Starting phenix.real_space_refine on Fri Sep 27 19:20:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bra_44839/09_2024/9bra_44839.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bra_44839/09_2024/9bra_44839.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/9bra_44839/09_2024/9bra_44839.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bra_44839/09_2024/9bra_44839.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bra_44839/09_2024/9bra_44839.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/9bra_44839/09_2024/9bra_44839.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 397 5.16 5 C 42830 2.51 5 N 11297 2.21 5 O 12328 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 114 residue(s): 0.15s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 66852 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: "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: "0" 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: "1" 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: "2" 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: "3" 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: "4" 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: "5" 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: "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: 6027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 741, 6027 Classifications: {'peptide': 741} Link IDs: {'PTRANS': 31, 'TRANS': 709} 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: "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: 28.09, per 1000 atoms: 0.42 Number of scatterers: 66852 At special positions: 0 Unit cell: (157.816, 216.719, 300.072, 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 397 16.00 O 12328 8.00 N 11297 7.00 C 42830 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: 12.67 Conformation dependent library (CDL) restraints added in 6.5 seconds 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 15820 Finding SS restraints... Secondary structure from input PDB file: 319 helices and 39 sheets defined 62.3% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 4.88 Creating SS restraints... Processing helix chain '8' and resid 2 through 106 Processing helix chain '8' and resid 108 through 128 removed outlier: 4.215A pdb=" N VAL 8 114 " --> pdb=" O THR 8 110 " (cutoff:3.500A) 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: 3.646A pdb=" N LYS 8 145 " --> pdb=" O PHE 8 141 " (cutoff:3.500A) removed outlier: 3.808A 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 207 Processing helix chain '8' and resid 207 through 217 Processing helix chain 'R' and resid 5 through 103 removed outlier: 4.294A pdb=" N LEU R 11 " --> pdb=" O GLY R 7 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N LYS R 34 " --> pdb=" O ALA R 30 " (cutoff:3.500A) removed outlier: 5.339A pdb=" N GLU R 93 " --> pdb=" O GLN R 89 " (cutoff:3.500A) removed outlier: 5.502A pdb=" N ARG R 94 " --> pdb=" O ARG R 90 " (cutoff:3.500A) Processing helix chain '9' and resid 4 through 108 removed outlier: 3.695A pdb=" N LYS 9 107 " --> pdb=" O SER 9 103 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ASP 9 108 " --> pdb=" O LYS 9 104 " (cutoff:3.500A) Processing helix chain '9' and resid 108 through 128 Processing helix chain '9' and resid 140 through 160 removed outlier: 3.587A pdb=" N ALA 9 146 " --> pdb=" O PRO 9 142 " (cutoff:3.500A) 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 Processing helix chain 'T' and resid 4 through 90 removed outlier: 4.097A pdb=" N ARG T 90 " --> pdb=" O SER T 86 " (cutoff:3.500A) Processing helix chain 'T' and resid 91 through 105 removed outlier: 4.379A pdb=" N VAL T 95 " --> pdb=" O ASN T 91 " (cutoff:3.500A) Processing helix chain 'Q' and resid 5 through 19 removed outlier: 3.776A pdb=" N LYS Q 10 " --> pdb=" O ALA Q 6 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N PHE Q 18 " --> pdb=" O HIS Q 14 " (cutoff:3.500A) Processing helix chain 'Q' and resid 19 through 107 removed outlier: 3.796A pdb=" N LEU Q 45 " --> pdb=" O GLU Q 41 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N VAL Q 46 " --> pdb=" O LYS Q 42 " (cutoff:3.500A) removed outlier: 4.923A pdb=" N GLN Q 47 " --> pdb=" O GLY Q 43 " (cutoff:3.500A) removed outlier: 4.095A pdb=" N LYS Q 107 " --> pdb=" O SER Q 103 " (cutoff:3.500A) Processing helix chain 'Q' and resid 108 through 128 removed outlier: 3.510A pdb=" N LEU Q 128 " --> pdb=" O LEU Q 124 " (cutoff:3.500A) 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 196 through 217 Proline residue: Q 209 - end of helix Processing helix chain 'V' and resid 5 through 105 removed outlier: 3.575A pdb=" N GLN V 9 " --> pdb=" O THR V 5 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ASN V 91 " --> pdb=" O SER V 87 " (cutoff:3.500A) removed outlier: 6.099A pdb=" N GLU V 93 " --> pdb=" O GLN V 89 " (cutoff:3.500A) removed outlier: 6.191A pdb=" N ARG V 94 " --> pdb=" O ARG V 90 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLU V 105 " --> pdb=" O GLY V 101 " (cutoff:3.500A) Processing helix chain '0' and resid 106 through 111 removed outlier: 3.652A pdb=" N SER 0 111 " --> pdb=" O SER 0 107 " (cutoff:3.500A) Processing helix chain '0' and resid 231 through 237 Processing helix chain '0' and resid 255 through 266 Processing helix chain '0' and resid 281 through 291 Processing helix chain '0' and resid 292 through 294 No H-bonds generated for 'chain '0' and resid 292 through 294' Processing helix chain '0' and resid 319 through 339 removed outlier: 4.672A pdb=" N ILE 0 327 " --> pdb=" O ARG 0 323 " (cutoff:3.500A) removed outlier: 5.013A pdb=" N TYR 0 328 " --> pdb=" O GLU 0 324 " (cutoff:3.500A) Processing helix chain '0' and resid 350 through 366 removed outlier: 3.719A pdb=" N TRP 0 354 " --> pdb=" O SER 0 350 " (cutoff:3.500A) Processing helix chain '0' and resid 370 through 374 Processing helix chain '0' and resid 377 through 388 Processing helix chain '0' and resid 412 through 416 Processing helix chain '0' and resid 419 through 427 Processing helix chain '0' and resid 436 through 442 removed outlier: 3.547A pdb=" N ARG 0 442 " --> pdb=" O LYS 0 438 " (cutoff:3.500A) Processing helix chain '0' and resid 461 through 469 Processing helix chain '0' and resid 471 through 496 removed outlier: 3.950A pdb=" N LEU 0 475 " --> pdb=" O GLU 0 471 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N THR 0 477 " --> pdb=" O VAL 0 473 " (cutoff:3.500A) Processing helix chain '0' and resid 497 through 501 Processing helix chain '0' and resid 502 through 519 Processing helix chain '0' and resid 535 through 551 Processing helix chain '0' and resid 566 through 583 removed outlier: 3.660A pdb=" N ILE 0 570 " --> pdb=" O THR 0 566 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N GLU 0 576 " --> pdb=" O GLU 0 572 " (cutoff:3.500A) removed outlier: 6.469A pdb=" N ILE 0 577 " --> pdb=" O HIS 0 573 " (cutoff:3.500A) Processing helix chain '0' and resid 584 through 586 No H-bonds generated for 'chain '0' and resid 584 through 586' Processing helix chain '0' and resid 593 through 615 Processing helix chain '1' and resid 105 through 114 Processing helix chain '1' and resid 231 through 238 Processing helix chain '1' and resid 255 through 266 Processing helix chain '1' and resid 280 through 294 removed outlier: 4.167A pdb=" N MET 1 284 " --> pdb=" O ARG 1 280 " (cutoff:3.500A) Proline residue: 1 292 - end of helix Processing helix chain '1' and resid 321 through 339 removed outlier: 4.258A pdb=" N ALA 1 325 " --> pdb=" O ALA 1 321 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ILE 1 331 " --> pdb=" O ILE 1 327 " (cutoff:3.500A) Processing helix chain '1' and resid 350 through 365 removed outlier: 3.969A pdb=" N TRP 1 354 " --> pdb=" O SER 1 350 " (cutoff:3.500A) Processing helix chain '1' and resid 370 through 374 Processing helix chain '1' and resid 375 through 376 No H-bonds generated for 'chain '1' and resid 375 through 376' Processing helix chain '1' and resid 377 through 388 removed outlier: 3.849A pdb=" N ARG 1 388 " --> pdb=" O SER 1 384 " (cutoff:3.500A) Processing helix chain '1' and resid 412 through 416 removed outlier: 4.305A pdb=" N ASP 1 416 " --> pdb=" O PRO 1 413 " (cutoff:3.500A) Processing helix chain '1' and resid 419 through 427 Processing helix chain '1' and resid 436 through 442 removed outlier: 3.510A pdb=" N ALA 1 440 " --> pdb=" O ASP 1 436 " (cutoff:3.500A) Processing helix chain '1' and resid 461 through 468 removed outlier: 3.559A pdb=" N TYR 1 465 " --> pdb=" O LEU 1 461 " (cutoff:3.500A) Processing helix chain '1' and resid 471 through 496 removed outlier: 3.636A pdb=" N LEU 1 475 " --> pdb=" O GLU 1 471 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N THR 1 477 " --> pdb=" O VAL 1 473 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N GLU 1 491 " --> pdb=" O GLU 1 487 " (cutoff:3.500A) removed outlier: 5.043A pdb=" N ILE 1 492 " --> pdb=" O ASP 1 488 " (cutoff:3.500A) Processing helix chain '1' and resid 502 through 519 Processing helix chain '1' and resid 533 through 558 removed outlier: 3.553A pdb=" N THR 1 558 " --> pdb=" O ALA 1 554 " (cutoff:3.500A) Processing helix chain '1' and resid 566 through 584 removed outlier: 6.628A pdb=" N GLU 1 576 " --> pdb=" O GLU 1 572 " (cutoff:3.500A) removed outlier: 6.052A 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 258 through 266 Processing helix chain '2' and resid 280 through 291 Processing helix chain '2' and resid 292 through 294 No H-bonds generated for 'chain '2' and resid 292 through 294' Processing helix chain '2' and resid 304 through 307 removed outlier: 3.526A pdb=" N LYS 2 307 " --> pdb=" O SER 2 304 " (cutoff:3.500A) No H-bonds generated for 'chain '2' and resid 304 through 307' Processing helix chain '2' and resid 319 through 340 removed outlier: 4.132A pdb=" N ILE 2 327 " --> pdb=" O ARG 2 323 " (cutoff:3.500A) removed outlier: 4.092A pdb=" N TYR 2 328 " --> pdb=" O GLU 2 324 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE 2 331 " --> pdb=" O ILE 2 327 " (cutoff:3.500A) Processing helix chain '2' and resid 350 through 365 removed outlier: 3.972A 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 386 Processing helix chain '2' and resid 419 through 427 Processing helix chain '2' and resid 461 through 466 Processing helix chain '2' and resid 471 through 495 removed outlier: 3.735A pdb=" N LEU 2 475 " --> pdb=" O GLU 2 471 " (cutoff:3.500A) removed outlier: 4.640A pdb=" N GLU 2 491 " --> pdb=" O GLU 2 487 " (cutoff:3.500A) removed outlier: 4.609A 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 553 removed outlier: 3.515A pdb=" N THR 2 537 " --> pdb=" O PRO 2 533 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N ALA 2 551 " --> pdb=" O PHE 2 547 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N ARG 2 553 " --> pdb=" O ASP 2 549 " (cutoff:3.500A) Processing helix chain '2' and resid 566 through 574 removed outlier: 3.549A pdb=" N ILE 2 570 " --> pdb=" O THR 2 566 " (cutoff:3.500A) Processing helix chain '2' and resid 574 through 584 Processing helix chain '2' and resid 585 through 587 No H-bonds generated for 'chain '2' and resid 585 through 587' Processing helix chain '2' and resid 593 through 614 Processing helix chain '3' and resid 124 through 128 removed outlier: 3.511A pdb=" N MET 3 127 " --> pdb=" O SER 3 124 " (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 174 through 180 Processing helix chain '3' and resid 198 through 210 Processing helix chain '3' and resid 223 through 225 No H-bonds generated for 'chain '3' and resid 223 through 225' Processing helix chain '3' and resid 241 through 252 removed outlier: 3.740A pdb=" N ASN 3 251 " --> pdb=" O ASP 3 247 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N GLY 3 252 " --> pdb=" O PHE 3 248 " (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 288 removed outlier: 3.559A pdb=" N ARG 3 271 " --> pdb=" O PRO 3 267 " (cutoff:3.500A) Proline residue: 3 275 - end of helix Processing helix chain '3' and resid 299 through 314 removed outlier: 3.785A pdb=" N TYR 3 303 " --> pdb=" O ASP 3 299 " (cutoff:3.500A) Processing helix chain '3' and resid 319 through 323 Processing helix chain '3' and resid 324 through 325 No H-bonds generated for 'chain '3' and resid 324 through 325' Processing helix chain '3' and resid 326 through 335 Processing helix chain '3' and resid 363 through 373 Processing helix chain '3' and resid 380 through 386 Processing helix chain '3' and resid 401 through 406 removed outlier: 3.547A pdb=" N ILE 3 406 " --> pdb=" O MET 3 402 " (cutoff:3.500A) Processing helix chain '3' and resid 414 through 439 removed outlier: 3.893A pdb=" N VAL 3 438 " --> pdb=" O ALA 3 434 " (cutoff:3.500A) Processing helix chain '3' and resid 440 through 444 Processing helix chain '3' and resid 445 through 462 Processing helix chain '3' and resid 472 through 485 Processing helix chain '3' and resid 496 through 504 removed outlier: 3.584A pdb=" N LEU 3 500 " --> pdb=" O PRO 3 496 " (cutoff:3.500A) Processing helix chain '4' and resid 124 through 128 Processing helix chain '4' and resid 133 through 137 removed outlier: 3.662A pdb=" N LYS 4 137 " --> pdb=" O GLY 4 134 " (cutoff:3.500A) Processing helix chain '4' and resid 159 through 163 removed outlier: 3.636A pdb=" N ARG 4 163 " --> pdb=" O PRO 4 160 " (cutoff:3.500A) Processing helix chain '4' and resid 174 through 179 Processing helix chain '4' and resid 199 through 209 Processing helix chain '4' and resid 237 through 252 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 269 through 288 removed outlier: 4.378A pdb=" N ILE 4 273 " --> pdb=" O ILE 4 269 " (cutoff:3.500A) Proline residue: 4 275 - end of helix removed outlier: 3.718A pdb=" N ALA 4 278 " --> pdb=" O THR 4 274 " (cutoff:3.500A) Processing helix chain '4' and resid 299 through 315 removed outlier: 3.752A pdb=" N TYR 4 303 " --> pdb=" O ASP 4 299 " (cutoff:3.500A) Processing helix chain '4' and resid 319 through 323 removed outlier: 4.462A pdb=" N GLY 4 322 " --> pdb=" O GLY 4 319 " (cutoff:3.500A) Processing helix chain '4' and resid 326 through 336 Processing helix chain '4' and resid 363 through 373 Processing helix chain '4' and resid 380 through 386 removed outlier: 3.598A pdb=" N HIS 4 384 " --> pdb=" O ASP 4 380 " (cutoff:3.500A) Processing helix chain '4' and resid 414 through 440 removed outlier: 3.578A pdb=" N VAL 4 438 " --> pdb=" O ALA 4 434 " (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 496 through 504 removed outlier: 3.951A pdb=" N GLU 4 502 " --> pdb=" O SER 4 498 " (cutoff:3.500A) Processing helix chain '5' and resid 124 through 128 Processing helix chain '5' and resid 159 through 161 No H-bonds generated for 'chain '5' and resid 159 through 161' Processing helix chain '5' and resid 198 through 210 Processing helix chain '5' and resid 237 through 251 removed outlier: 3.562A pdb=" N ALA 5 241 " --> pdb=" O ASN 5 237 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ASN 5 251 " --> pdb=" O ASP 5 247 " (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 288 removed outlier: 4.329A pdb=" N ILE 5 273 " --> pdb=" O ILE 5 269 " (cutoff:3.500A) Proline residue: 5 275 - end of helix removed outlier: 3.665A pdb=" N ALA 5 278 " --> pdb=" O THR 5 274 " (cutoff:3.500A) Processing helix chain '5' and resid 299 through 315 removed outlier: 3.856A pdb=" N TYR 5 303 " --> pdb=" O ASP 5 299 " (cutoff:3.500A) Processing helix chain '5' and resid 319 through 323 Processing helix chain '5' and resid 324 through 325 No H-bonds generated for 'chain '5' and resid 324 through 325' Processing helix chain '5' and resid 326 through 336 Processing helix chain '5' and resid 363 through 373 Processing helix chain '5' and resid 380 through 386 removed outlier: 3.628A pdb=" N HIS 5 384 " --> pdb=" O ASP 5 380 " (cutoff:3.500A) Processing helix chain '5' and resid 414 through 439 removed outlier: 3.529A pdb=" N ALA 5 437 " --> pdb=" O GLN 5 433 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N VAL 5 438 " --> pdb=" O ALA 5 434 " (cutoff:3.500A) Processing helix chain '5' and resid 440 through 444 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 