0.004 0.057 11796 Dihedral : 4.392 22.675 9269 Min Nonbonded Distance : 2.346 Molprobity Statistics. All-atom Clashscore : 10.94 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.21 % Favored : 95.78 % Rotamer: Outliers : 0.00 % Allowed : 0.12 % Favored : 99.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.31 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.09), residues: 8475 helix: 1.81 (0.07), residues: 4842 sheet: -0.08 (0.20), residues: 734 loop : -1.05 (0.12), residues: 2899 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.059 0.002 TRP e 83 HIS 0.011 0.001 HIS a 802 PHE 0.037 0.001 PHE i 108 TYR 0.027 0.001 TYR j 144 ARG 0.007 0.000 ARG g 119 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 14907.40 seconds wall clock time: 260 minutes 17.91 seconds (15617.91 seconds total)