Processing helix chain '5' and resid 496 through 504 Processing helix chain '6' and resid 14 through 22 Processing helix chain '6' and resid 28 through 32 removed outlier: 3.659A pdb=" N ASN 6 31 " --> pdb=" O THR 6 28 " (cutoff:3.500A) Processing helix chain '6' and resid 49 through 81 Processing helix chain '6' and resid 93 through 97 Processing helix chain '6' and resid 98 through 106 Processing helix chain '6' and resid 118 through 158 removed outlier: 3.808A pdb=" N ASN 6 158 " --> pdb=" O LEU 6 154 " (cutoff:3.500A) Processing helix chain '6' and resid 194 through 202 removed outlier: 3.668A pdb=" N ILE 6 199 " --> pdb=" O HIS 6 195 " (cutoff:3.500A) Processing helix chain '6' and resid 203 through 205 No H-bonds generated for 'chain '6' and resid 203 through 205' Processing helix chain '6' and resid 233 through 245 removed outlier: 4.060A pdb=" N ASP 6 237 " --> pdb=" O LYS 6 233 " (cutoff:3.500A) Processing helix chain '6' and resid 255 through 311 removed outlier: 4.018A pdb=" N MET 6 259 " --> pdb=" O ASN 6 255 " (cutoff:3.500A) Proline residue: 6 279 - end of helix Processing helix chain '6' and resid 328 through 345 removed outlier: 5.298A pdb=" N HIS 6 342 " --> pdb=" O GLU 6 338 " (cutoff:3.500A) removed outlier: 4.916A pdb=" N LEU 6 343 " --> pdb=" O LEU 6 339 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N SER 6 345 " --> pdb=" O LYS 6 341 " (cutoff:3.500A) Processing helix chain '7' and resid 12 through 77 removed outlier: 3.573A pdb=" N LYS 7 50 " --> pdb=" O GLN 7 46 " (cutoff:3.500A) removed outlier: 4.400A pdb=" N ILE 7 52 " --> pdb=" O LEU 7 48 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N GLU 7 53 " --> pdb=" O LYS 7 49 " (cutoff:3.500A) Processing helix chain '7' and resid 78 through 86 removed outlier: 4.188A pdb=" N THR 7 82 " --> pdb=" O ASP 7 78 " (cutoff:3.500A) Processing helix chain '7' and resid 127 through 175 removed outlier: 3.543A pdb=" N LYS 7 133 " --> pdb=" O GLU 7 129 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N VAL 7 175 " --> pdb=" O ALA 7 171 " (cutoff:3.500A) Processing helix chain '7' and resid 175 through 209 removed outlier: 3.543A pdb=" N ARG 7 179 " --> pdb=" O VAL 7 175 " (cutoff:3.500A) Processing helix chain 'U' and resid 34 through 45 Processing helix chain 'U' and resid 59 through 66 Processing helix chain 'U' and resid 74 through 84 removed outlier: 3.802A pdb=" N LYS U 78 " --> pdb=" O SER U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 95 through 100 removed outlier: 3.603A pdb=" N HIS U 99 " --> pdb=" O ASN U 95 " (cutoff:3.500A) Processing helix chain 'U' and resid 102 through 120 removed outlier: 3.742A pdb=" N VAL U 106 " --> pdb=" O LYS U 102 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN U 120 " --> pdb=" O MET U 116 " (cutoff:3.500A) Processing helix chain 'U' and resid 131 through 138 removed outlier: 4.811A pdb=" N SER U 136 " --> pdb=" O ARG U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 139 through 143 Processing helix chain 'U' and resid 152 through 161 removed outlier: 4.946A pdb=" N ARG U 159 " --> pdb=" O HIS U 155 " (cutoff:3.500A) Processing helix chain 'U' and resid 183 through 188 removed outlier: 3.880A pdb=" N LEU U 188 " --> pdb=" O ILE U 184 " (cutoff:3.500A) Processing helix chain 'U' and resid 229 through 244 Processing helix chain 'U' and resid 245 through 255 Processing helix chain 'U' and resid 256 through 267 Processing helix chain 'U' and resid 270 through 285 removed outlier: 3.575A pdb=" N ALA U 285 " --> pdb=" O ILE U 281 " (cutoff:3.500A) Processing helix chain 'U' and resid 287 through 295 Processing helix chain 'U' and resid 299 through 309 Processing helix chain 'U' and resid 314 through 329 Processing helix chain 'U' and resid 332 through 346 removed outlier: 4.406A pdb=" N GLU U 338 " --> pdb=" O GLU U 334 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N TYR U 339 " --> pdb=" O THR U 335 " (cutoff:3.500A) removed outlier: 4.112A pdb=" N ALA U 340 " --> pdb=" O ARG U 336 " (cutoff:3.500A) Processing helix chain 'U' and resid 347 through 358 removed outlier: 3.908A pdb=" N GLN U 351 " --> pdb=" O LYS U 347 " (cutoff:3.500A) Processing helix chain 'U' and resid 362 through 383 Processing helix chain 'U' and resid 385 through 395 removed outlier: 3.623A pdb=" N TYR U 389 " --> pdb=" O SER U 385 " (cutoff:3.500A) Processing helix chain 'U' and resid 406 through 412 Processing helix chain 'U' and resid 419 through 421 No H-bonds generated for 'chain 'U' and resid 419 through 421' Processing helix chain 'U' and resid 422 through 435 removed outlier: 4.063A pdb=" N GLU U 433 " --> pdb=" O THR U 429 " (cutoff:3.500A) Processing helix chain 'U' and resid 437 through 455 Processing helix chain 'U' and resid 455 through 486 Processing helix chain 'U' and resid 486 through 496 removed outlier: 3.961A pdb=" N LEU U 490 " --> pdb=" O GLY U 486 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ASN U 493 " --> pdb=" O GLN U 489 " (cutoff:3.500A) Processing helix chain 'U' and resid 499 through 514 Processing helix chain 'X' and resid 16 through 26 Processing helix chain 'X' and resid 47 through 61 Processing helix chain 'X' and resid 71 through 77 Processing helix chain 'X' and resid 77 through 84 Processing helix chain 'a' and resid 18 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 removed outlier: 3.528A pdb=" N ARG a 185 " --> pdb=" O PRO a 181 " (cutoff:3.500A) Processing helix chain 'a' and resid 226 through 239 Processing helix chain 'a' and resid 251 through 309 removed outlier: 4.343A pdb=" N LYS a 255 " --> pdb=" O PRO a 251 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASN a 289 " --> pdb=" O ALA a 285 " (cutoff:3.500A) removed outlier: 4.314A pdb=" N ARG a 291 " --> pdb=" O ALA a 287 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N VAL a 292 " --> pdb=" O LYS a 288 " (cutoff:3.500A) removed outlier: 4.183A pdb=" N ILE a 295 " --> pdb=" O ARG a 291 " (cutoff:3.500A) Processing helix chain 'a' and resid 326 through 328 No H-bonds generated for 'chain 'a' and resid 326 through 328' Processing helix chain 'a' and resid 329 through 344 removed outlier: 3.665A pdb=" N ILE a 333 " --> pdb=" O ASP a 329 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N SER a 344 " --> pdb=" O GLY a 340 " (cutoff:3.500A) Processing helix chain 'a' and resid 371 through 382 Processing helix chain 'a' and resid 391 through 407 removed outlier: 4.501A 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: 3.566A pdb=" N GLY a 413 " --> pdb=" O ASP a 409 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N ARG a 426 " --> pdb=" O TRP a 422 " (cutoff:3.500A) Processing helix chain 'a' and resid 426 through 432 Processing helix chain 'a' and resid 437 through 446 Processing helix chain 'a' and resid 446 through 465 removed outlier: 4.013A pdb=" N LEU a 452 " --> pdb=" O TYR a 448 " (cutoff:3.500A) Processing helix chain 'a' and resid 481 through 488 Processing helix chain 'a' and resid 492 through 499 removed outlier: 4.069A pdb=" N SER a 498 " --> pdb=" O LEU a 495 " (cutoff:3.500A) Processing helix chain 'a' and resid 520 through 525 Processing helix chain 'a' and resid 528 through 554 removed outlier: 3.948A pdb=" N PHE a 532 " --> pdb=" O ASN a 528 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N SER a 554 " --> pdb=" O LEU a 550 " (cutoff:3.500A) Processing helix chain 'a' and resid 554 through 563 removed outlier: 3.933A pdb=" N PHE a 558 " --> pdb=" O SER a 554 " (cutoff:3.500A) Processing helix chain 'a' and resid 566 through 571 removed outlier: 3.958A pdb=" N PHE a 571 " --> pdb=" O LEU a 567 " (cutoff:3.500A) Processing helix chain 'a' and resid 572 through 598 removed outlier: 4.324A pdb=" N LEU a 587 " --> pdb=" O LEU a 583 " (cutoff:3.500A) Processing helix chain 'a' and resid 599 through 603 Processing helix chain 'a' and resid 608 through 618 Processing helix chain 'a' and resid 632 through 653 removed outlier: 3.761A pdb=" N ILE a 636 " --> pdb=" O GLY a 632 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL a 648 " --> pdb=" O ALA a 644 " (cutoff:3.500A) Proline residue: a 649 - end of helix removed outlier: 3.572A pdb=" N LEU a 652 " --> pdb=" O VAL a 648 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N LEU a 653 " --> pdb=" O PRO a 649 " (cutoff:3.500A) Processing helix chain 'a' and resid 653 through 667 Processing helix chain 'a' and resid 713 through 739 Processing helix chain 'a' and resid 740 through 760 Processing helix chain 'a' and resid 761 through 765 Processing helix chain 'a' and resid 770 through 792 removed outlier: 4.460A pdb=" N LEU a 774 " --> pdb=" O LEU a 770 " (cutoff:3.500A) removed outlier: 4.509A 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: 4.553A pdb=" N PHE a 815 " --> pdb=" O PHE a 811 " (cutoff:3.500A) Processing helix chain 'a' and resid 827 through 832 removed outlier: 4.347A pdb=" N HIS a 830 " --> pdb=" O SER a 827 " (cutoff:3.500A) Processing helix chain 'b' and resid 3 through 29 removed outlier: 3.960A pdb=" N THR b 27 " --> pdb=" O GLY b 23 " (cutoff:3.500A) Processing helix chain 'b' and resid 36 through 44 Processing helix chain 'b' and resid 45 through 80 removed outlier: 4.109A pdb=" N TRP b 49 " --> pdb=" O SER b 45 " (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 84 No H-bonds generated for 'chain 'b' and resid 83 through 84' Processing helix chain 'b' and resid 85 through 91 removed outlier: 4.126A pdb=" N LYS b 89 " --> pdb=" O ARG b 85 " (cutoff:3.500A) Processing helix chain 'b' and resid 91 through 113 removed outlier: 3.798A pdb=" N ILE b 95 " --> pdb=" O LEU b 91 " (cutoff:3.500A) Processing helix chain 'b' and resid 127 through 166 removed outlier: 3.569A pdb=" N TYR b 131 " --> pdb=" O GLY b 127 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N HIS b 132 " --> pdb=" O HIS b 128 " (cutoff:3.500A) Processing helix chain 'b' and resid 169 through 177 removed outlier: 3.646A pdb=" N ILE b 176 " --> pdb=" O PHE b 173 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N LEU b 177 " --> pdb=" O VAL b 174 " (cutoff:3.500A) Processing helix chain 'b' and resid 178 through 200 removed outlier: 4.154A pdb=" N PHE b 182 " --> pdb=" O ILE b 178 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY b 183 " --> pdb=" O VAL b 179 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N ARG b 200 " --> pdb=" O LEU b 196 " (cutoff:3.500A) Processing helix chain 'd' and resid 9 through 27 removed outlier: 4.015A pdb=" N ASP d 13 " --> pdb=" O TYR d 9 " (cutoff:3.500A) removed outlier: 6.713A pdb=" N TYR d 16 " --> pdb=" O VAL d 12 " (cutoff:3.500A) removed outlier: 5.871A pdb=" N LEU d 17 " --> pdb=" O ASP d 13 " (cutoff:3.500A) Processing helix chain 'd' and resid 30 through 41 removed outlier: 3.643A pdb=" N CYS d 40 " --> pdb=" O ASN d 36 " (cutoff:3.500A) removed outlier: 4.434A pdb=" N GLU d 41 " --> pdb=" O LEU d 37 " (cutoff:3.500A) Processing helix chain 'd' and resid 42 through 51 Processing helix chain 'd' and resid 67 through 89 removed outlier: 3.721A pdb=" N HIS d 89 " --> pdb=" O HIS d 85 " (cutoff:3.500A) Processing helix chain 'd' and resid 91 through 114 removed outlier: 3.801A pdb=" N SER d 104 " --> pdb=" O PHE d 100 " (cutoff:3.500A) removed outlier: 4.853A pdb=" N TYR d 105 " --> pdb=" O ILE d 101 " (cutoff:3.500A) Processing helix chain 'd' and resid 126 through 130 Processing helix chain 'd' and resid 147 through 158 Processing helix chain 'd' and resid 159 through 167 removed outlier: 4.443A pdb=" N ALA d 163 " --> pdb=" O PRO d 160 " (cutoff:3.500A) Processing helix chain 'd' and resid 172 through 177 Processing helix chain 'd' and resid 178 through 201 Processing helix chain 'd' and resid 203 through 228 Proline residue: d 211 - end of helix Processing helix chain 'd' and resid 229 through 231 No H-bonds generated for 'chain 'd' and resid 229 through 231' Processing helix chain 'd' and resid 234 through 241 removed outlier: 3.920A pdb=" N LEU d 241 " --> pdb=" O ASP d 237 " (cutoff:3.500A) Processing helix chain 'd' and resid 252 through 259 Processing helix chain 'd' and resid 261 through 271 removed outlier: 3.702A pdb=" N VAL d 265 " --> pdb=" O ASP d 261 " (cutoff:3.500A) Processing helix chain 'd' and resid 272 through 281 removed outlier: 3.559A pdb=" N LEU d 277 " --> pdb=" O PRO d 273 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N LEU d 278 " --> pdb=" O GLU d 274 " (cutoff:3.500A) Processing helix chain 'd' and resid 290 through 309 removed outlier: 3.579A pdb=" N ASN d 309 " --> pdb=" O LEU d 305 " (cutoff:3.500A) Processing helix chain 'd' and resid 313 through 340 removed outlier: 4.024A pdb=" N TYR d 317 " --> pdb=" O PHE d 313 " (cutoff:3.500A) Processing helix chain 'd' and resid 341 through 345 removed outlier: 3.579A pdb=" N LYS d 344 " --> pdb=" O HIS d 341 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N ILE d 345 " --> pdb=" O ARG d 342 " (cutoff:3.500A) No H-bonds generated for 'chain 'd' and resid 341 through 345' Processing helix chain 'g' and resid 10 through 45 removed outlier: 3.644A pdb=" N PHE g 14 " --> pdb=" O TYR g 10 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLY g 15 " --> pdb=" O SER g 11 " (cutoff:3.500A) Processing helix chain 'g' and resid 46 through 47 No H-bonds generated for 'chain 'g' and resid 46 through 47' Processing helix chain 'g' and resid 48 through 52 Processing helix chain 'g' and resid 55 through 80 removed outlier: 3.910A pdb=" N VAL g 59 " --> pdb=" O SER g 55 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N TYR g 68 " --> pdb=" O ILE g 64 " (cutoff:3.500A) removed outlier: 4.872A pdb=" N GLY g 69 " --> pdb=" O ILE g 65 " (cutoff:3.500A) removed outlier: 4.979A pdb=" N LEU g 70 " --> pdb=" O ALA g 66 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N VAL g 71 " --> pdb=" O ILE g 67 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N VAL g 72 " --> pdb=" O TYR g 68 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N SER g 79 " --> pdb=" O LEU g 75 " (cutoff:3.500A) Processing helix chain 'g' and resid 87 through 124 removed outlier: 4.487A pdb=" N ILE g 112 " --> pdb=" O PHE g 108 " (cutoff:3.500A) Processing helix chain 'g' and resid 127 through 155 removed outlier: 4.207A pdb=" N THR g 154 " --> pdb=" O LEU g 150 " (cutoff:3.500A) Processing helix chain 'h' and resid 10 through 45 removed outlier: 4.232A pdb=" N PHE h 14 " --> pdb=" O TYR h 10 " (cutoff:3.500A) removed outlier: 3.864A pdb=" N GLY h 15 " --> pdb=" O SER h 11 " (cutoff:3.500A) Processing helix chain 'h' and resid 48 through 50 No H-bonds generated for 'chain 'h' and resid 48 through 50' Processing helix chain 'h' and resid 51 through 56 Processing helix chain 'h' and resid 56 through 79 removed outlier: 3.823A pdb=" N SER h 79 " --> pdb=" O LEU h 75 " (cutoff:3.500A) Processing helix chain 'h' and resid 87 through 121 removed outlier: 4.163A pdb=" N LEU h 91 " --> pdb=" O TYR h 87 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N GLY h 100 " --> pdb=" O GLY h 96 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N ARG h 119 " --> pdb=" O ASP h 115 " (cutoff:3.500A) Processing helix chain 'h' and resid 122 through 123 No H-bonds generated for 'chain 'h' and resid 122 through 123' Processing helix chain 'h' and resid 124 through 126 No H-bonds generated for 'chain 'h' and resid 124 through 126' Processing helix chain 'h' and resid 127 through 155 removed outlier: 3.956A pdb=" N VAL h 148 " --> pdb=" O TYR h 144 " (cutoff:3.500A) Processing helix chain 'i' and resid 13 through 45 removed outlier: 3.595A pdb=" N GLY i 40 " --> pdb=" O LYS i 36 " (cutoff:3.500A) Processing helix chain 'i' and resid 48 through 50 No H-bonds generated for 'chain 'i' and resid 48 through 50' Processing helix chain 'i' and resid 51 through 56 Processing helix chain 'i' and resid 56 through 79 Processing helix chain 'i' and resid 86 through 122 removed outlier: 3.895A pdb=" N PHE i 90 " --> pdb=" O LEU i 86 " (cutoff:3.500A) Processing helix chain 'i' and resid 124 through 126 No H-bonds generated for 'chain 'i' and resid 124 through 126' Processing helix chain 'i' and resid 127 through 155 Processing helix chain 'j' and resid 11 through 45 removed outlier: 3.905A pdb=" N GLY j 15 " --> pdb=" O SER j 11 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N PHE j 25 " --> pdb=" O SER j 21 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N SER j 26 " --> pdb=" O ALA j 22 " (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 50 No H-bonds generated for 'chain 'j' and resid 48 through 50' Processing helix chain 'j' and resid 51 through 79 removed outlier: 4.481A pdb=" N ILE j 57 " --> pdb=" O MET j 53 " (cutoff:3.500A) Proline residue: j 58 - end of helix removed outlier: 4.550A pdb=" N ILE j 65 " --> pdb=" O MET j 61 " (cutoff:3.500A) removed outlier: 4.157A pdb=" N ALA j 66 " --> pdb=" O ALA j 62 " (cutoff:3.500A) Processing helix chain 'j' and resid 88 through 122 Processing helix chain 'j' and resid 126 through 155 removed outlier: 4.492A pdb=" N GLY j 130 " --> pdb=" O ARG j 126 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ALA j 138 " --> pdb=" O ILE j 134 " (cutoff:3.500A) Processing helix chain 'k' and resid 12 through 48 removed outlier: 4.344A pdb=" N VAL k 16 " --> pdb=" O SER k 12 " (cutoff:3.500A) removed outlier: 4.363A pdb=" N PHE k 25 " --> pdb=" O SER k 21 " (cutoff:3.500A) removed outlier: 3.813A pdb=" N SER k 26 " --> pdb=" O ALA k 22 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N THR k 39 " --> pdb=" O ALA k 35 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N VAL k 46 " --> pdb=" O ALA k 42 " (cutoff:3.500A) removed outlier: 4.266A pdb=" N MET k 47 " --> pdb=" O ALA k 43 " (cutoff:3.500A) Processing helix chain 'k' and resid 49 through 55 removed outlier: 3.594A pdb=" N ILE k 52 " --> pdb=" O PRO k 49 " (cutoff:3.500A) removed outlier: 5.447A pdb=" N MET k 53 " --> pdb=" O GLU k 50 " (cutoff:3.500A) Processing helix chain 'k' and resid 56 through 79 Processing helix chain 'k' and resid 87 through 122 Processing helix chain 'k' and resid 124 through 128 removed outlier: 3.680A pdb=" N LEU k 127 " --> pdb=" O GLN k 124 " (cutoff:3.500A) Processing helix chain 'k' and resid 129 through 154 removed outlier: 3.908A pdb=" N VAL k 148 " --> pdb=" O TYR k 144 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ALA k 149 " --> pdb=" O GLY k 145 " (cutoff:3.500A) Processing helix chain 'l' and resid 12 through 48 Processing helix chain 'l' and resid 49 through 55 removed outlier: 4.133A pdb=" N MET l 53 " --> pdb=" O GLU l 50 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N SER l 55 " --> pdb=" O ILE l 52 " (cutoff:3.500A) Processing helix chain 'l' and resid 56 through 80 removed outlier: 3.811A pdb=" N GLY l 69 " --> pdb=" O ILE l 65 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU l 70 " --> pdb=" O ALA l 66 " (cutoff:3.500A) Processing helix chain 'l' and resid 88 through 121 Processing helix chain 'l' and resid 122 through 123 No H-bonds generated for 'chain 'l' and resid 122 through 123' Processing helix chain 'l' and resid 124 through 125 No H-bonds generated for 'chain 'l' and resid 124 through 125' Processing helix chain 'l' and resid 126 through 155 removed outlier: 4.661A pdb=" N GLY l 130 " --> pdb=" O ARG l 126 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N LYS l 155 " --> pdb=" O ILE l 151 " (cutoff:3.500A) Processing helix chain 'm' and resid 12 through 46 removed outlier: 4.316A pdb=" N GLY m 18 " --> pdb=" O PHE m 14 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N VAL m 46 " --> pdb=" O ALA m 42 " (cutoff:3.500A) Processing helix chain 'm' and resid 47 through 50 removed outlier: 6.453A pdb=" N GLU m 50 " --> pdb=" O MET m 47 " (cutoff:3.500A) No H-bonds generated for 'chain 'm' and resid 47 through 50' Processing helix chain 'm' and resid 51 through 56 Processing helix chain 'm' and resid 56 through 80 removed outlier: 3.647A pdb=" N MET m 61 " --> pdb=" O ILE m 57 " (cutoff:3.500A) removed outlier: 3.636A pdb=" N GLY m 63 " --> pdb=" O VAL m 59 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ILE m 64 " --> pdb=" O VAL m 60 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE m 65 " --> pdb=" O MET m 61 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N ALA m 66 " --> pdb=" O ALA m 62 " (cutoff:3.500A) Processing helix chain 'm' and resid 87 through 121 removed outlier: 3.854A pdb=" N LEU m 91 " --> pdb=" O TYR m 87 " (cutoff:3.500A) Processing helix chain 'm' and resid 124 through 126 No H-bonds generated for 'chain 'm' and resid 124 through 126' Processing helix chain 'm' and resid 127 through 155 removed outlier: 3.573A pdb=" N ALA m 138 " --> pdb=" O ILE m 134 " (cutoff:3.500A) removed outlier: 3.760A pdb=" N GLU m 139 " --> pdb=" O LEU m 135 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL m 140 " --> pdb=" O ILE m 136 " (cutoff:3.500A) removed outlier: 4.835A pdb=" N LEU m 141 " --> pdb=" O PHE m 137 " (cutoff:3.500A) removed outlier: 4.153A pdb=" N GLY m 142 " --> pdb=" O ALA m 138 " (cutoff:3.500A) Processing helix chain 'n' and resid 11 through 45 removed outlier: 3.791A pdb=" N GLY n 15 " --> pdb=" O SER n 11 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N SER n 26 " --> pdb=" O ALA n 22 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N LYS n 36 " --> pdb=" O TYR n 32 " (cutoff:3.500A) removed outlier: 3.575A pdb=" N ALA n 43 " --> pdb=" O THR n 39 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N MET n 44 " --> pdb=" O GLY n 40 " (cutoff:3.500A) Processing helix chain 'n' and resid 48 through 52 Processing helix chain 'n' and resid 53 through 54 No H-bonds generated for 'chain 'n' and resid 53 through 54' Processing helix chain 'n' and resid 55 through 80 removed outlier: 4.394A pdb=" N VAL n 59 " --> pdb=" O SER n 55 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N MET n 61 " --> pdb=" O ILE n 57 " (cutoff:3.500A) Processing helix chain 'n' and resid 88 through 124 removed outlier: 3.559A pdb=" N GLN n 92 " --> pdb=" O ARG n 88 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ARG n 119 " --> pdb=" O ASP n 115 " (cutoff:3.500A) Processing helix chain 'n' and resid 127 through 155 Processing helix chain 'o' and resid 12 through 46 removed outlier: 3.911A pdb=" N SER o 20 " --> pdb=" O VAL o 16 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N SER o 26 " --> pdb=" O ALA o 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER o 37 " --> pdb=" O GLY o 33 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ALA o 42 " --> pdb=" O GLY o 38 " (cutoff:3.500A) removed outlier: 4.202A pdb=" N VAL o 46 " --> pdb=" O ALA o 42 " (cutoff:3.500A) Processing helix chain 'o' and resid 51 through 56 Processing helix chain 'o' and resid 56 through 80 removed outlier: 3.821A pdb=" N VAL o 60 " --> pdb=" O ILE o 56 " (cutoff:3.500A) Processing helix chain 'o' and resid 87 through 124 Processing helix chain 'o' and resid 127 through 154 Processing helix chain 'p' and resid 600 through 628 removed outlier: 4.220A pdb=" N VAL p 604 " --> pdb=" O GLU p 600 " (cutoff:3.500A) removed outlier: 4.657A pdb=" N ASN p 606 " --> pdb=" O SER p 602 " (cutoff:3.500A) Processing helix chain 'c' and resid 309 through 313 Processing helix chain 'c' and resid 416 through 441 removed outlier: 4.549A pdb=" N GLY c 422 " --> pdb=" O GLY c 418 " (cutoff:3.500A) Processing helix chain 'f' and resid 8 through 11 removed outlier: 3.570A pdb=" N LEU f 11 " --> pdb=" O GLY f 8 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 8 through 11' Processing helix chain 'f' and resid 12 through 35 Processing helix chain 'f' and resid 55 through 67 Processing helix chain 'f' and resid 67 through 89 removed outlier: 4.381A pdb=" N ILE f 71 " --> pdb=" O TYR f 67 " (cutoff:3.500A) removed outlier: 3.879A 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 Processing helix chain 's' and resid 101 through 128 Processing helix chain 's' and resid 129 through 135 Processing helix chain 's' and resid 138 through 172 removed outlier: 3.506A pdb=" N MET s 142 " --> pdb=" O LYS s 138 " (cutoff:3.500A) Processing helix chain 's' and resid 173 through 181 removed outlier: 3.736A pdb=" N ILE s 177 " --> pdb=" O ASP s 173 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N MET s 181 " --> pdb=" O ILE s 177 " (cutoff:3.500A) Processing helix chain 's' and resid 182 through 186 Processing helix chain 's' and resid 199 through 228 removed outlier: 3.691A pdb=" N GLY s 228 " --> pdb=" O PHE s 224 " (cutoff:3.500A) Processing helix chain 'e' and resid 6 through 28 removed outlier: 3.880A pdb=" N VAL e 10 " --> pdb=" O PHE e 6 " (cutoff:3.500A) Proline residue: e 25 - end of helix Processing helix chain 'e' and resid 33 through 60 removed outlier: 3.779A pdb=" N GLN e 59 " --> pdb=" O ALA e 55 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LEU e 60 " --> pdb=" O ILE e 56 " (cutoff:3.500A) Processing helix chain 'e' and resid 69 through 80 removed outlier: 3.915A pdb=" N PHE e 78 " --> pdb=" O TRP e 74 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N TRP e 80 " --> pdb=" O VAL e 76 " (cutoff:3.500A) 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 190 through 195 WARNING: can't find start of bonding for strands! previous: chain '8' and resid 190 through 195 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 190 through 195 WARNING: can't find start of bonding for strands! previous: chain 'Q' and resid 190 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: 6.908A pdb=" N THR 0 63 " --> pdb=" O ILE 0 55 " (cutoff:3.500A) removed outlier: 5.189A pdb=" N LEU 0 57 " --> pdb=" O MET 0 61 " (cutoff:3.500A) removed outlier: 7.168A 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: 6.730A pdb=" N THR 1 63 " --> pdb=" O ILE 1 55 " (cutoff:3.500A) removed outlier: 5.185A pdb=" N LEU 1 57 " --> pdb=" O MET 1 61 " (cutoff:3.500A) removed outlier: 7.185A 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: 6.697A pdb=" N THR 2 63 " --> pdb=" O ILE 2 55 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N LEU 2 57 " --> pdb=" O MET 2 61 " (cutoff:3.500A) removed outlier: 7.107A 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 60 WARNING: can't find start of bonding for strands! previous: chain '3' and resid 57 through 60 current: chain '3' and resid 81 through 90 removed outlier: 6.927A pdb=" N VAL 3 95 " --> pdb=" O LEU 3 87 " (cutoff:3.500A) removed outlier: 5.170A pdb=" N VAL 3 89 " --> pdb=" O LYS 3 93 " (cutoff:3.500A) removed outlier: 7.347A pdb=" N LYS 3 93 " --> pdb=" O VAL 3 89 " (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: 5.873A pdb=" N VAL 4 86 " --> pdb=" O GLN 4 97 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N GLN 4 97 " --> pdb=" O VAL 4 86 " (cutoff:3.500A) removed outlier: 4.122A pdb=" N GLU 4 88 " --> pdb=" O VAL 4 95 " (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: 5.577A pdb=" N VAL 5 86 " --> pdb=" O GLN 5 97 " (cutoff:3.500A) removed outlier: 6.555A pdb=" N GLN 5 97 " --> pdb=" O VAL 5 86 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N GLU 5 88 " --> pdb=" O VAL 5 95 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain '9' and resid 164 through 167 removed outlier: 6.339A pdb=" N MET 9 132 " --> pdb=" O GLN 9 166 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ILE 9 183 " --> pdb=" O VAL 9 192 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain '0' and resid 87 through 90 Processing sheet with id=AA4, 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 312 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 309 through 312 current: chain '0' and resid 401 through 410 WARNING: can't find start of bonding for strands! previous: chain '0' and resid 401 through 410 current: chain '0' and resid 454 through 455 No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain '0' and resid 146 through 148 removed outlier: 4.098A pdb=" N TYR 0 178 " --> pdb=" O LEU 0 192 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N VAL 0 191 " --> pdb=" O PHE 0 203 " (cutoff:3.500A) removed outlier: 3.505A pdb=" N PHE 0 203 " --> pdb=" O VAL 0 191 " (cutoff:3.500A) removed outlier: 3.741A pdb=" N GLU 0 193 " --> pdb=" O GLU 0 201 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain '0' and resid 152 through 156 removed outlier: 4.607A pdb=" N GLY 0 154 " --> pdb=" O ILE 0 166 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain '0' and resid 226 through 227 removed outlier: 4.091A pdb=" N CYS 0 240 " --> pdb=" O LEU 0 227 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain '1' and resid 87 through 90 Processing sheet with id=AA9, first strand: chain '1' and resid 98 through 99 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 98 through 99 current: chain '1' and resid 309 through 315 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 309 through 315 current: chain '1' and resid 401 through 409 WARNING: can't find start of bonding for strands! previous: chain '1' and resid 401 through 409 current: chain '1' and resid 454 through 455 No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain '1' and resid 164 through 167 removed outlier: 3.812A pdb=" N GLY 1 154 " --> pdb=" O ILE 1 166 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain '1' and resid 175 through 179 removed outlier: 6.748A pdb=" N GLU 1 193 " --> pdb=" O THR 1 177 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N LEU 1 192 " --> pdb=" O PHE 1 203 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain '1' and resid 226 through 227 removed outlier: 4.547A pdb=" N CYS 1 240 " --> pdb=" O LEU 1 227 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain '1' and resid 295 through 298 Processing sheet with id=AB5, first strand: chain '2' and resid 87 through 90 Processing sheet with id=AB6, first strand: chain '2' and resid 98 through 100 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 98 through 100 current: chain '2' and resid 309 through 313 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 309 through 313 current: chain '2' and resid 401 through 409 WARNING: can't find start of bonding for strands! previous: chain '2' and resid 401 through 409 current: chain '2' and resid 454 through 455 No H-bonds generated for sheet with id=AB6 Processing sheet with id=AB7, first strand: chain '2' and resid 165 through 167 removed outlier: 6.781A pdb=" N ILE 2 166 " --> pdb=" O TYR 2 153 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N TYR 2 153 " --> pdb=" O ILE 2 166 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain '2' and resid 178 through 179 removed outlier: 3.703A pdb=" N TYR 2 178 " --> pdb=" O GLU 2 193 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N LEU 2 192 " --> pdb=" O PHE 2 203 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain '2' and resid 226 through 227 removed outlier: 4.399A pdb=" N CYS 2 240 " --> pdb=" O LEU 2 227 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain '3' and resid 120 through 123 Processing sheet with id=AC2, first strand: chain '3' and resid 131 through 132 removed outlier: 6.413A pdb=" N PHE 3 132 " --> pdb=" O LEU 3 261 " (cutoff:3.500A) removed outlier: 7.997A pdb=" N LEU 3 263 " --> pdb=" O PHE 3 132 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N ALA 3 228 " --> pdb=" O LEU 3 294 " (cutoff:3.500A) removed outlier: 8.040A pdb=" N ILE 3 296 " --> pdb=" O ALA 3 228 " (cutoff:3.500A) removed outlier: 6.323A pdb=" N VAL 3 230 " --> pdb=" O ILE 3 296 " (cutoff:3.500A) removed outlier: 7.886A pdb=" N THR 3 298 " --> pdb=" O VAL 3 230 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N ALA 3 232 " --> pdb=" O THR 3 298 " (cutoff:3.500A) removed outlier: 6.865A pdb=" N VAL 3 293 " --> pdb=" O THR 3 349 " (cutoff:3.500A) removed outlier: 8.302A pdb=" N ILE 3 351 " --> pdb=" O VAL 3 293 " (cutoff:3.500A) removed outlier: 6.756A pdb=" N VAL 3 295 " --> pdb=" O ILE 3 351 " (cutoff:3.500A) removed outlier: 7.998A pdb=" N ILE 3 353 " --> pdb=" O VAL 3 295 " (cutoff:3.500A) removed outlier: 6.981A pdb=" N LEU 3 297 " --> pdb=" O ILE 3 353 " (cutoff:3.500A) removed outlier: 8.692A pdb=" N THR 3 355 " --> pdb=" O LEU 3 297 " (cutoff:3.500A) removed outlier: 6.204A pdb=" N ILE 3 191 " --> pdb=" O LEU 3 354 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain '3' and resid 163 through 164 removed outlier: 4.056A pdb=" N ARG 3 340 " --> pdb=" O ILE 3 164 " (cutoff:3.500A) Processing sheet with id=AC4, first strand: chain '4' and resid 120 through 123 Processing sheet with id=AC5, first strand: chain '4' and resid 131 through 132 removed outlier: 6.590A pdb=" N ILE 4 229 " --> pdb=" O CYS 4 258 " (cutoff:3.500A) removed outlier: 8.028A pdb=" N PHE 4 260 " --> pdb=" O ILE 4 229 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N PHE 4 231 " --> pdb=" O PHE 4 260 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N ALA 4 228 " --> pdb=" O LEU 4 294 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ILE 4 296 " --> pdb=" O ALA 4 228 " (cutoff:3.500A) removed outlier: 6.417A pdb=" N VAL 4 230 " --> pdb=" O ILE 4 296 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N LEU 4 297 " --> pdb=" O ILE 4 351 " (cutoff:3.500A) removed outlier: 5.943A pdb=" N ILE 4 191 " --> pdb=" O LEU 4 354 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain '4' and resid 170 through 171 Processing sheet with id=AC7, first strand: chain '5' and resid 120 through 123 Processing sheet with id=AC8, first strand: chain '5' and resid 131 through 132 removed outlier: 6.160A pdb=" N ILE 5 229 " --> pdb=" O CYS 5 258 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N PHE 5 260 " --> pdb=" O ILE 5 229 " (cutoff:3.500A) removed outlier: 6.678A pdb=" N PHE 5 231 " --> pdb=" O PHE 5 260 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N THR 5 298 " --> pdb=" O ALA 5 232 " (cutoff:3.500A) Processing sheet with id=AC9, first strand: chain '5' and resid 163 through 164 removed outlier: 3.931A pdb=" N ARG 5 340 " --> pdb=" O ILE 5 164 " (cutoff:3.500A) Processing sheet with id=AD1, first strand: chain '5' and resid 170 through 171 Processing sheet with id=AD2, first strand: chain '6' and resid 35 through 39 removed outlier: 3.696A pdb=" N GLN 6 318 " --> pdb=" O ALA 6 10 " (cutoff:3.500A) removed outlier: 3.643A pdb=" N TYR 6 394 " --> pdb=" O LEU 6 7 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL 6 392 " --> pdb=" O SER 6 9 " (cutoff:3.500A) Processing sheet with id=AD3, first strand: chain '6' and resid 215 through 219 removed outlier: 7.022A pdb=" N LEU 6 225 " --> pdb=" O LEU 6 217 " (cutoff:3.500A) removed outlier: 5.614A pdb=" N GLU 6 219 " --> pdb=" O SER 6 223 " (cutoff:3.500A) removed outlier: 7.434A pdb=" N SER 6 223 " --> pdb=" O GLU 6 219 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N LEU 6 230 " --> pdb=" O VAL 6 184 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N ARG 6 250 " --> pdb=" O LEU 6 187 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N ILE 6 248 " --> pdb=" O VAL 6 189 " (cutoff:3.500A) Processing sheet with id=AD4, first strand: chain '7' and resid 92 through 99 Processing sheet with id=AD5, first strand: chain 'X' and resid 39 through 41 removed outlier: 6.353A pdb=" N ILE X 67 " --> pdb=" O LEU X 92 " (cutoff:3.500A) removed outlier: 7.310A pdb=" N ILE X 94 " --> pdb=" O ILE X 67 " (cutoff:3.500A) removed outlier: 5.838A pdb=" N ILE X 69 " --> pdb=" O ILE X 94 " (cutoff:3.500A) Processing sheet with id=AD6, first strand: chain 'a' and resid 36 through 38 removed outlier: 4.316A pdb=" N GLU a 322 " --> pdb=" O ARG a 38 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ALA a 13 " --> pdb=" O VAL a 323 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N ASN a 353 " --> pdb=" O GLN a 14 " (cutoff:3.500A) Processing sheet with id=AD7, first strand: chain 'a' and resid 197 through 202 Processing sheet with id=AD8, first strand: chain 'c' and resid 252 through 255 removed outlier: 4.289A pdb=" N ILE c 261 " --> pdb=" O TYR c 254 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 259 through 264 current: chain 'c' and resid 276 through 278 WARNING: can't find start of bonding for strands! previous: chain 'c' and resid 276 through 278 current: chain 'c' and resid 388 through 396 Processing sheet with id=AD9, first strand: chain 'c' and resid 301 through 307 removed outlier: 3.934A pdb=" N VAL c 315 " --> pdb=" O TYR c 307 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER c 343 " --> pdb=" O SER c 346 " (cutoff:3.500A) Processing sheet with id=AE1, first strand: chain 'c' and resid 324 through 325 Processing sheet with id=AE2, first strand: chain 's' and resid 64 through 72 removed outlier: 4.745A pdb=" N LEU s 65 " --> pdb=" O VAL s 55 " (cutoff:3.500A) removed outlier: 5.978A pdb=" N VAL s 55 " --> pdb=" O LEU s 65 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ARG s 52 " --> pdb=" O LEU s 194 " (cutoff:3.500A) Processing sheet with id=AE3, first strand: chain 's' and resid 81 through 82 4050 hydrogen bonds defined for protein. 11808 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: 27.56 Time building geometry restraints manager: 15.29 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: 20555 1.34 - 1.46: 12816 1.46 - 1.58: 34042 1.58 - 1.70: 0 1.70 - 1.82: 701 Bond restraints: 68114 Sorted by residual: bond pdb=" C PHE l 137 " pdb=" O PHE l 137 " ideal model delta sigma weight residual 1.236 1.298 -0.062 1.26e-02 6.30e+03 2.41e+01 bond pdb=" C VAL 6 66 " pdb=" O VAL 6 66 " ideal model delta sigma weight residual 1.237 1.279 -0.042 1.13e-02 7.83e+03 1.40e+01 bond pdb=" N VAL 6 70 " pdb=" CA VAL 6 70 " ideal model delta sigma weight residual 1.458 1.510 -0.052 1.41e-02 5.03e+03 1.38e+01 bond pdb=" C ALA k 62 " pdb=" O ALA k 62 " ideal model delta sigma weight residual 1.237 1.277 -0.040 1.19e-02 7.06e+03 1.15e+01 bond pdb=" CA PHE l 137 " pdb=" C PHE l 137 " ideal model delta sigma weight residual 1.523 1.568 -0.046 1.35e-02 5.49e+03 1.14e+01 ... (remaining 68109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.09: 89424 2.09 - 4.18: 2251 4.18 - 6.27: 320 6.27 - 8.36: 54 8.36 - 10.46: 10 Bond angle restraints: 92059 Sorted by residual: angle pdb=" N VAL k 71 " pdb=" CA VAL k 71 " pdb=" C VAL k 71 " ideal model delta sigma weight residual 110.62 103.92 6.70 1.14e+00 7.69e-01 3.46e+01 angle pdb=" N VAL 6 70 " pdb=" CA VAL 6 70 " pdb=" CB VAL 6 70 " ideal model delta sigma weight residual 111.05 121.51 -10.46 2.10e+00 2.27e-01 2.48e+01 angle pdb=" N MET U 495 " pdb=" CA MET U 495 " pdb=" C MET U 495 " ideal model delta sigma weight residual 112.38 106.36 6.02 1.22e+00 6.72e-01 2.44e+01 angle pdb=" CB GLU 1 491 " pdb=" CG GLU 1 491 " pdb=" CD GLU 1 491 " ideal model delta sigma weight residual 112.60 120.82 -8.22 1.70e+00 3.46e-01 2.34e+01 angle pdb=" N VAL 6 66 " pdb=" CA VAL 6 66 " pdb=" CB VAL 6 66 " ideal model delta sigma weight residual 110.55 104.94 5.61 1.17e+00 7.31e-01 2.30e+01 ... (remaining 92054 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.08: 37638 18.08 - 36.16: 2844 36.16 - 54.24: 459 54.24 - 72.32: 94 72.32 - 90.40: 54 Dihedral angle restraints: 41089 sinusoidal: 16442 harmonic: 24647 Sorted by residual: dihedral pdb=" CA ILE U 58 " pdb=" C ILE U 58 " pdb=" N SER U 59 " pdb=" CA SER U 59 " ideal model delta harmonic sigma weight residual 180.00 154.08 25.92 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CA PRO l 49 " pdb=" C PRO l 49 " pdb=" N GLU l 50 " pdb=" CA GLU l 50 " ideal model delta harmonic sigma weight residual -180.00 -154.28 -25.72 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" N VAL 6 70 " pdb=" C VAL 6 70 " pdb=" CA VAL 6 70 " pdb=" CB VAL 6 70 " ideal model delta harmonic sigma weight residual 123.40 136.12 -12.72 0 2.50e+00 1.60e-01 2.59e+01 ... (remaining 41086 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.064: 8894 0.064 - 0.128: 1431 0.128 - 0.191: 98 0.191 - 0.255: 14 0.255 - 0.319: 5 Chirality restraints: 10442 Sorted by residual: chirality pdb=" CA VAL 6 66 " pdb=" N VAL 6 66 " pdb=" C VAL 6 66 " pdb=" CB VAL 6 66 " both_signs ideal model delta sigma weight residual False 2.44 2.76 -0.32 2.00e-01 2.50e+01 2.55e+00 chirality pdb=" CB THR 0 425 " pdb=" CA THR 0 425 " pdb=" OG1 THR 0 425 " pdb=" CG2 THR 0 425 " both_signs ideal model delta sigma weight residual False 2.55 2.26 0.29 2.00e-01 2.50e+01 2.15e+00 chirality pdb=" CB THR j 39 " pdb=" CA THR j 39 " pdb=" OG1 THR j 39 " pdb=" CG2 THR j 39 " both_signs ideal model delta sigma weight residual False 2.55 2.27 0.28 2.00e-01 2.50e+01 1.97e+00 ... (remaining 10439 not shown) Planarity restraints: 11782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA MET k 61 " 0.021 2.00e-02 2.50e+03 4.21e-02 1.77e+01 pdb=" C MET k 61 " -0.073 2.00e-02 2.50e+03 pdb=" O MET k 61 " 0.027 2.00e-02 2.50e+03 pdb=" N ALA k 62 " 0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE l 136 " -0.021 2.00e-02 2.50e+03 4.00e-02 1.60e+01 pdb=" C ILE l 136 " 0.069 2.00e-02 2.50e+03 pdb=" O ILE l 136 " -0.026 2.00e-02 2.50e+03 pdb=" N PHE l 137 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG V 28 " -0.279 9.50e-02 1.11e+02 1.25e-01 9.62e+00 pdb=" NE ARG V 28 " 0.017 2.00e-02 2.50e+03 pdb=" CZ ARG V 28 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG V 28 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG V 28 " -0.010 2.00e-02 2.50e+03 ... (remaining 11779 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 19180 2.82 - 3.34: 73300 3.34 - 3.86: 111350 3.86 - 4.38: 129687 4.38 - 4.90: 206304 Nonbonded interactions: 539821 Sorted by model distance: nonbonded pdb=" OE1 GLU l 139 " pdb=" CD1 LEU l 143 " model vdw 2.297 3.460 nonbonded pdb=" OE2 GLU l 139 " pdb=" CD1 LEU l 143 " model vdw 2.346 3.460 nonbonded pdb=" O ASN 7 86 " pdb=" OD1 ASN 7 86 " model vdw 2.360 3.040 nonbonded pdb=" O LEU 5 455 " pdb=" OE1 GLU 5 459 " model vdw 2.362 3.040 nonbonded pdb=" OE2 GLU l 139 " pdb=" CG LEU l 143 " model vdw 2.386 3.470 ... (remaining 539816 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 251 or resid 256 through 495 or resid 501 throu \ gh 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 558 or resid 565 through 615)) } ncs_group { reference = (chain '3' and (resid 39 through 214 or resid 225 through 505)) selection = chain '4' selection = (chain '5' and (resid 39 through 214 or resid 225 through 505)) } 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: 7.430 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: 0.080 Extract box with map and model: 1.940 Check model and map are aligned: 0.380 Set scattering table: 0.490 Process input model: 117.130 Find NCS groups from input model: 2.080 Set up NCS constraints: 0.480 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:2.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 132.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7229 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.096 68114 Z= 0.333 Angle : 0.811 10.455 92059 Z= 0.462 Chirality : 0.046 0.319 10442 Planarity : 0.006 0.125 11782 Dihedral : 13.343 90.397 25269 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.02 % Allowed : 5.15 % Favored : 94.83 % Rotamer: Outliers : 0.10 % Allowed : 0.26 % Favored : 99.64 % Cbeta Deviations : 0.01 % 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: -0.52 (0.09), residues: 8466 helix: 0.42 (0.07), residues: 4797 sheet: -1.46 (0.18), residues: 726 loop : -1.19 (0.12), residues: 2943 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP 6 295 HIS 0.019 0.002 HIS d 49 PHE 0.036 0.002 PHE 7 67 TYR 0.043 0.002 TYR 2 525 ARG 0.020 0.001 ARG 0 364 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1112 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 1105 time to evaluate : 5.792 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: 8 76 MET cc_start: 0.9490 (mmm) cc_final: 0.9157 (mmm) REVERT: 8 93 ASP cc_start: 0.9016 (m-30) cc_final: 0.8766 (m-30) REVERT: 8 124 LEU cc_start: 0.9360 (mm) cc_final: 0.9152 (mm) REVERT: 8 208 MET cc_start: 0.8948 (ttt) cc_final: 0.8501 (mpp) REVERT: 9 89 ASP cc_start: 0.9068 (m-30) cc_final: 0.8839 (m-30) REVERT: 9 96 ASN cc_start: 0.9117 (m-40) cc_final: 0.8885 (m-40) REVERT: T 84 MET cc_start: 0.8560 (tpt) cc_final: 0.8280 (tpp) REVERT: Q 207 MET cc_start: 0.9209 (tpt) cc_final: 0.8799 (tpp) REVERT: V 33 LEU cc_start: 0.6860 (mt) cc_final: 0.6470 (tt) REVERT: 0 340 MET cc_start: 0.8307 (ttm) cc_final: 0.7535 (ttm) REVERT: 0 443 LYS cc_start: 0.9150 (mttt) cc_final: 0.8943 (mppt) REVERT: 0 444 HIS cc_start: 0.7621 (t-170) cc_final: 0.7116 (t-170) REVERT: 0 458 MET cc_start: 0.9346 (mmm) cc_final: 0.8249 (mmt) REVERT: 1 61 MET cc_start: 0.9144 (mmm) cc_final: 0.8891 (mmm) REVERT: 1 246 THR cc_start: 0.9200 (t) cc_final: 0.8934 (m) REVERT: 1 318 MET cc_start: 0.9335 (mtt) cc_final: 0.8942 (mtt) REVERT: 1 368 MET cc_start: 0.9451 (tpp) cc_final: 0.8865 (tpp) REVERT: 1 485 GLU cc_start: 0.9055 (tm-30) cc_final: 0.8501 (tm-30) REVERT: 1 550 MET cc_start: 0.9274 (tpt) cc_final: 0.8991 (tpp) REVERT: 1 584 MET cc_start: 0.8866 (ttp) cc_final: 0.7839 (ttt) REVERT: 2 34 MET cc_start: 0.8814 (mmm) cc_final: 0.8556 (mmm) REVERT: 2 228 LEU cc_start: 0.9183 (tp) cc_final: 0.8949 (tp) REVERT: 2 318 MET cc_start: 0.9007 (mmm) cc_final: 0.8781 (mmm) REVERT: 2 346 MET cc_start: 0.8869 (ttt) cc_final: 0.8480 (ttm) REVERT: 2 347 MET cc_start: 0.8042 (pmm) cc_final: 0.7317 (pmm) REVERT: 2 454 TYR cc_start: 0.8940 (p90) cc_final: 0.7944 (p90) REVERT: 3 234 MET cc_start: 0.8652 (mtm) cc_final: 0.8250 (mpp) REVERT: 3 270 GLU cc_start: 0.9435 (mt-10) cc_final: 0.9123 (tp30) REVERT: 3 285 LEU cc_start: 0.9456 (tp) cc_final: 0.9240 (tt) REVERT: 3 389 TYR cc_start: 0.8688 (t80) cc_final: 0.8263 (t80) REVERT: 3 435 MET cc_start: 0.9078 (mmm) cc_final: 0.8693 (mmm) REVERT: 4 127 MET cc_start: 0.9199 (mtp) cc_final: 0.8921 (mtp) REVERT: 4 247 ASP cc_start: 0.8489 (m-30) cc_final: 0.8254 (m-30) REVERT: 4 309 GLU cc_start: 0.9192 (tm-30) cc_final: 0.8984 (tm-30) REVERT: 4 351 ILE cc_start: 0.9678 (mt) cc_final: 0.9363 (tp) REVERT: 4 410 MET cc_start: 0.8915 (mpp) cc_final: 0.8590 (mpp) REVERT: 4 425 CYS cc_start: 0.9359 (m) cc_final: 0.8965 (m) REVERT: 5 127 MET cc_start: 0.8964 (mmm) cc_final: 0.8728 (mmt) REVERT: 5 234 MET cc_start: 0.7831 (mmm) cc_final: 0.7301 (mmt) REVERT: 5 266 ASP cc_start: 0.9360 (m-30) cc_final: 0.9091 (m-30) REVERT: 5 270 GLU cc_start: 0.8743 (tp30) cc_final: 0.8433 (tp30) REVERT: 5 299 ASP cc_start: 0.7609 (t0) cc_final: 0.7150 (t0) REVERT: 5 300 MET cc_start: 0.8772 (mmm) cc_final: 0.8552 (mmm) REVERT: 5 492 LEU cc_start: 0.8957 (mt) cc_final: 0.8738 (mt) REVERT: 6 163 LEU cc_start: 0.7638 (mm) cc_final: 0.6703 (tp) REVERT: 6 331 LYS cc_start: 0.8626 (tttt) cc_final: 0.8164 (tppt) REVERT: 7 79 PHE cc_start: 0.9264 (p90) cc_final: 0.8952 (p90) REVERT: 7 144 LEU cc_start: 0.8887 (tp) cc_final: 0.8662 (tp) REVERT: U 57 MET cc_start: 0.7082 (tpp) cc_final: 0.6320 (tmm) REVERT: U 97 MET cc_start: 0.3838 (tpt) cc_final: 0.1851 (ttp) REVERT: U 242 MET cc_start: 0.7477 (tmm) cc_final: 0.6805 (tpp) REVERT: U 306 ILE cc_start: 0.8141 (mm) cc_final: 0.7882 (tp) REVERT: X 28 ILE cc_start: 0.9248 (mm) cc_final: 0.9020 (mp) REVERT: a 80 MET cc_start: 0.8454 (mpp) cc_final: 0.8171 (mmt) REVERT: a 186 MET cc_start: 0.8720 (mtm) cc_final: 0.8242 (mmm) REVERT: a 484 MET cc_start: 0.6035 (tmm) cc_final: 0.5539 (tmm) REVERT: a 580 MET cc_start: 0.7886 (ptp) cc_final: 0.7518 (ptp) REVERT: a 584 PHE cc_start: 0.8165 (m-80) cc_final: 0.7919 (m-80) REVERT: a 616 MET cc_start: 0.8646 (tmm) cc_final: 0.8222 (tmm) REVERT: a 651 MET cc_start: 0.8764 (mtt) cc_final: 0.7474 (mpp) REVERT: a 804 LEU cc_start: 0.9285 (mt) cc_final: 0.9054 (mt) REVERT: b 26 TYR cc_start: 0.5045 (t80) cc_final: 0.4614 (t80) REVERT: b 203 MET cc_start: 0.5289 (mtm) cc_final: 0.5084 (mtm) REVERT: d 106 MET cc_start: 0.8084 (mmp) cc_final: 0.7650 (mmp) REVERT: g 41 ILE cc_start: 0.8470 (tp) cc_final: 0.8192 (tp) REVERT: g 53 MET cc_start: 0.7488 (mmm) cc_final: 0.6802 (ppp) REVERT: g 115 ASP cc_start: 0.7632 (t0) cc_final: 0.6756 (t0) REVERT: g 150 LEU cc_start: 0.8458 (mm) cc_final: 0.8127 (tt) REVERT: i 131 MET cc_start: 0.7022 (ttt) cc_final: 0.6410 (tmm) REVERT: j 53 MET cc_start: 0.7544 (mmp) cc_final: 0.7002 (tpp) REVERT: k 44 MET cc_start: 0.7035 (mmm) cc_final: 0.6176 (mmm) REVERT: k 61 MET cc_start: 0.6956 (mpp) cc_final: 0.6592 (mpp) REVERT: l 146 LEU cc_start: 0.8491 (OUTLIER) cc_final: 0.8244 (mm) REVERT: m 65 ILE cc_start: 0.8717 (mm) cc_final: 0.8502 (mm) REVERT: n 44 MET cc_start: 0.6644 (ptp) cc_final: 0.5859 (ptp) REVERT: n 119 ARG cc_start: 0.8207 (ppt170) cc_final: 0.8007 (mpt180) REVERT: o 47 MET cc_start: 0.7696 (mmm) cc_final: 0.7281 (ptp) REVERT: c 365 CYS cc_start: 0.9228 (m) cc_final: 0.8273 (t) REVERT: c 446 MET cc_start: 0.2216 (mmp) cc_final: 0.1582 (mmm) REVERT: f 18 LEU cc_start: 0.9119 (mt) cc_final: 0.8821 (pp) REVERT: f 24 ILE cc_start: 0.8740 (mt) cc_final: 0.8430 (mt) REVERT: f 26 LEU cc_start: 0.8074 (mm) cc_final: 0.7702 (mt) REVERT: f 27 ILE cc_start: 0.8724 (mm) cc_final: 0.8311 (pt) REVERT: f 28 MET cc_start: 0.8886 (mtp) cc_final: 0.8627 (mtm) REVERT: f 29 LEU cc_start: 0.9159 (mt) cc_final: 0.8917 (mt) REVERT: f 65 VAL cc_start: 0.8365 (m) cc_final: 0.8156 (m) REVERT: f 76 TYR cc_start: 0.7163 (m-80) cc_final: 0.6766 (m-10) REVERT: s 32 LEU cc_start: 0.6656 (mt) cc_final: 0.6324 (pp) REVERT: s 142 MET cc_start: 0.3742 (mmt) cc_final: 0.3476 (mmt) REVERT: s 153 MET cc_start: 0.6651 (ppp) cc_final: 0.6352 (ppp) outliers start: 7 outliers final: 2 residues processed: 1112 average time/residue: 0.6541 time to fit residues: 1254.6036 Evaluate side-chains 779 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 776 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 713 optimal weight: 0.8980 chunk 640 optimal weight: 5.9990 chunk 355 optimal weight: 0.6980 chunk 218 optimal weight: 8.9990 chunk 432 optimal weight: 0.0470 chunk 342 optimal weight: 0.6980 chunk 662 optimal weight: 3.9990 chunk 256 optimal weight: 30.0000 chunk 402 optimal weight: 6.9990 chunk 492 optimal weight: 6.9990 chunk 767 optimal weight: 5.9990 overall best weight: 1.2680 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 75 GLN Q 14 HIS V 113 ASN ** 1 543 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 521 GLN ** 2 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 2 573 HIS 3 171 GLN 6 195 HIS U 107 GLN U 496 HIS a 720 HIS a 724 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS d 172 GLN ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 92 GLN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** c 392 ASN s 78 HIS ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7201 moved from start: 0.1359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 68114 Z= 0.199 Angle : 0.626 9.057 92059 Z= 0.331 Chirality : 0.043 0.410 10442 Planarity : 0.005 0.070 11782 Dihedral : 4.676 28.152 9259 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.47 % Favored : 96.52 % Rotamer: Outliers : 0.32 % Allowed : 3.32 % Favored : 96.36 % 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: 0.23 (0.09), residues: 8466 helix: 1.00 (0.07), residues: 4800 sheet: -0.73 (0.19), residues: 716 loop : -0.94 (0.12), residues: 2950 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP b 67 HIS 0.017 0.001 HIS 6 337 PHE 0.050 0.002 PHE g 25 TYR 0.053 0.002 TYR i 144 ARG 0.009 0.000 ARG n 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 1053 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 1030 time to evaluate : 5.824 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: 8 72 MET cc_start: 0.8896 (tpt) cc_final: 0.8645 (tpt) REVERT: 8 76 MET cc_start: 0.9474 (mmm) cc_final: 0.9006 (mmm) REVERT: 8 93 ASP cc_start: 0.8967 (m-30) cc_final: 0.8710 (m-30) REVERT: 8 208 MET cc_start: 0.8872 (ttt) cc_final: 0.8438 (mpp) REVERT: 9 54 MET cc_start: 0.9157 (mmp) cc_final: 0.8846 (mmp) REVERT: 9 89 ASP cc_start: 0.9027 (m-30) cc_final: 0.8797 (m-30) REVERT: 9 96 ASN cc_start: 0.9142 (m-40) cc_final: 0.8925 (m-40) REVERT: T 84 MET cc_start: 0.8533 (tpt) cc_final: 0.8277 (tpp) REVERT: Q 16 MET cc_start: -0.0021 (mmm) cc_final: -0.0372 (mmm) REVERT: Q 207 MET cc_start: 0.9205 (tpt) cc_final: 0.8773 (tpp) REVERT: V 33 LEU cc_start: 0.6947 (mt) cc_final: 0.6362 (tt) REVERT: 0 162 ILE cc_start: 0.9237 (mm) cc_final: 0.8921 (tp) REVERT: 0 284 MET cc_start: 0.9060 (mmm) cc_final: 0.8794 (mmm) REVERT: 0 340 MET cc_start: 0.8599 (ttm) cc_final: 0.7763 (ttm) REVERT: 0 443 LYS cc_start: 0.9178 (mttt) cc_final: 0.8936 (mppt) REVERT: 0 444 HIS cc_start: 0.7741 (t-170) cc_final: 0.7358 (t-170) REVERT: 0 458 MET cc_start: 0.9382 (mmm) cc_final: 0.8299 (mmt) REVERT: 0 478 LYS cc_start: 0.9381 (mtmm) cc_final: 0.9174 (mtmt) REVERT: 0 544 MET cc_start: 0.9626 (mtm) cc_final: 0.9421 (mtm) REVERT: 0 573 HIS cc_start: 0.8200 (t-170) cc_final: 0.7709 (t-170) REVERT: 0 608 MET cc_start: 0.9068 (tmm) cc_final: 0.8792 (tmm) REVERT: 1 61 MET cc_start: 0.9163 (mmm) cc_final: 0.8932 (mmm) REVERT: 1 246 THR cc_start: 0.9176 (t) cc_final: 0.8974 (m) REVERT: 1 318 MET cc_start: 0.9371 (mtt) cc_final: 0.8968 (mtt) REVERT: 1 347 MET cc_start: 0.8951 (mmm) cc_final: 0.8324 (mmm) REVERT: 1 368 MET cc_start: 0.9412 (tpp) cc_final: 0.9055 (tpp) REVERT: 1 436 ASP cc_start: 0.8623 (t0) cc_final: 0.8407 (t0) REVERT: 1 485 GLU cc_start: 0.9103 (tm-30) cc_final: 0.8471 (tm-30) REVERT: 1 550 MET cc_start: 0.9274 (tpt) cc_final: 0.8982 (tpp) REVERT: 1 584 MET cc_start: 0.8460 (ttp) cc_final: 0.7339 (ttt) REVERT: 2 34 MET cc_start: 0.8944 (mmm) cc_final: 0.8681 (mmm) REVERT: 2 228 LEU cc_start: 0.9250 (tp) cc_final: 0.9015 (tp) REVERT: 2 318 MET cc_start: 0.8738 (mmm) cc_final: 0.8386 (mmm) REVERT: 2 346 MET cc_start: 0.8935 (ttt) cc_final: 0.8681 (ttm) REVERT: 2 454 TYR cc_start: 0.8895 (p90) cc_final: 0.7694 (p90) REVERT: 3 234 MET cc_start: 0.8530 (mtm) cc_final: 0.8320 (mpp) REVERT: 3 270 GLU cc_start: 0.9392 (mt-10) cc_final: 0.9110 (tp30) REVERT: 3 389 TYR cc_start: 0.8534 (t80) cc_final: 0.8129 (t80) REVERT: 3 410 MET cc_start: 0.7958 (mpp) cc_final: 0.7719 (mpp) REVERT: 3 432 VAL cc_start: 0.9307 (p) cc_final: 0.9062 (m) REVERT: 4 309 GLU cc_start: 0.9140 (tm-30) cc_final: 0.8909 (tm-30) REVERT: 4 351 ILE cc_start: 0.9591 (mt) cc_final: 0.9262 (tp) REVERT: 4 410 MET cc_start: 0.8918 (mpp) cc_final: 0.8616 (mpp) REVERT: 4 425 CYS cc_start: 0.9367 (m) cc_final: 0.8993 (m) REVERT: 5 234 MET cc_start: 0.7769 (mmm) cc_final: 0.7230 (mmm) REVERT: 5 270 GLU cc_start: 0.8758 (tp30) cc_final: 0.8479 (tp30) REVERT: 5 299 ASP cc_start: 0.7739 (t0) cc_final: 0.7262 (t0) REVERT: 5 300 MET cc_start: 0.8866 (mmm) cc_final: 0.8631 (mmm) REVERT: 5 410 MET cc_start: 0.8667 (mpp) cc_final: 0.7942 (mpp) REVERT: 5 431 ASP cc_start: 0.9290 (t0) cc_final: 0.9023 (t0) REVERT: 5 435 MET cc_start: 0.8868 (mpp) cc_final: 0.8662 (mpp) REVERT: 6 163 LEU cc_start: 0.8036 (mm) cc_final: 0.7047 (tp) REVERT: 6 259 MET cc_start: 0.5830 (mtm) cc_final: 0.5619 (mtt) REVERT: 6 331 LYS cc_start: 0.8682 (tttt) cc_final: 0.8267 (tppt) REVERT: 7 79 PHE cc_start: 0.9214 (p90) cc_final: 0.8854 (p90) REVERT: U 57 MET cc_start: 0.6757 (tpp) cc_final: 0.6493 (tpp) REVERT: U 97 MET cc_start: 0.5382 (tpt) cc_final: 0.3747 (ttp) REVERT: U 181 PHE cc_start: 0.7492 (m-10) cc_final: 0.7107 (m-80) REVERT: U 242 MET cc_start: 0.7426 (tmm) cc_final: 0.6801 (tpp) REVERT: U 306 ILE cc_start: 0.8043 (mm) cc_final: 0.7805 (tp) REVERT: U 387 ASP cc_start: 0.7266 (m-30) cc_final: 0.6735 (p0) REVERT: X 28 ILE cc_start: 0.9047 (mm) cc_final: 0.8800 (mp) REVERT: a 186 MET cc_start: 0.8774 (mtm) cc_final: 0.8451 (mtp) REVERT: a 359 GLN cc_start: 0.8647 (mm-40) cc_final: 0.8113 (mm110) REVERT: a 466 ASP cc_start: 0.8459 (t0) cc_final: 0.7804 (p0) REVERT: a 540 MET cc_start: 0.8122 (ppp) cc_final: 0.7905 (ppp) REVERT: a 651 MET cc_start: 0.8872 (mtt) cc_final: 0.7593 (mpp) REVERT: a 804 LEU cc_start: 0.9186 (mt) cc_final: 0.8926 (mt) REVERT: b 26 TYR cc_start: 0.5034 (t80) cc_final: 0.4157 (t80) REVERT: b 90 ASN cc_start: 0.7569 (m110) cc_final: 0.7287 (m110) REVERT: b 137 MET cc_start: 0.5208 (ttm) cc_final: 0.4861 (ptm) REVERT: g 47 MET cc_start: 0.7856 (ppp) cc_final: 0.7594 (ppp) REVERT: g 53 MET cc_start: 0.7414 (mmm) cc_final: 0.6675 (ppp) REVERT: g 61 MET cc_start: 0.6543 (tpp) cc_final: 0.6071 (mmt) REVERT: g 115 ASP cc_start: 0.7381 (t0) cc_final: 0.6233 (t0) REVERT: g 150 LEU cc_start: 0.8444 (mm) cc_final: 0.8096 (tt) REVERT: i 131 MET cc_start: 0.7079 (ttt) cc_final: 0.6500 (tmm) REVERT: j 53 MET cc_start: 0.7439 (mmp) cc_final: 0.6873 (tpp) REVERT: k 28 MET cc_start: 0.8592 (mmp) cc_final: 0.7969 (mtp) REVERT: k 44 MET cc_start: 0.7375 (mmm) cc_final: 0.6563 (mmm) REVERT: k 61 MET cc_start: 0.7024 (mpp) cc_final: 0.6752 (mpp) REVERT: m 44 MET cc_start: 0.8110 (mmm) cc_final: 0.7779 (mmm) REVERT: n 44 MET cc_start: 0.6335 (ptp) cc_final: 0.5542 (ptp) REVERT: n 61 MET cc_start: 0.6375 (ttm) cc_final: 0.6044 (ttm) REVERT: o 37 SER cc_start: 0.8038 (m) cc_final: 0.7456 (t) REVERT: c 274 ASP cc_start: 0.8859 (m-30) cc_final: 0.8590 (m-30) REVERT: c 336 MET cc_start: 0.6153 (tpt) cc_final: 0.5831 (tpp) REVERT: c 365 CYS cc_start: 0.9210 (m) cc_final: 0.8336 (t) REVERT: f 18 LEU cc_start: 0.9107 (mt) cc_final: 0.8816 (pp) REVERT: f 24 ILE cc_start: 0.8695 (mt) cc_final: 0.8364 (mt) REVERT: f 26 LEU cc_start: 0.8061 (mm) cc_final: 0.7731 (mm) REVERT: f 29 LEU cc_start: 0.9176 (mt) cc_final: 0.8965 (mt) REVERT: s 32 LEU cc_start: 0.6365 (mt) cc_final: 0.5853 (pp) REVERT: e 40 MET cc_start: 0.6762 (ppp) cc_final: 0.6473 (ppp) outliers start: 23 outliers final: 3 residues processed: 1046 average time/residue: 0.6239 time to fit residues: 1133.1686 Evaluate side-chains 767 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 764 time to evaluate : 5.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 426 optimal weight: 0.7980 chunk 238 optimal weight: 8.9990 chunk 638 optimal weight: 5.9990 chunk 522 optimal weight: 20.0000 chunk 211 optimal weight: 3.9990 chunk 768 optimal weight: 1.9990 chunk 830 optimal weight: 40.0000 chunk 684 optimal weight: 0.9980 chunk 762 optimal weight: 5.9990 chunk 262 optimal weight: 9.9990 chunk 616 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 46 GLN R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 140 ASN 1 268 ASN 1 543 ASN 2 573 HIS ** 3 209 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 6 337 HIS ** 7 46 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 418 ASN ** a 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS ** d 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** i 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** j 124 GLN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** s 78 HIS ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7237 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 68114 Z= 0.230 Angle : 0.626 18.031 92059 Z= 0.330 Chirality : 0.043 0.261 10442 Planarity : 0.004 0.093 11782 Dihedral : 4.588 26.560 9259 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 10.20 Ramachandran Plot: Outliers : 0.01 % Allowed : 3.90 % Favored : 96.09 % Rotamer: Outliers : 0.19 % Allowed : 3.25 % Favored : 96.55 % 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: 0.42 (0.09), residues: 8466 helix: 1.14 (0.07), residues: 4802 sheet: -0.38 (0.19), residues: 740 loop : -0.90 (0.12), residues: 2924 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP 6 20 HIS 0.010 0.001 HIS 6 337 PHE 0.039 0.002 PHE a 399 TYR 0.050 0.002 TYR 6 76 ARG 0.007 0.000 ARG R 17 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 969 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 955 time to evaluate : 5.741 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: 8 72 MET cc_start: 0.8933 (tpt) cc_final: 0.8520 (tpt) REVERT: 8 76 MET cc_start: 0.9504 (mmm) cc_final: 0.9039 (mmm) REVERT: 8 93 ASP cc_start: 0.8972 (m-30) cc_final: 0.8703 (m-30) REVERT: 8 132 MET cc_start: 0.9046 (mtp) cc_final: 0.8682 (mtt) REVERT: 8 208 MET cc_start: 0.8852 (ttt) cc_final: 0.8406 (mpp) REVERT: 9 54 MET cc_start: 0.9172 (mmp) cc_final: 0.8862 (mmp) REVERT: 9 89 ASP cc_start: 0.9035 (m-30) cc_final: 0.8817 (m-30) REVERT: T 84 MET cc_start: 0.8529 (tpt) cc_final: 0.8315 (tpp) REVERT: Q 16 MET cc_start: -0.0256 (mmm) cc_final: -0.0463 (mmm) REVERT: Q 207 MET cc_start: 0.9173 (tpt) cc_final: 0.8680 (tpp) REVERT: V 33 LEU cc_start: 0.7024 (mt) cc_final: 0.6334 (tt) REVERT: V 50 GLU cc_start: 0.8683 (OUTLIER) cc_final: 0.8459 (pm20) REVERT: 0 162 ILE cc_start: 0.9277 (mm) cc_final: 0.8942 (tp) REVERT: 0 296 MET cc_start: 0.7840 (pmm) cc_final: 0.7582 (pmm) REVERT: 0 340 MET cc_start: 0.8707 (ttm) cc_final: 0.7797 (ttm) REVERT: 0 444 HIS cc_start: 0.7921 (t-170) cc_final: 0.7473 (t-170) REVERT: 0 458 MET cc_start: 0.9340 (mmm) cc_final: 0.8205 (mmt) REVERT: 0 459 ARG cc_start: 0.8964 (mmp80) cc_final: 0.8690 (mmp80) REVERT: 0 462 ASP cc_start: 0.9064 (p0) cc_final: 0.8861 (p0) REVERT: 0 478 LYS cc_start: 0.9439 (mtmm) cc_final: 0.9204 (mtmt) REVERT: 0 544 MET cc_start: 0.9666 (mtm) cc_final: 0.9182 (mtm) REVERT: 0 608 MET cc_start: 0.9061 (tmm) cc_final: 0.8834 (tmm) REVERT: 1 34 MET cc_start: 0.9065 (mmm) cc_final: 0.8513 (tpp) REVERT: 1 246 THR cc_start: 0.9144 (t) cc_final: 0.8883 (m) REVERT: 1 318 MET cc_start: 0.9399 (mtt) cc_final: 0.8984 (mtt) REVERT: 1 340 MET cc_start: 0.8775 (tpp) cc_final: 0.8532 (tpp) REVERT: 1 368 MET cc_start: 0.9401 (tpp) cc_final: 0.9036 (tpp) REVERT: 1 485 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8539 (tm-30) REVERT: 1 489 LEU cc_start: 0.9405 (mt) cc_final: 0.9070 (mp) REVERT: 1 540 MET cc_start: 0.8491 (mmt) cc_final: 0.8246 (mmm) REVERT: 1 550 MET cc_start: 0.9270 (tpt) cc_final: 0.9006 (tpp) REVERT: 1 584 MET cc_start: 0.8239 (ttp) cc_final: 0.7970 (ttp) REVERT: 2 34 MET cc_start: 0.8996 (mmm) cc_final: 0.8725 (mmm) REVERT: 2 318 MET cc_start: 0.8814 (mmm) cc_final: 0.8409 (mmm) REVERT: 2 454 TYR cc_start: 0.8821 (p90) cc_final: 0.7831 (p90) REVERT: 2 608 MET cc_start: 0.8609 (mpp) cc_final: 0.8345 (mpp) REVERT: 3 270 GLU cc_start: 0.9419 (mt-10) cc_final: 0.9108 (tp30) REVERT: 3 389 TYR cc_start: 0.8636 (t80) cc_final: 0.8212 (t80) REVERT: 3 410 MET cc_start: 0.8136 (mpp) cc_final: 0.7792 (mpp) REVERT: 3 431 ASP cc_start: 0.9535 (m-30) cc_final: 0.9203 (m-30) REVERT: 4 247 ASP cc_start: 0.8609 (m-30) cc_final: 0.8401 (m-30) REVERT: 4 283 GLU cc_start: 0.9163 (tt0) cc_final: 0.8945 (tm-30) REVERT: 4 309 GLU cc_start: 0.9152 (tm-30) cc_final: 0.8927 (tm-30) REVERT: 4 351 ILE cc_start: 0.9603 (mt) cc_final: 0.9308 (tp) REVERT: 4 402 MET cc_start: 0.8833 (mmm) cc_final: 0.8515 (mmm) REVERT: 4 410 MET cc_start: 0.8989 (mpp) cc_final: 0.8611 (mpp) REVERT: 4 425 CYS cc_start: 0.9415 (m) cc_final: 0.9062 (m) REVERT: 5 127 MET cc_start: 0.8458 (mtt) cc_final: 0.8075 (mmm) REVERT: 5 234 MET cc_start: 0.8117 (mmm) cc_final: 0.7663 (mmt) REVERT: 5 270 GLU cc_start: 0.8758 (tp30) cc_final: 0.8507 (tp30) REVERT: 5 299 ASP cc_start: 0.7851 (t0) cc_final: 0.7362 (t0) REVERT: 5 300 MET cc_start: 0.9006 (mmm) cc_final: 0.8728 (mmm) REVERT: 5 354 LEU cc_start: 0.8892 (tp) cc_final: 0.8685 (tp) REVERT: 5 410 MET cc_start: 0.8701 (mpp) cc_final: 0.7897 (mpp) REVERT: 6 163 LEU cc_start: 0.8001 (mm) cc_final: 0.7010 (tp) REVERT: 6 259 MET cc_start: 0.5731 (mtm) cc_final: 0.5459 (mtt) REVERT: 6 331 LYS cc_start: 0.8708 (tttt) cc_final: 0.8293 (tppt) REVERT: U 97 MET cc_start: 0.6076 (tpt) cc_final: 0.4662 (ttp) REVERT: U 181 PHE cc_start: 0.7550 (m-10) cc_final: 0.7188 (m-80) REVERT: U 306 ILE cc_start: 0.8030 (mm) cc_final: 0.7803 (tp) REVERT: X 28 ILE cc_start: 0.9184 (mm) cc_final: 0.8939 (mp) REVERT: a 55 VAL cc_start: 0.9181 (t) cc_final: 0.8921 (t) REVERT: a 80 MET cc_start: 0.8416 (mpp) cc_final: 0.8166 (mmt) REVERT: a 186 MET cc_start: 0.8785 (mtm) cc_final: 0.8448 (mtp) REVERT: a 423 MET cc_start: 0.8554 (mpp) cc_final: 0.8119 (mpp) REVERT: a 466 ASP cc_start: 0.8500 (t0) cc_final: 0.7791 (p0) REVERT: a 793 ILE cc_start: 0.7988 (pt) cc_final: 0.7747 (pt) REVERT: a 804 LEU cc_start: 0.9041 (mt) cc_final: 0.8760 (mt) REVERT: b 90 ASN cc_start: 0.7533 (m110) cc_final: 0.7279 (m110) REVERT: b 203 MET cc_start: 0.5548 (mtm) cc_final: 0.5340 (mtm) REVERT: d 86 MET cc_start: 0.7135 (mmp) cc_final: 0.6339 (mmm) REVERT: d 153 ASN cc_start: 0.8832 (m-40) cc_final: 0.8619 (p0) REVERT: g 53 MET cc_start: 0.7604 (mmm) cc_final: 0.6748 (ppp) REVERT: g 68 TYR cc_start: 0.8054 (m-80) cc_final: 0.7729 (m-80) REVERT: g 115 ASP cc_start: 0.7214 (t0) cc_final: 0.6360 (t0) REVERT: g 150 LEU cc_start: 0.8439 (mm) cc_final: 0.8130 (tt) REVERT: h 47 MET cc_start: 0.7879 (ppp) cc_final: 0.7238 (pmm) REVERT: h 132 ILE cc_start: 0.8357 (mm) cc_final: 0.8147 (mm) REVERT: i 131 MET cc_start: 0.6897 (ttt) cc_final: 0.6664 (ppp) REVERT: i 144 TYR cc_start: 0.6810 (m-80) cc_final: 0.6401 (m-80) REVERT: j 53 MET cc_start: 0.7511 (mmp) cc_final: 0.7217 (tpp) REVERT: k 44 MET cc_start: 0.7501 (mmm) cc_final: 0.6700 (mmm) REVERT: l 131 MET cc_start: 0.8462 (ptp) cc_final: 0.8095 (ptp) REVERT: m 28 MET cc_start: 0.8119 (mmp) cc_final: 0.7599 (mmp) REVERT: m 44 MET cc_start: 0.8391 (mmm) cc_final: 0.8113 (mmm) REVERT: n 44 MET cc_start: 0.6668 (ptp) cc_final: 0.6019 (ptp) REVERT: n 61 MET cc_start: 0.6486 (ttm) cc_final: 0.6114 (ttm) REVERT: o 37 SER cc_start: 0.8064 (m) cc_final: 0.7424 (t) REVERT: p 615 LEU cc_start: 0.7774 (pp) cc_final: 0.7508 (tt) REVERT: c 274 ASP cc_start: 0.8889 (m-30) cc_final: 0.8644 (m-30) REVERT: c 336 MET cc_start: 0.6218 (tpt) cc_final: 0.5818 (tpp) REVERT: c 365 CYS cc_start: 0.9254 (m) cc_final: 0.8257 (t) REVERT: c 444 LYS cc_start: 0.6155 (pptt) cc_final: 0.5730 (ptmm) REVERT: c 446 MET cc_start: 0.1181 (mmp) cc_final: 0.0632 (mmm) REVERT: f 25 MET cc_start: 0.8722 (ptm) cc_final: 0.8263 (ptm) REVERT: f 26 LEU cc_start: 0.8072 (mm) cc_final: 0.7763 (mm) REVERT: f 29 LEU cc_start: 0.9177 (mt) cc_final: 0.8921 (mt) REVERT: s 32 LEU cc_start: 0.6183 (mt) cc_final: 0.5903 (pp) REVERT: e 40 MET cc_start: 0.6617 (ppp) cc_final: 0.6336 (ppp) outliers start: 14 outliers final: 4 residues processed: 963 average time/residue: 0.6190 time to fit residues: 1037.6940 Evaluate side-chains 751 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 746 time to evaluate : 5.825 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 759 optimal weight: 2.9990 chunk 577 optimal weight: 2.9990 chunk 398 optimal weight: 4.9990 chunk 85 optimal weight: 0.7980 chunk 366 optimal weight: 9.9990 chunk 516 optimal weight: 10.0000 chunk 771 optimal weight: 6.9990 chunk 816 optimal weight: 10.0000 chunk 403 optimal weight: 0.9980 chunk 731 optimal weight: 6.9990 chunk 220 optimal weight: 6.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN Q 14 HIS V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 468 HIS 1 543 ASN ** 2 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 2 543 ASN 4 209 GLN 7 152 GLN a 274 GLN a 720 HIS a 735 ASN d 85 HIS d 298 HIS ** d 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7236 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 68114 Z= 0.218 Angle : 0.610 11.695 92059 Z= 0.321 Chirality : 0.042 0.250 10442 Planarity : 0.004 0.057 11782 Dihedral : 4.528 25.314 9259 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.00 % Favored : 95.98 % Rotamer: Outliers : 0.10 % Allowed : 3.11 % Favored : 96.79 % 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: 0.54 (0.09), residues: 8466 helix: 1.21 (0.07), residues: 4803 sheet: -0.15 (0.19), residues: 735 loop : -0.87 (0.12), residues: 2928 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.054 0.002 TRP b 67 HIS 0.015 0.001 HIS 6 337 PHE 0.029 0.002 PHE h 108 TYR 0.049 0.002 TYR l 68 ARG 0.010 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 949 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 942 time to evaluate : 5.875 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: 8 72 MET cc_start: 0.8961 (tpt) cc_final: 0.8534 (tpt) REVERT: 8 76 MET cc_start: 0.9485 (mmm) cc_final: 0.9023 (mmm) REVERT: 8 93 ASP cc_start: 0.8950 (m-30) cc_final: 0.8696 (m-30) REVERT: 8 132 MET cc_start: 0.9058 (mtp) cc_final: 0.8738 (mtt) REVERT: 8 208 MET cc_start: 0.8870 (ttt) cc_final: 0.8408 (mpp) REVERT: 9 54 MET cc_start: 0.9188 (mmp) cc_final: 0.8878 (mmp) REVERT: 9 89 ASP cc_start: 0.9024 (m-30) cc_final: 0.8792 (m-30) REVERT: T 84 MET cc_start: 0.8498 (tpt) cc_final: 0.8263 (tpp) REVERT: Q 207 MET cc_start: 0.9155 (tpt) cc_final: 0.8680 (tpp) REVERT: V 33 LEU cc_start: 0.6834 (mt) cc_final: 0.6151 (tt) REVERT: 0 444 HIS cc_start: 0.8037 (t-170) cc_final: 0.7689 (t70) REVERT: 0 458 MET cc_start: 0.9327 (mmm) cc_final: 0.8175 (mmt) REVERT: 0 459 ARG cc_start: 0.8934 (mmp80) cc_final: 0.8688 (mmp80) REVERT: 0 478 LYS cc_start: 0.9451 (mtmm) cc_final: 0.9223 (mtmt) REVERT: 0 540 MET cc_start: 0.8745 (ptm) cc_final: 0.8327 (ppp) REVERT: 0 541 LEU cc_start: 0.9696 (mt) cc_final: 0.9118 (mt) REVERT: 0 544 MET cc_start: 0.9672 (mtm) cc_final: 0.9382 (mtp) REVERT: 0 608 MET cc_start: 0.9077 (tmm) cc_final: 0.8838 (tmm) REVERT: 1 246 THR cc_start: 0.9114 (t) cc_final: 0.8888 (m) REVERT: 1 318 MET cc_start: 0.9407 (mtt) cc_final: 0.8954 (mtt) REVERT: 1 368 MET cc_start: 0.9400 (tpp) cc_final: 0.9013 (tpp) REVERT: 1 485 GLU cc_start: 0.9074 (tm-30) cc_final: 0.8350 (tm-30) REVERT: 1 489 LEU cc_start: 0.9376 (mt) cc_final: 0.9131 (mp) REVERT: 1 550 MET cc_start: 0.9268 (tpt) cc_final: 0.9009 (tpp) REVERT: 1 584 MET cc_start: 0.8224 (ttp) cc_final: 0.7631 (ttp) REVERT: 2 34 MET cc_start: 0.9008 (mmm) cc_final: 0.8732 (mmm) REVERT: 2 228 LEU cc_start: 0.9285 (tp) cc_final: 0.9067 (tp) REVERT: 2 318 MET cc_start: 0.8838 (mmm) cc_final: 0.8422 (mmm) REVERT: 2 346 MET cc_start: 0.9135 (ttt) cc_final: 0.8893 (ttm) REVERT: 2 454 TYR cc_start: 0.8775 (p90) cc_final: 0.7911 (p90) REVERT: 2 576 GLU cc_start: 0.9150 (tt0) cc_final: 0.8550 (tp30) REVERT: 2 608 MET cc_start: 0.8505 (mpp) cc_final: 0.8283 (mpp) REVERT: 3 270 GLU cc_start: 0.9400 (mt-10) cc_final: 0.9178 (tt0) REVERT: 3 389 TYR cc_start: 0.8609 (t80) cc_final: 0.8189 (t80) REVERT: 3 410 MET cc_start: 0.8071 (mpp) cc_final: 0.7718 (mpp) REVERT: 3 435 MET cc_start: 0.9415 (ttp) cc_final: 0.9105 (mtp) REVERT: 4 127 MET cc_start: 0.9531 (mtp) cc_final: 0.9111 (mtt) REVERT: 4 247 ASP cc_start: 0.8627 (m-30) cc_final: 0.8384 (m-30) REVERT: 4 283 GLU cc_start: 0.9181 (tt0) cc_final: 0.8922 (tm-30) REVERT: 4 351 ILE cc_start: 0.9596 (mt) cc_final: 0.9313 (tp) REVERT: 4 410 MET cc_start: 0.9015 (mpp) cc_final: 0.8656 (mpp) REVERT: 4 425 CYS cc_start: 0.9407 (m) cc_final: 0.9065 (m) REVERT: 5 127 MET cc_start: 0.8525 (mtt) cc_final: 0.8166 (mmt) REVERT: 5 234 MET cc_start: 0.8127 (mmm) cc_final: 0.7568 (mmt) REVERT: 5 270 GLU cc_start: 0.8711 (tp30) cc_final: 0.8461 (tp30) REVERT: 5 299 ASP cc_start: 0.7874 (t0) cc_final: 0.7408 (t0) REVERT: 5 300 MET cc_start: 0.9016 (mmm) cc_final: 0.8679 (mmm) REVERT: 5 354 LEU cc_start: 0.8867 (tp) cc_final: 0.8640 (tp) REVERT: 5 410 MET cc_start: 0.8656 (mpp) cc_final: 0.7754 (mpp) REVERT: 5 422 LEU cc_start: 0.9753 (mm) cc_final: 0.9537 (mt) REVERT: 5 431 ASP cc_start: 0.9533 (t0) cc_final: 0.9160 (t0) REVERT: 5 459 GLU cc_start: 0.9207 (mp0) cc_final: 0.8873 (mp0) REVERT: 6 163 LEU cc_start: 0.8051 (mm) cc_final: 0.7048 (tp) REVERT: 6 259 MET cc_start: 0.5729 (mtm) cc_final: 0.5421 (mtt) REVERT: 6 331 LYS cc_start: 0.8702 (tttt) cc_final: 0.8298 (tppt) REVERT: 7 23 LEU cc_start: 0.8789 (tt) cc_final: 0.8247 (tt) REVERT: U 97 MET cc_start: 0.6421 (tpt) cc_final: 0.4907 (ttp) REVERT: U 145 MET cc_start: 0.4138 (mmm) cc_final: 0.3820 (mmm) REVERT: U 181 PHE cc_start: 0.7540 (m-10) cc_final: 0.7136 (m-80) REVERT: U 306 ILE cc_start: 0.7994 (mm) cc_final: 0.7778 (tp) REVERT: U 387 ASP cc_start: 0.7530 (m-30) cc_final: 0.7014 (p0) REVERT: X 28 ILE cc_start: 0.9217 (mm) cc_final: 0.8973 (mp) REVERT: a 55 VAL cc_start: 0.9108 (t) cc_final: 0.8852 (t) REVERT: a 186 MET cc_start: 0.8764 (mtm) cc_final: 0.8427 (mtp) REVERT: a 367 THR cc_start: 0.7372 (p) cc_final: 0.6966 (t) REVERT: a 804 LEU cc_start: 0.9158 (mt) cc_final: 0.8902 (mt) REVERT: a 806 LEU cc_start: 0.9369 (tp) cc_final: 0.9136 (tp) REVERT: b 26 TYR cc_start: 0.5187 (t80) cc_final: 0.4263 (t80) REVERT: d 86 MET cc_start: 0.7209 (mmp) cc_final: 0.6395 (mmm) REVERT: d 153 ASN cc_start: 0.8834 (m-40) cc_final: 0.8613 (p0) REVERT: g 53 MET cc_start: 0.7539 (mmm) cc_final: 0.6693 (ppp) REVERT: g 68 TYR cc_start: 0.8202 (m-80) cc_final: 0.7938 (m-80) REVERT: g 115 ASP cc_start: 0.7104 (t0) cc_final: 0.6195 (t0) REVERT: g 150 LEU cc_start: 0.8341 (mm) cc_final: 0.8020 (tt) REVERT: h 44 MET cc_start: 0.8331 (tpp) cc_final: 0.8096 (tpp) REVERT: h 47 MET cc_start: 0.8032 (ppp) cc_final: 0.7249 (ppp) REVERT: h 132 ILE cc_start: 0.8544 (mm) cc_final: 0.8311 (mm) REVERT: i 144 TYR cc_start: 0.6711 (m-80) cc_final: 0.6489 (m-80) REVERT: j 53 MET cc_start: 0.7497 (mmp) cc_final: 0.6871 (mmt) REVERT: j 131 MET cc_start: 0.7611 (ppp) cc_final: 0.7064 (ppp) REVERT: k 44 MET cc_start: 0.7551 (mmm) cc_final: 0.6722 (mmm) REVERT: l 28 MET cc_start: 0.8916 (mmp) cc_final: 0.8621 (mmm) REVERT: l 131 MET cc_start: 0.8354 (ptp) cc_final: 0.7874 (ptp) REVERT: m 28 MET cc_start: 0.8231 (mmp) cc_final: 0.7663 (mmp) REVERT: n 44 MET cc_start: 0.6879 (ptp) cc_final: 0.6159 (ptp) REVERT: n 61 MET cc_start: 0.6717 (ttm) cc_final: 0.6310 (ttm) REVERT: o 37 SER cc_start: 0.7984 (m) cc_final: 0.7405 (t) REVERT: c 274 ASP cc_start: 0.8979 (m-30) cc_final: 0.8757 (m-30) REVERT: c 336 MET cc_start: 0.6192 (tpt) cc_final: 0.5785 (tpp) REVERT: c 365 CYS cc_start: 0.9268 (m) cc_final: 0.8278 (t) REVERT: f 24 ILE cc_start: 0.8585 (mt) cc_final: 0.8278 (mt) REVERT: f 26 LEU cc_start: 0.8049 (mm) cc_final: 0.7775 (mm) REVERT: f 28 MET cc_start: 0.8260 (mpp) cc_final: 0.8024 (mpp) REVERT: f 29 LEU cc_start: 0.9223 (mt) cc_final: 0.8988 (mt) REVERT: s 32 LEU cc_start: 0.6199 (mt) cc_final: 0.5902 (pp) REVERT: e 9 PRO cc_start: 0.8035 (Cg_exo) cc_final: 0.7578 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7827 (m-10) cc_final: 0.7549 (m-10) outliers start: 7 outliers final: 0 residues processed: 945 average time/residue: 0.6100 time to fit residues: 1003.4755 Evaluate side-chains 745 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 745 time to evaluate : 5.723 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 680 optimal weight: 7.9990 chunk 463 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 608 optimal weight: 5.9990 chunk 337 optimal weight: 5.9990 chunk 696 optimal weight: 7.9990 chunk 564 optimal weight: 6.9990 chunk 0 optimal weight: 30.0000 chunk 417 optimal weight: 5.9990 chunk 733 optimal weight: 5.9990 chunk 206 optimal weight: 20.0000 overall best weight: 3.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 172 ASN 0 282 ASN 1 441 GLN 1 468 HIS 1 543 ASN 2 242 GLN 2 397 ASN ** 2 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 3 292 HIS ** 4 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 720 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS ** d 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** m 124 GLN ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7275 moved from start: 0.2374 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 68114 Z= 0.271 Angle : 0.642 10.037 92059 Z= 0.339 Chirality : 0.043 0.237 10442 Planarity : 0.004 0.062 11782 Dihedral : 4.591 25.779 9259 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 12.86 Ramachandran Plot: Outliers : 0.01 % Allowed : 4.33 % Favored : 95.65 % Rotamer: Outliers : 0.06 % Allowed : 2.63 % Favored : 97.32 % 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: 0.58 (0.09), residues: 8466 helix: 1.24 (0.07), residues: 4809 sheet: 0.00 (0.20), residues: 718 loop : -0.90 (0.12), residues: 2939 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.002 TRP 6 20 HIS 0.012 0.001 HIS 6 337 PHE 0.032 0.002 PHE 3 244 TYR 0.042 0.002 TYR l 68 ARG 0.011 0.001 ARG a 805 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 922 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 918 time to evaluate : 5.721 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: 8 72 MET cc_start: 0.9022 (tpt) cc_final: 0.8487 (tpt) REVERT: 8 76 MET cc_start: 0.9494 (mmm) cc_final: 0.9030 (mmm) REVERT: 8 93 ASP cc_start: 0.8979 (m-30) cc_final: 0.8724 (m-30) REVERT: 8 132 MET cc_start: 0.9076 (mtp) cc_final: 0.8744 (mtt) REVERT: 8 208 MET cc_start: 0.8844 (ttt) cc_final: 0.8364 (mpp) REVERT: 9 54 MET cc_start: 0.9190 (mmp) cc_final: 0.8881 (mmp) REVERT: 9 89 ASP cc_start: 0.9048 (m-30) cc_final: 0.8825 (m-30) REVERT: Q 207 MET cc_start: 0.9096 (tpt) cc_final: 0.8653 (tpp) REVERT: V 33 LEU cc_start: 0.6796 (mt) cc_final: 0.6113 (tt) REVERT: 0 39 MET cc_start: 0.8499 (ptp) cc_final: 0.8235 (ptp) REVERT: 0 284 MET cc_start: 0.8773 (mmm) cc_final: 0.8556 (mmm) REVERT: 0 444 HIS cc_start: 0.8217 (t-170) cc_final: 0.7964 (t-170) REVERT: 0 458 MET cc_start: 0.9291 (mmm) cc_final: 0.8113 (mmt) REVERT: 0 462 ASP cc_start: 0.8837 (p0) cc_final: 0.8610 (p0) REVERT: 0 478 LYS cc_start: 0.9452 (mtmm) cc_final: 0.9205 (mtmt) REVERT: 0 544 MET cc_start: 0.9676 (mtm) cc_final: 0.9145 (mtm) REVERT: 0 573 HIS cc_start: 0.8195 (t-170) cc_final: 0.7842 (t-170) REVERT: 0 574 MET cc_start: 0.8982 (mmp) cc_final: 0.8763 (ptp) REVERT: 0 608 MET cc_start: 0.9093 (tmm) cc_final: 0.8856 (tmm) REVERT: 1 34 MET cc_start: 0.9071 (mmm) cc_final: 0.8542 (tpp) REVERT: 1 246 THR cc_start: 0.9102 (t) cc_final: 0.8862 (m) REVERT: 1 340 MET cc_start: 0.8767 (tpp) cc_final: 0.8490 (tpp) REVERT: 1 436 ASP cc_start: 0.8858 (t0) cc_final: 0.8639 (t0) REVERT: 1 485 GLU cc_start: 0.9054 (tm-30) cc_final: 0.8452 (tm-30) REVERT: 1 489 LEU cc_start: 0.9429 (mt) cc_final: 0.9195 (mt) REVERT: 1 540 MET cc_start: 0.8909 (mmm) cc_final: 0.8531 (mmt) REVERT: 1 550 MET cc_start: 0.9258 (tpt) cc_final: 0.9019 (tpp) REVERT: 1 584 MET cc_start: 0.8006 (ttp) cc_final: 0.7632 (ttp) REVERT: 2 34 MET cc_start: 0.9114 (mmm) cc_final: 0.8805 (mmm) REVERT: 2 228 LEU cc_start: 0.9325 (tp) cc_final: 0.9068 (tp) REVERT: 2 318 MET cc_start: 0.8865 (mmm) cc_final: 0.8392 (mmm) REVERT: 2 346 MET cc_start: 0.9116 (ttt) cc_final: 0.8891 (ttm) REVERT: 2 576 GLU cc_start: 0.9163 (tt0) cc_final: 0.8572 (tp30) REVERT: 3 270 GLU cc_start: 0.9471 (mt-10) cc_final: 0.9020 (tp30) REVERT: 3 378 TYR cc_start: 0.8307 (m-80) cc_final: 0.8094 (m-80) REVERT: 3 389 TYR cc_start: 0.8537 (t80) cc_final: 0.8128 (t80) REVERT: 3 410 MET cc_start: 0.8064 (mpp) cc_final: 0.7682 (mpp) REVERT: 3 431 ASP cc_start: 0.9408 (m-30) cc_final: 0.9146 (m-30) REVERT: 3 453 GLU cc_start: 0.8697 (pp20) cc_final: 0.8350 (pp20) REVERT: 3 478 ASP cc_start: 0.9200 (m-30) cc_final: 0.8826 (m-30) REVERT: 4 127 MET cc_start: 0.9546 (mtp) cc_final: 0.9344 (mtp) REVERT: 4 283 GLU cc_start: 0.9209 (tt0) cc_final: 0.8934 (tm-30) REVERT: 4 351 ILE cc_start: 0.9612 (mt) cc_final: 0.9284 (tp) REVERT: 4 410 MET cc_start: 0.9044 (mpp) cc_final: 0.8639 (mpp) REVERT: 4 425 CYS cc_start: 0.9468 (m) cc_final: 0.9138 (m) REVERT: 5 127 MET cc_start: 0.8499 (mtt) cc_final: 0.8126 (mmm) REVERT: 5 234 MET cc_start: 0.8263 (mmm) cc_final: 0.7759 (mmt) REVERT: 5 270 GLU cc_start: 0.8734 (tp30) cc_final: 0.8523 (tp30) REVERT: 5 299 ASP cc_start: 0.8047 (t0) cc_final: 0.7666 (t0) REVERT: 5 300 MET cc_start: 0.9101 (mmm) cc_final: 0.8722 (mmm) REVERT: 5 327 MET cc_start: 0.9560 (ptp) cc_final: 0.9317 (ptp) REVERT: 5 354 LEU cc_start: 0.8928 (tp) cc_final: 0.8654 (tp) REVERT: 5 431 ASP cc_start: 0.9553 (t0) cc_final: 0.9148 (t0) REVERT: 6 163 LEU cc_start: 0.8089 (mm) cc_final: 0.7142 (tp) REVERT: 6 259 MET cc_start: 0.5760 (mtm) cc_final: 0.5439 (mtt) REVERT: U 97 MET cc_start: 0.6108 (tpt) cc_final: 0.4630 (ttp) REVERT: U 145 MET cc_start: 0.4396 (mmm) cc_final: 0.4081 (mmm) REVERT: U 181 PHE cc_start: 0.7614 (m-10) cc_final: 0.7230 (m-80) REVERT: U 387 ASP cc_start: 0.7495 (m-30) cc_final: 0.6882 (p0) REVERT: a 55 VAL cc_start: 0.9129 (t) cc_final: 0.8850 (t) REVERT: a 186 MET cc_start: 0.8762 (mtm) cc_final: 0.8394 (mtp) REVERT: a 367 THR cc_start: 0.7290 (p) cc_final: 0.6954 (t) REVERT: a 584 PHE cc_start: 0.8709 (m-80) cc_final: 0.8481 (m-10) REVERT: a 793 ILE cc_start: 0.7898 (pt) cc_final: 0.7687 (pt) REVERT: a 804 LEU cc_start: 0.9234 (mt) cc_final: 0.8985 (mt) REVERT: a 806 LEU cc_start: 0.9345 (tp) cc_final: 0.9077 (tp) REVERT: b 90 ASN cc_start: 0.7652 (m110) cc_final: 0.7413 (m110) REVERT: d 86 MET cc_start: 0.7322 (mmp) cc_final: 0.6420 (mmm) REVERT: d 153 ASN cc_start: 0.8891 (m-40) cc_final: 0.8656 (p0) REVERT: d 209 MET cc_start: 0.6273 (mmm) cc_final: 0.5752 (tpt) REVERT: g 53 MET cc_start: 0.7655 (mmm) cc_final: 0.6815 (ppp) REVERT: g 61 MET cc_start: 0.8589 (mmt) cc_final: 0.8076 (mmt) REVERT: g 68 TYR cc_start: 0.8239 (m-10) cc_final: 0.7979 (m-80) REVERT: g 115 ASP cc_start: 0.7219 (t0) cc_final: 0.6300 (t0) REVERT: h 132 ILE cc_start: 0.8501 (mm) cc_final: 0.8256 (mm) REVERT: i 131 MET cc_start: 0.6920 (ppp) cc_final: 0.6612 (ppp) REVERT: j 39 THR cc_start: 0.9040 (t) cc_final: 0.8677 (p) REVERT: j 53 MET cc_start: 0.7559 (mmp) cc_final: 0.6949 (mmt) REVERT: j 131 MET cc_start: 0.7692 (ppp) cc_final: 0.7158 (ppp) REVERT: k 28 MET cc_start: 0.8188 (mmp) cc_final: 0.7497 (mtp) REVERT: k 44 MET cc_start: 0.7627 (mmm) cc_final: 0.6787 (mmm) REVERT: l 28 MET cc_start: 0.8937 (mmp) cc_final: 0.8555 (mmm) REVERT: l 131 MET cc_start: 0.8438 (ptp) cc_final: 0.8237 (ptp) REVERT: n 36 LYS cc_start: 0.8716 (pttm) cc_final: 0.8472 (ptpp) REVERT: n 44 MET cc_start: 0.6719 (ptp) cc_final: 0.6101 (ptp) REVERT: n 61 MET cc_start: 0.6844 (ttm) cc_final: 0.6523 (ttm) REVERT: o 37 SER cc_start: 0.7952 (m) cc_final: 0.7443 (t) REVERT: c 274 ASP cc_start: 0.9052 (m-30) cc_final: 0.8823 (m-30) REVERT: c 336 MET cc_start: 0.6227 (tpt) cc_final: 0.5811 (tpp) REVERT: c 365 CYS cc_start: 0.9270 (m) cc_final: 0.8327 (t) REVERT: f 24 ILE cc_start: 0.8653 (mt) cc_final: 0.8175 (mt) REVERT: f 28 MET cc_start: 0.8374 (mpp) cc_final: 0.7975 (mpp) REVERT: s 32 LEU cc_start: 0.6132 (mt) cc_final: 0.5850 (pp) REVERT: e 13 PHE cc_start: 0.7818 (m-10) cc_final: 0.7448 (m-10) REVERT: e 40 MET cc_start: 0.6385 (ppp) cc_final: 0.6102 (ppp) outliers start: 4 outliers final: 1 residues processed: 919 average time/residue: 0.6049 time to fit residues: 970.1904 Evaluate side-chains 723 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 722 time to evaluate : 5.715 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 274 optimal weight: 6.9990 chunk 735 optimal weight: 0.9980 chunk 161 optimal weight: 8.9990 chunk 479 optimal weight: 9.9990 chunk 201 optimal weight: 0.7980 chunk 817 optimal weight: 10.0000 chunk 678 optimal weight: 6.9990 chunk 378 optimal weight: 0.0770 chunk 67 optimal weight: 7.9990 chunk 270 optimal weight: 10.0000 chunk 429 optimal weight: 40.0000 overall best weight: 3.1742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 543 ASN 1 610 ASN ** 2 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 5 171 GLN ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 HIS U 439 GLN a 274 GLN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7267 moved from start: 0.2576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 68114 Z= 0.236 Angle : 0.628 10.148 92059 Z= 0.330 Chirality : 0.043 0.247 10442 Planarity : 0.004 0.098 11782 Dihedral : 4.581 25.667 9259 Min Nonbonded Distance : 2.377 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.06 % Allowed : 2.22 % Favored : 97.72 % 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: 0.63 (0.09), residues: 8466 helix: 1.29 (0.07), residues: 4795 sheet: 0.07 (0.20), residues: 714 loop : -0.89 (0.12), residues: 2957 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.053 0.002 TRP 6 20 HIS 0.007 0.001 HIS d 49 PHE 0.039 0.002 PHE h 108 TYR 0.055 0.002 TYR f 62 ARG 0.009 0.000 ARG i 126 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 916 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 912 time to evaluate : 5.787 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: 8 72 MET cc_start: 0.9018 (tpt) cc_final: 0.8514 (tpt) REVERT: 8 76 MET cc_start: 0.9495 (mmm) cc_final: 0.9050 (mmm) REVERT: 8 93 ASP cc_start: 0.8959 (m-30) cc_final: 0.8713 (m-30) REVERT: 8 132 MET cc_start: 0.9071 (mtp) cc_final: 0.8754 (mtt) REVERT: 8 208 MET cc_start: 0.8886 (ttt) cc_final: 0.8374 (mpp) REVERT: 9 89 ASP cc_start: 0.9042 (m-30) cc_final: 0.8819 (m-30) REVERT: Q 207 MET cc_start: 0.9120 (tpt) cc_final: 0.8668 (tpp) REVERT: V 33 LEU cc_start: 0.6707 (mt) cc_final: 0.5964 (tt) REVERT: 0 39 MET cc_start: 0.8411 (ptp) cc_final: 0.8205 (ptp) REVERT: 0 340 MET cc_start: 0.8542 (ttm) cc_final: 0.7991 (ttm) REVERT: 0 346 MET cc_start: 0.8845 (tmm) cc_final: 0.8172 (tmm) REVERT: 0 406 ILE cc_start: 0.9466 (mm) cc_final: 0.9227 (mm) REVERT: 0 444 HIS cc_start: 0.8221 (t-170) cc_final: 0.7986 (t-170) REVERT: 0 458 MET cc_start: 0.9269 (mmm) cc_final: 0.8017 (mmt) REVERT: 0 462 ASP cc_start: 0.8825 (p0) cc_final: 0.8618 (p0) REVERT: 0 478 LYS cc_start: 0.9461 (mtmm) cc_final: 0.9221 (mtmt) REVERT: 0 540 MET cc_start: 0.8626 (ptm) cc_final: 0.8332 (ppp) REVERT: 0 541 LEU cc_start: 0.9671 (mt) cc_final: 0.9132 (mt) REVERT: 0 544 MET cc_start: 0.9690 (mtm) cc_final: 0.9374 (mtp) REVERT: 0 573 HIS cc_start: 0.8284 (t-170) cc_final: 0.7887 (t-170) REVERT: 1 34 MET cc_start: 0.9065 (mmm) cc_final: 0.8561 (tpp) REVERT: 1 246 THR cc_start: 0.9128 (t) cc_final: 0.8876 (m) REVERT: 1 340 MET cc_start: 0.8865 (tpp) cc_final: 0.8618 (tpp) REVERT: 1 368 MET cc_start: 0.9363 (tpp) cc_final: 0.8964 (tpp) REVERT: 1 485 GLU cc_start: 0.9123 (tm-30) cc_final: 0.8503 (tm-30) REVERT: 1 489 LEU cc_start: 0.9404 (mt) cc_final: 0.9140 (mt) REVERT: 1 540 MET cc_start: 0.8837 (mmm) cc_final: 0.8627 (mmt) REVERT: 1 550 MET cc_start: 0.9254 (tpt) cc_final: 0.9019 (tpp) REVERT: 1 584 MET cc_start: 0.7995 (ttp) cc_final: 0.7720 (ttm) REVERT: 2 34 MET cc_start: 0.9047 (mmm) cc_final: 0.8691 (mmm) REVERT: 2 228 LEU cc_start: 0.9295 (tp) cc_final: 0.9062 (tp) REVERT: 2 231 GLN cc_start: 0.8843 (tp40) cc_final: 0.8591 (tp40) REVERT: 2 318 MET cc_start: 0.8915 (mmm) cc_final: 0.8421 (mmm) REVERT: 2 346 MET cc_start: 0.9067 (ttt) cc_final: 0.8835 (ttm) REVERT: 2 576 GLU cc_start: 0.9145 (tt0) cc_final: 0.8524 (tp30) REVERT: 3 270 GLU cc_start: 0.9438 (mt-10) cc_final: 0.8980 (tp30) REVERT: 3 389 TYR cc_start: 0.8619 (t80) cc_final: 0.8214 (t80) REVERT: 3 431 ASP cc_start: 0.9402 (m-30) cc_final: 0.9129 (m-30) REVERT: 3 435 MET cc_start: 0.9371 (ttp) cc_final: 0.9057 (ttp) REVERT: 3 478 ASP cc_start: 0.9160 (m-30) cc_final: 0.8790 (m-30) REVERT: 4 127 MET cc_start: 0.9543 (mtp) cc_final: 0.9180 (mtp) REVERT: 4 283 GLU cc_start: 0.9211 (tt0) cc_final: 0.8891 (tm-30) REVERT: 4 351 ILE cc_start: 0.9592 (mt) cc_final: 0.9266 (tp) REVERT: 4 410 MET cc_start: 0.9023 (mpp) cc_final: 0.8599 (mpp) REVERT: 5 127 MET cc_start: 0.8502 (mtt) cc_final: 0.8187 (mmt) REVERT: 5 234 MET cc_start: 0.8293 (mmm) cc_final: 0.7777 (mmt) REVERT: 5 299 ASP cc_start: 0.8062 (t0) cc_final: 0.7647 (t0) REVERT: 5 300 MET cc_start: 0.9097 (mmm) cc_final: 0.8724 (mmm) REVERT: 5 431 ASP cc_start: 0.9543 (t0) cc_final: 0.9139 (t0) REVERT: 6 163 LEU cc_start: 0.8041 (mm) cc_final: 0.7085 (tp) REVERT: 6 259 MET cc_start: 0.5799 (mtm) cc_final: 0.5448 (mtt) REVERT: 7 79 PHE cc_start: 0.9235 (p90) cc_final: 0.8927 (p90) REVERT: U 97 MET cc_start: 0.6000 (tpt) cc_final: 0.4521 (ttp) REVERT: U 145 MET cc_start: 0.4369 (mmm) cc_final: 0.4068 (mmm) REVERT: U 181 PHE cc_start: 0.7541 (m-10) cc_final: 0.7153 (m-80) REVERT: U 387 ASP cc_start: 0.7444 (m-30) cc_final: 0.6956 (p0) REVERT: X 98 GLU cc_start: 0.7777 (mp0) cc_final: 0.7493 (mp0) REVERT: a 186 MET cc_start: 0.8743 (mtm) cc_final: 0.8380 (mtp) REVERT: a 367 THR cc_start: 0.7398 (p) cc_final: 0.7123 (t) REVERT: a 423 MET cc_start: 0.8655 (mpp) cc_final: 0.8257 (mpp) REVERT: a 584 PHE cc_start: 0.8691 (m-80) cc_final: 0.8463 (m-10) REVERT: a 745 LEU cc_start: 0.8934 (mp) cc_final: 0.8642 (mp) REVERT: a 793 ILE cc_start: 0.7891 (pt) cc_final: 0.7554 (pt) REVERT: a 804 LEU cc_start: 0.9225 (mt) cc_final: 0.8958 (mt) REVERT: a 806 LEU cc_start: 0.9432 (tp) cc_final: 0.9212 (tp) REVERT: b 26 TYR cc_start: 0.5229 (t80) cc_final: 0.4216 (t80) REVERT: b 90 ASN cc_start: 0.7497 (m110) cc_final: 0.7278 (m110) REVERT: d 86 MET cc_start: 0.7326 (mmp) cc_final: 0.6421 (mmm) REVERT: d 153 ASN cc_start: 0.8868 (m-40) cc_final: 0.8604 (p0) REVERT: d 209 MET cc_start: 0.6269 (mmm) cc_final: 0.6069 (mmm) REVERT: g 53 MET cc_start: 0.7635 (mmm) cc_final: 0.6776 (ppp) REVERT: g 68 TYR cc_start: 0.8235 (m-10) cc_final: 0.8003 (m-80) REVERT: h 47 MET cc_start: 0.8353 (ppp) cc_final: 0.7743 (pmm) REVERT: h 132 ILE cc_start: 0.8513 (mm) cc_final: 0.8280 (mm) REVERT: i 131 MET cc_start: 0.6887 (ppp) cc_final: 0.6610 (ppp) REVERT: i 144 TYR cc_start: 0.6731 (m-80) cc_final: 0.6338 (m-80) REVERT: j 39 THR cc_start: 0.9013 (t) cc_final: 0.8644 (p) REVERT: j 53 MET cc_start: 0.7570 (mmp) cc_final: 0.6947 (mmt) REVERT: j 131 MET cc_start: 0.7690 (ppp) cc_final: 0.7158 (ppp) REVERT: k 44 MET cc_start: 0.7512 (mmm) cc_final: 0.6851 (mmm) REVERT: l 28 MET cc_start: 0.8945 (mmp) cc_final: 0.8537 (mmm) REVERT: m 28 MET cc_start: 0.8130 (mmp) cc_final: 0.7628 (mmp) REVERT: m 44 MET cc_start: 0.8568 (mmm) cc_final: 0.8142 (mmm) REVERT: m 115 ASP cc_start: 0.8000 (m-30) cc_final: 0.7522 (p0) REVERT: n 44 MET cc_start: 0.6643 (ptp) cc_final: 0.6209 (ptp) REVERT: n 61 MET cc_start: 0.6892 (ttm) cc_final: 0.6664 (ttm) REVERT: o 37 SER cc_start: 0.7903 (m) cc_final: 0.7338 (p) REVERT: p 615 LEU cc_start: 0.7573 (pp) cc_final: 0.7314 (tt) REVERT: c 274 ASP cc_start: 0.8996 (m-30) cc_final: 0.8781 (m-30) REVERT: c 336 MET cc_start: 0.6219 (tpt) cc_final: 0.5340 (tpp) REVERT: c 365 CYS cc_start: 0.9286 (m) cc_final: 0.8333 (t) REVERT: s 32 LEU cc_start: 0.6047 (mt) cc_final: 0.5780 (pp) REVERT: e 9 PRO cc_start: 0.8072 (Cg_exo) cc_final: 0.7355 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7804 (m-10) cc_final: 0.7374 (m-10) REVERT: e 19 LEU cc_start: 0.7517 (tp) cc_final: 0.7188 (pp) REVERT: e 40 MET cc_start: 0.6906 (ppp) cc_final: 0.6681 (ppp) outliers start: 4 outliers final: 2 residues processed: 915 average time/residue: 0.6159 time to fit residues: 982.6489 Evaluate side-chains 715 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 713 time to evaluate : 5.745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 788 optimal weight: 20.0000 chunk 92 optimal weight: 8.9990 chunk 465 optimal weight: 1.9990 chunk 597 optimal weight: 2.9990 chunk 462 optimal weight: 2.9990 chunk 688 optimal weight: 10.0000 chunk 456 optimal weight: 5.9990 chunk 814 optimal weight: 8.9990 chunk 509 optimal weight: 5.9990 chunk 496 optimal weight: 3.9990 chunk 376 optimal weight: 10.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN V 41 GLN 1 468 HIS 1 543 ASN ** 3 262 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 HIS 6 287 ASN U 404 HIS a 343 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 197 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS ** d 89 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** f 68 ASN ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7281 moved from start: 0.2757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 68114 Z= 0.254 Angle : 0.642 9.459 92059 Z= 0.338 Chirality : 0.043 0.211 10442 Planarity : 0.004 0.096 11782 Dihedral : 4.602 25.569 9259 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.00 % Allowed : 1.56 % Favored : 98.44 % 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: 0.60 (0.09), residues: 8466 helix: 1.27 (0.07), residues: 4792 sheet: 0.06 (0.20), residues: 699 loop : -0.91 (0.12), residues: 2975 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.055 0.002 TRP 6 20 HIS 0.007 0.001 HIS d 49 PHE 0.033 0.002 PHE 0 291 TYR 0.048 0.002 TYR l 68 ARG 0.016 0.000 ARG V 28 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 898 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 898 time to evaluate : 5.800 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: 8 51 LEU cc_start: 0.8953 (mt) cc_final: 0.8752 (mt) REVERT: 8 72 MET cc_start: 0.9052 (tpt) cc_final: 0.8524 (tpt) REVERT: 8 76 MET cc_start: 0.9496 (mmm) cc_final: 0.9050 (mmm) REVERT: 8 93 ASP cc_start: 0.8960 (m-30) cc_final: 0.8715 (m-30) REVERT: 8 132 MET cc_start: 0.9062 (mtp) cc_final: 0.8743 (mtt) REVERT: 8 208 MET cc_start: 0.8924 (ttt) cc_final: 0.8383 (mpp) REVERT: 9 54 MET cc_start: 0.9122 (mmp) cc_final: 0.8846 (mmp) REVERT: 9 89 ASP cc_start: 0.9033 (m-30) cc_final: 0.8818 (m-30) REVERT: T 84 MET cc_start: 0.8485 (tpt) cc_final: 0.7956 (tpp) REVERT: Q 207 MET cc_start: 0.9091 (tpt) cc_final: 0.8664 (tpp) REVERT: V 33 LEU cc_start: 0.6708 (mt) cc_final: 0.6012 (tt) REVERT: 0 340 MET cc_start: 0.8539 (ttm) cc_final: 0.7964 (ttm) REVERT: 0 444 HIS cc_start: 0.8284 (t-170) cc_final: 0.8035 (t70) REVERT: 0 458 MET cc_start: 0.9266 (mmm) cc_final: 0.8003 (mmt) REVERT: 0 541 LEU cc_start: 0.9667 (mt) cc_final: 0.9127 (mt) REVERT: 0 544 MET cc_start: 0.9679 (mtm) cc_final: 0.9382 (mtp) REVERT: 1 34 MET cc_start: 0.8996 (mmm) cc_final: 0.8494 (tpp) REVERT: 1 246 THR cc_start: 0.9141 (t) cc_final: 0.8883 (m) REVERT: 1 485 GLU cc_start: 0.9093 (tm-30) cc_final: 0.8435 (tm-30) REVERT: 1 489 LEU cc_start: 0.9401 (mt) cc_final: 0.9135 (mt) REVERT: 1 540 MET cc_start: 0.8824 (mmm) cc_final: 0.8591 (mmt) REVERT: 1 550 MET cc_start: 0.9246 (tpt) cc_final: 0.9023 (tpp) REVERT: 1 584 MET cc_start: 0.7971 (ttp) cc_final: 0.7660 (ttm) REVERT: 2 34 MET cc_start: 0.9096 (mmm) cc_final: 0.8763 (mmm) REVERT: 2 228 LEU cc_start: 0.9312 (tp) cc_final: 0.9068 (tp) REVERT: 2 231 GLN cc_start: 0.8863 (tp40) cc_final: 0.8594 (tp40) REVERT: 2 318 MET cc_start: 0.8884 (mmm) cc_final: 0.8412 (mmm) REVERT: 2 576 GLU cc_start: 0.9133 (tt0) cc_final: 0.8512 (tp30) REVERT: 3 270 GLU cc_start: 0.9452 (mt-10) cc_final: 0.8988 (tp30) REVERT: 3 431 ASP cc_start: 0.9409 (m-30) cc_final: 0.9142 (m-30) REVERT: 3 435 MET cc_start: 0.9386 (ttp) cc_final: 0.9105 (ttp) REVERT: 3 478 ASP cc_start: 0.9191 (m-30) cc_final: 0.8811 (m-30) REVERT: 4 127 MET cc_start: 0.9552 (mtp) cc_final: 0.9138 (mtp) REVERT: 4 283 GLU cc_start: 0.9225 (tt0) cc_final: 0.8818 (tm-30) REVERT: 4 309 GLU cc_start: 0.9261 (tm-30) cc_final: 0.9026 (tm-30) REVERT: 4 351 ILE cc_start: 0.9600 (mt) cc_final: 0.9274 (tp) REVERT: 4 410 MET cc_start: 0.9011 (mpp) cc_final: 0.8564 (mpp) REVERT: 4 425 CYS cc_start: 0.9497 (m) cc_final: 0.9164 (m) REVERT: 5 127 MET cc_start: 0.8496 (mtt) cc_final: 0.8127 (mmm) REVERT: 5 234 MET cc_start: 0.8355 (mmm) cc_final: 0.7842 (mmt) REVERT: 5 270 GLU cc_start: 0.8680 (tp30) cc_final: 0.8451 (tp30) REVERT: 5 299 ASP cc_start: 0.8041 (t0) cc_final: 0.7619 (t0) REVERT: 5 300 MET cc_start: 0.9086 (mmm) cc_final: 0.8693 (mmm) REVERT: 5 431 ASP cc_start: 0.9557 (t0) cc_final: 0.9136 (t0) REVERT: 6 163 LEU cc_start: 0.7972 (mm) cc_final: 0.7051 (tp) REVERT: 6 259 MET cc_start: 0.5839 (mtm) cc_final: 0.5459 (mtt) REVERT: 7 79 PHE cc_start: 0.9263 (p90) cc_final: 0.8953 (p90) REVERT: U 97 MET cc_start: 0.5972 (tpt) cc_final: 0.4491 (ttp) REVERT: U 145 MET cc_start: 0.4347 (mmm) cc_final: 0.4095 (mmm) REVERT: U 181 PHE cc_start: 0.7495 (m-10) cc_final: 0.7131 (m-80) REVERT: U 387 ASP cc_start: 0.7553 (m-30) cc_final: 0.7046 (p0) REVERT: X 98 GLU cc_start: 0.7792 (mp0) cc_final: 0.7512 (mp0) REVERT: a 186 MET cc_start: 0.8737 (mtm) cc_final: 0.8372 (mtp) REVERT: a 367 THR cc_start: 0.7420 (p) cc_final: 0.7162 (t) REVERT: a 423 MET cc_start: 0.8580 (mpp) cc_final: 0.8191 (mpp) REVERT: a 540 MET cc_start: 0.8182 (ppp) cc_final: 0.7911 (ppp) REVERT: a 584 PHE cc_start: 0.8649 (m-80) cc_final: 0.8407 (m-10) REVERT: a 651 MET cc_start: 0.8137 (mtm) cc_final: 0.7732 (mpp) REVERT: a 745 LEU cc_start: 0.9037 (mp) cc_final: 0.8716 (mp) REVERT: a 804 LEU cc_start: 0.9215 (mt) cc_final: 0.8998 (mt) REVERT: a 806 LEU cc_start: 0.9430 (tp) cc_final: 0.9200 (tp) REVERT: b 26 TYR cc_start: 0.5296 (t80) cc_final: 0.4247 (t80) REVERT: b 90 ASN cc_start: 0.7575 (m110) cc_final: 0.7326 (m110) REVERT: b 149 LEU cc_start: 0.8373 (tt) cc_final: 0.7910 (tt) REVERT: d 86 MET cc_start: 0.7452 (mmp) cc_final: 0.6485 (mmm) REVERT: d 153 ASN cc_start: 0.8831 (m-40) cc_final: 0.8579 (p0) REVERT: g 53 MET cc_start: 0.7591 (mmm) cc_final: 0.6640 (ppp) REVERT: g 68 TYR cc_start: 0.8223 (m-10) cc_final: 0.7992 (m-80) REVERT: g 115 ASP cc_start: 0.7233 (t0) cc_final: 0.6728 (t0) REVERT: g 150 LEU cc_start: 0.8483 (mm) cc_final: 0.8048 (tt) REVERT: h 47 MET cc_start: 0.8343 (ppp) cc_final: 0.7566 (pmm) REVERT: h 132 ILE cc_start: 0.8612 (mm) cc_final: 0.8317 (mm) REVERT: i 131 MET cc_start: 0.6932 (ppp) cc_final: 0.6641 (ppp) REVERT: i 144 TYR cc_start: 0.6751 (m-80) cc_final: 0.6514 (m-80) REVERT: j 39 THR cc_start: 0.8924 (t) cc_final: 0.8593 (p) REVERT: j 44 MET cc_start: 0.5402 (ptm) cc_final: 0.5149 (ptp) REVERT: j 53 MET cc_start: 0.7507 (mmp) cc_final: 0.6893 (mmt) REVERT: j 131 MET cc_start: 0.7601 (ppp) cc_final: 0.7211 (ppp) REVERT: j 136 ILE cc_start: 0.7658 (mm) cc_final: 0.7365 (mm) REVERT: k 28 MET cc_start: 0.8287 (mmp) cc_final: 0.7619 (mmm) REVERT: k 44 MET cc_start: 0.7663 (mmm) cc_final: 0.6851 (mmm) REVERT: l 28 MET cc_start: 0.8942 (mmp) cc_final: 0.8557 (mmm) REVERT: m 28 MET cc_start: 0.8335 (mmp) cc_final: 0.7760 (mmp) REVERT: m 115 ASP cc_start: 0.8107 (m-30) cc_final: 0.7620 (p0) REVERT: n 44 MET cc_start: 0.6552 (ptp) cc_final: 0.6184 (ptp) REVERT: n 61 MET cc_start: 0.6536 (ttm) cc_final: 0.6183 (ttm) REVERT: o 37 SER cc_start: 0.7915 (m) cc_final: 0.7356 (p) REVERT: p 615 LEU cc_start: 0.7686 (pp) cc_final: 0.7403 (tt) REVERT: c 274 ASP cc_start: 0.9003 (m-30) cc_final: 0.8795 (m-30) REVERT: c 336 MET cc_start: 0.6426 (tpt) cc_final: 0.5872 (tpp) REVERT: c 365 CYS cc_start: 0.9319 (m) cc_final: 0.8391 (t) REVERT: f 24 ILE cc_start: 0.8721 (mt) cc_final: 0.8462 (mt) REVERT: f 26 LEU cc_start: 0.7116 (tt) cc_final: 0.6723 (tt) REVERT: f 28 MET cc_start: 0.8405 (mpp) cc_final: 0.8124 (mpp) REVERT: s 32 LEU cc_start: 0.6062 (mt) cc_final: 0.5809 (pp) REVERT: e 9 PRO cc_start: 0.7982 (Cg_exo) cc_final: 0.7300 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7885 (m-10) cc_final: 0.7458 (m-10) REVERT: e 57 LEU cc_start: 0.7670 (pp) cc_final: 0.7428 (pp) outliers start: 0 outliers final: 0 residues processed: 898 average time/residue: 0.6218 time to fit residues: 976.8487 Evaluate side-chains 706 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 706 time to evaluate : 5.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 503 optimal weight: 0.8980 chunk 325 optimal weight: 5.9990 chunk 486 optimal weight: 9.9990 chunk 245 optimal weight: 8.9990 chunk 160 optimal weight: 0.9990 chunk 157 optimal weight: 9.9990 chunk 517 optimal weight: 0.2980 chunk 554 optimal weight: 0.9990 chunk 402 optimal weight: 9.9990 chunk 75 optimal weight: 7.9990 chunk 640 optimal weight: 5.9990 overall best weight: 1.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN Q 14 HIS V 41 GLN ** 0 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 468 HIS ** 1 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 543 ASN 3 262 ASN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 465 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 HIS 6 287 ASN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 289 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 493 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** a 612 HIS ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS ** d 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 219 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 68114 Z= 0.196 Angle : 0.633 11.285 92059 Z= 0.330 Chirality : 0.043 0.252 10442 Planarity : 0.004 0.089 11782 Dihedral : 4.556 25.268 9259 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % 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: 0.67 (0.09), residues: 8466 helix: 1.32 (0.07), residues: 4800 sheet: 0.17 (0.20), residues: 699 loop : -0.90 (0.12), residues: 2967 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.002 TRP 6 20 HIS 0.018 0.001 HIS 6 337 PHE 0.040 0.002 PHE a 399 TYR 0.056 0.002 TYR f 76 ARG 0.011 0.000 ARG a 805 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 908 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 908 time to evaluate : 6.211 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: 8 72 MET cc_start: 0.8996 (tpt) cc_final: 0.8489 (tpt) REVERT: 8 76 MET cc_start: 0.9477 (mmm) cc_final: 0.9030 (mmm) REVERT: 8 93 ASP cc_start: 0.8924 (m-30) cc_final: 0.8672 (m-30) REVERT: 8 132 MET cc_start: 0.8953 (mtp) cc_final: 0.8605 (mtt) REVERT: 8 208 MET cc_start: 0.8879 (ttt) cc_final: 0.8339 (mpp) REVERT: 9 54 MET cc_start: 0.9098 (mmp) cc_final: 0.8852 (mmp) REVERT: 9 89 ASP cc_start: 0.9026 (m-30) cc_final: 0.8816 (m-30) REVERT: T 63 MET cc_start: 0.8841 (tpt) cc_final: 0.8248 (mtt) REVERT: T 84 MET cc_start: 0.8544 (tpt) cc_final: 0.8251 (tpp) REVERT: Q 207 MET cc_start: 0.9107 (tpt) cc_final: 0.8381 (tpp) REVERT: V 33 LEU cc_start: 0.6664 (mt) cc_final: 0.5973 (tt) REVERT: 0 340 MET cc_start: 0.8583 (ttm) cc_final: 0.7944 (ttm) REVERT: 0 444 HIS cc_start: 0.8169 (t-170) cc_final: 0.7912 (t70) REVERT: 0 458 MET cc_start: 0.9253 (mmm) cc_final: 0.7960 (mmt) REVERT: 0 478 LYS cc_start: 0.9451 (mtmm) cc_final: 0.9111 (mttt) REVERT: 0 544 MET cc_start: 0.9486 (mtm) cc_final: 0.9206 (mtm) REVERT: 0 571 ARG cc_start: 0.9483 (tpt90) cc_final: 0.9082 (ptp-170) REVERT: 1 246 THR cc_start: 0.9153 (t) cc_final: 0.8908 (m) REVERT: 1 334 SER cc_start: 0.9588 (t) cc_final: 0.9197 (p) REVERT: 1 340 MET cc_start: 0.8698 (tpp) cc_final: 0.8463 (tpp) REVERT: 1 368 MET cc_start: 0.9343 (tpp) cc_final: 0.8951 (tpp) REVERT: 1 485 GLU cc_start: 0.9034 (tm-30) cc_final: 0.8349 (tm-30) REVERT: 1 489 LEU cc_start: 0.9372 (mt) cc_final: 0.9104 (mt) REVERT: 1 540 MET cc_start: 0.8825 (mmm) cc_final: 0.8588 (mmt) REVERT: 1 550 MET cc_start: 0.9248 (tpt) cc_final: 0.9026 (tpp) REVERT: 1 584 MET cc_start: 0.8031 (ttp) cc_final: 0.7713 (ttm) REVERT: 2 34 MET cc_start: 0.9089 (mmm) cc_final: 0.8727 (mmm) REVERT: 2 228 LEU cc_start: 0.9294 (tp) cc_final: 0.9052 (tp) REVERT: 2 231 GLN cc_start: 0.8855 (tp40) cc_final: 0.8580 (tp40) REVERT: 2 318 MET cc_start: 0.8833 (mmm) cc_final: 0.8413 (mmm) REVERT: 2 544 MET cc_start: 0.9015 (mtt) cc_final: 0.8745 (mtt) REVERT: 2 576 GLU cc_start: 0.9113 (tt0) cc_final: 0.8477 (tp30) REVERT: 3 270 GLU cc_start: 0.9425 (mt-10) cc_final: 0.9146 (tt0) REVERT: 3 431 ASP cc_start: 0.9399 (m-30) cc_final: 0.9135 (m-30) REVERT: 3 435 MET cc_start: 0.9389 (ttp) cc_final: 0.9058 (ttp) REVERT: 3 450 LEU cc_start: 0.8777 (tp) cc_final: 0.8262 (tp) REVERT: 3 453 GLU cc_start: 0.8620 (pp20) cc_final: 0.8345 (pp20) REVERT: 3 478 ASP cc_start: 0.9165 (m-30) cc_final: 0.8783 (m-30) REVERT: 4 127 MET cc_start: 0.9511 (mtp) cc_final: 0.9130 (mtp) REVERT: 4 283 GLU cc_start: 0.9174 (tt0) cc_final: 0.8802 (tm-30) REVERT: 4 309 GLU cc_start: 0.9259 (tm-30) cc_final: 0.9045 (tm-30) REVERT: 4 351 ILE cc_start: 0.9596 (mt) cc_final: 0.9300 (tp) REVERT: 4 380 ASP cc_start: 0.8667 (t0) cc_final: 0.7967 (p0) REVERT: 4 410 MET cc_start: 0.8990 (mpp) cc_final: 0.8555 (mpp) REVERT: 4 425 CYS cc_start: 0.9458 (m) cc_final: 0.9104 (m) REVERT: 5 127 MET cc_start: 0.8426 (mtt) cc_final: 0.8042 (mmt) REVERT: 5 234 MET cc_start: 0.8287 (mmm) cc_final: 0.7664 (mmt) REVERT: 5 270 GLU cc_start: 0.8627 (tp30) cc_final: 0.8347 (tp30) REVERT: 5 299 ASP cc_start: 0.8031 (t0) cc_final: 0.7629 (t0) REVERT: 5 300 MET cc_start: 0.9020 (mmm) cc_final: 0.8693 (mmm) REVERT: 5 402 MET cc_start: 0.8419 (ttt) cc_final: 0.7699 (tmm) REVERT: 5 420 ASN cc_start: 0.9698 (m110) cc_final: 0.9492 (m-40) REVERT: 5 431 ASP cc_start: 0.9519 (t0) cc_final: 0.9078 (t0) REVERT: 6 163 LEU cc_start: 0.7954 (mm) cc_final: 0.7033 (tp) REVERT: 6 259 MET cc_start: 0.5993 (mtm) cc_final: 0.5650 (mtt) REVERT: 7 79 PHE cc_start: 0.9194 (p90) cc_final: 0.8893 (p90) REVERT: U 97 MET cc_start: 0.6019 (tpt) cc_final: 0.4471 (ptt) REVERT: U 181 PHE cc_start: 0.7570 (m-10) cc_final: 0.7195 (m-80) REVERT: U 387 ASP cc_start: 0.7473 (m-30) cc_final: 0.7048 (p0) REVERT: X 98 GLU cc_start: 0.7765 (mp0) cc_final: 0.7478 (mp0) REVERT: X 109 LEU cc_start: 0.9210 (mm) cc_final: 0.9005 (mt) REVERT: a 80 MET cc_start: 0.8544 (mpp) cc_final: 0.8070 (mmt) REVERT: a 186 MET cc_start: 0.8733 (mtm) cc_final: 0.8357 (mtp) REVERT: a 367 THR cc_start: 0.7451 (p) cc_final: 0.7166 (t) REVERT: a 423 MET cc_start: 0.8645 (mpp) cc_final: 0.8237 (mpp) REVERT: a 466 ASP cc_start: 0.8457 (t0) cc_final: 0.7788 (p0) REVERT: a 584 PHE cc_start: 0.8592 (m-80) cc_final: 0.8061 (m-80) REVERT: a 651 MET cc_start: 0.8031 (mtm) cc_final: 0.7546 (mpp) REVERT: a 745 LEU cc_start: 0.9023 (mp) cc_final: 0.8706 (mp) REVERT: b 26 TYR cc_start: 0.5227 (t80) cc_final: 0.4217 (t80) REVERT: b 90 ASN cc_start: 0.7389 (m110) cc_final: 0.7148 (m110) REVERT: b 149 LEU cc_start: 0.8330 (tt) cc_final: 0.7854 (tt) REVERT: d 86 MET cc_start: 0.7555 (mmp) cc_final: 0.6607 (mmm) REVERT: d 153 ASN cc_start: 0.8800 (m-40) cc_final: 0.8559 (p0) REVERT: g 53 MET cc_start: 0.7523 (mmm) cc_final: 0.6683 (ppp) REVERT: g 68 TYR cc_start: 0.8173 (m-10) cc_final: 0.7927 (m-80) REVERT: h 47 MET cc_start: 0.8305 (ppp) cc_final: 0.7546 (pmm) REVERT: h 132 ILE cc_start: 0.8659 (mm) cc_final: 0.8322 (mm) REVERT: i 44 MET cc_start: 0.5025 (ptp) cc_final: 0.4562 (ptp) REVERT: i 131 MET cc_start: 0.6867 (ppp) cc_final: 0.6596 (ppp) REVERT: i 144 TYR cc_start: 0.6577 (m-80) cc_final: 0.6325 (m-80) REVERT: j 39 THR cc_start: 0.8914 (t) cc_final: 0.8582 (p) REVERT: j 44 MET cc_start: 0.5490 (ptm) cc_final: 0.5192 (ptm) REVERT: j 53 MET cc_start: 0.7526 (mmp) cc_final: 0.6928 (mmt) REVERT: j 61 MET cc_start: 0.5996 (ppp) cc_final: 0.5746 (ppp) REVERT: j 131 MET cc_start: 0.7628 (ppp) cc_final: 0.7051 (ppp) REVERT: k 28 MET cc_start: 0.8234 (mmp) cc_final: 0.7531 (mmm) REVERT: k 44 MET cc_start: 0.7497 (mmm) cc_final: 0.6768 (mmm) REVERT: k 57 ILE cc_start: 0.8565 (mt) cc_final: 0.8327 (mt) REVERT: l 28 MET cc_start: 0.8923 (mmp) cc_final: 0.8528 (mmm) REVERT: m 28 MET cc_start: 0.8229 (mmp) cc_final: 0.7718 (mmp) REVERT: m 44 MET cc_start: 0.8394 (mmm) cc_final: 0.8154 (mmm) REVERT: m 115 ASP cc_start: 0.8060 (m-30) cc_final: 0.7026 (m-30) REVERT: n 44 MET cc_start: 0.6504 (ptp) cc_final: 0.6208 (ptp) REVERT: n 61 MET cc_start: 0.6070 (ttm) cc_final: 0.5808 (ttt) REVERT: o 37 SER cc_start: 0.7839 (m) cc_final: 0.7254 (p) REVERT: p 615 LEU cc_start: 0.7649 (pp) cc_final: 0.7367 (tt) REVERT: c 274 ASP cc_start: 0.9024 (m-30) cc_final: 0.8813 (m-30) REVERT: c 336 MET cc_start: 0.6295 (tpt) cc_final: 0.5794 (tpp) REVERT: c 365 CYS cc_start: 0.9306 (m) cc_final: 0.8479 (t) REVERT: f 24 ILE cc_start: 0.8745 (mt) cc_final: 0.8445 (mt) REVERT: f 28 MET cc_start: 0.8447 (mpp) cc_final: 0.8109 (mpp) REVERT: s 32 LEU cc_start: 0.6011 (mt) cc_final: 0.5774 (pp) REVERT: s 153 MET cc_start: 0.6630 (ppp) cc_final: 0.6278 (ppp) REVERT: e 9 PRO cc_start: 0.7901 (Cg_exo) cc_final: 0.7179 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7933 (m-10) cc_final: 0.7476 (m-10) REVERT: e 40 MET cc_start: 0.6823 (ppp) cc_final: 0.6305 (ppp) REVERT: e 57 LEU cc_start: 0.7676 (pp) cc_final: 0.7447 (pp) outliers start: 0 outliers final: 0 residues processed: 908 average time/residue: 0.6042 time to fit residues: 956.0614 Evaluate side-chains 727 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 727 time to evaluate : 5.759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 740 optimal weight: 6.9990 chunk 780 optimal weight: 6.9990 chunk 711 optimal weight: 2.9990 chunk 758 optimal weight: 8.9990 chunk 456 optimal weight: 9.9990 chunk 330 optimal weight: 2.9990 chunk 595 optimal weight: 6.9990 chunk 232 optimal weight: 7.9990 chunk 685 optimal weight: 1.9990 chunk 717 optimal weight: 6.9990 chunk 756 optimal weight: 20.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** T 66 GLN V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 114 GLN ** 0 444 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 1 468 HIS 1 543 ASN 3 251 ASN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 HIS 6 287 ASN ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** U 493 ASN ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS ** d 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** l 78 ASN ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7299 moved from start: 0.3045 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 68114 Z= 0.294 Angle : 0.686 11.110 92059 Z= 0.360 Chirality : 0.044 0.283 10442 Planarity : 0.005 0.086 11782 Dihedral : 4.679 25.755 9259 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer: Outliers : 0.01 % Allowed : 0.64 % Favored : 99.35 % 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: 0.52 (0.09), residues: 8466 helix: 1.22 (0.07), residues: 4804 sheet: 0.01 (0.20), residues: 727 loop : -0.99 (0.12), residues: 2935 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.002 TRP 6 20 HIS 0.018 0.001 HIS 6 337 PHE 0.036 0.002 PHE 0 291 TYR 0.049 0.002 TYR f 62 ARG 0.010 0.001 ARG a 805 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 877 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 876 time to evaluate : 5.814 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: 8 51 LEU cc_start: 0.8915 (mt) cc_final: 0.8709 (mt) REVERT: 8 72 MET cc_start: 0.9063 (tpt) cc_final: 0.8492 (tpt) REVERT: 8 76 MET cc_start: 0.9496 (mmm) cc_final: 0.9059 (mmm) REVERT: 8 93 ASP cc_start: 0.8972 (m-30) cc_final: 0.8729 (m-30) REVERT: 8 132 MET cc_start: 0.8998 (mtp) cc_final: 0.8659 (mtt) REVERT: 8 208 MET cc_start: 0.8928 (ttt) cc_final: 0.8361 (mpp) REVERT: 9 54 MET cc_start: 0.9109 (mmp) cc_final: 0.8821 (mmp) REVERT: 9 89 ASP cc_start: 0.9055 (m-30) cc_final: 0.8850 (m-30) REVERT: T 84 MET cc_start: 0.8625 (tpt) cc_final: 0.8358 (tpp) REVERT: Q 207 MET cc_start: 0.9104 (tpt) cc_final: 0.8629 (tpp) REVERT: V 33 LEU cc_start: 0.6636 (mt) cc_final: 0.5865 (tt) REVERT: 0 340 MET cc_start: 0.8549 (ttm) cc_final: 0.7923 (ttm) REVERT: 0 444 HIS cc_start: 0.8273 (t-170) cc_final: 0.8017 (t70) REVERT: 0 458 MET cc_start: 0.9261 (mmm) cc_final: 0.7984 (mmt) REVERT: 1 246 THR cc_start: 0.9143 (t) cc_final: 0.8850 (m) REVERT: 1 340 MET cc_start: 0.8705 (tpp) cc_final: 0.8414 (tpp) REVERT: 1 485 GLU cc_start: 0.9076 (tm-30) cc_final: 0.8402 (tm-30) REVERT: 1 489 LEU cc_start: 0.9410 (mt) cc_final: 0.9129 (mt) REVERT: 1 550 MET cc_start: 0.9274 (tpt) cc_final: 0.9027 (tpp) REVERT: 1 584 MET cc_start: 0.7909 (ttp) cc_final: 0.7634 (ttm) REVERT: 2 34 MET cc_start: 0.9149 (mmm) cc_final: 0.8874 (mmm) REVERT: 2 205 MET cc_start: 0.8627 (ptp) cc_final: 0.8246 (pmm) REVERT: 2 228 LEU cc_start: 0.9328 (tp) cc_final: 0.9121 (tp) REVERT: 2 318 MET cc_start: 0.8897 (mmm) cc_final: 0.8476 (mmm) REVERT: 2 525 TYR cc_start: 0.6367 (p90) cc_final: 0.6107 (p90) REVERT: 2 544 MET cc_start: 0.9025 (mtt) cc_final: 0.8750 (mtt) REVERT: 2 576 GLU cc_start: 0.9119 (tt0) cc_final: 0.8519 (tp30) REVERT: 3 270 GLU cc_start: 0.9463 (mt-10) cc_final: 0.8969 (tp30) REVERT: 3 431 ASP cc_start: 0.9426 (m-30) cc_final: 0.9172 (m-30) REVERT: 3 435 MET cc_start: 0.9387 (ttp) cc_final: 0.9072 (ttp) REVERT: 3 450 LEU cc_start: 0.8771 (tp) cc_final: 0.8233 (tp) REVERT: 3 453 GLU cc_start: 0.8683 (pp20) cc_final: 0.8397 (pp20) REVERT: 3 478 ASP cc_start: 0.9190 (m-30) cc_final: 0.8821 (m-30) REVERT: 4 127 MET cc_start: 0.9549 (mtp) cc_final: 0.9124 (mtp) REVERT: 4 169 MET cc_start: 0.9076 (tmm) cc_final: 0.8723 (tmm) REVERT: 4 283 GLU cc_start: 0.9240 (tt0) cc_final: 0.8838 (tm-30) REVERT: 4 309 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8985 (tm-30) REVERT: 4 351 ILE cc_start: 0.9610 (mt) cc_final: 0.9270 (tp) REVERT: 4 410 MET cc_start: 0.8983 (mpp) cc_final: 0.8490 (mpp) REVERT: 4 425 CYS cc_start: 0.9550 (m) cc_final: 0.9222 (m) REVERT: 5 127 MET cc_start: 0.8471 (mtt) cc_final: 0.7958 (mmm) REVERT: 5 234 MET cc_start: 0.8397 (mmm) cc_final: 0.7858 (mmt) REVERT: 5 270 GLU cc_start: 0.8701 (tp30) cc_final: 0.8494 (tp30) REVERT: 5 299 ASP cc_start: 0.8262 (t0) cc_final: 0.7817 (t0) REVERT: 5 300 MET cc_start: 0.9076 (mmm) cc_final: 0.8685 (mmm) REVERT: 5 402 MET cc_start: 0.8484 (ttt) cc_final: 0.7711 (tmm) REVERT: 5 420 ASN cc_start: 0.9705 (m110) cc_final: 0.9496 (m-40) REVERT: 5 431 ASP cc_start: 0.9558 (t0) cc_final: 0.9017 (t0) REVERT: 6 163 LEU cc_start: 0.7931 (mm) cc_final: 0.6946 (tp) REVERT: 6 259 MET cc_start: 0.6054 (mtm) cc_final: 0.5615 (mtt) REVERT: 7 23 LEU cc_start: 0.8600 (tt) cc_final: 0.8075 (tt) REVERT: 7 79 PHE cc_start: 0.9325 (p90) cc_final: 0.9083 (p90) REVERT: U 156 MET cc_start: 0.7937 (pmm) cc_final: 0.7714 (pmm) REVERT: U 181 PHE cc_start: 0.7640 (m-10) cc_final: 0.7282 (m-80) REVERT: X 98 GLU cc_start: 0.7813 (mp0) cc_final: 0.7529 (mp0) REVERT: a 186 MET cc_start: 0.8759 (mtm) cc_final: 0.8372 (mtp) REVERT: a 367 THR cc_start: 0.7633 (p) cc_final: 0.7376 (t) REVERT: a 423 MET cc_start: 0.8682 (mpp) cc_final: 0.8300 (mpp) REVERT: a 484 MET cc_start: 0.6095 (tmm) cc_final: 0.5478 (tmm) REVERT: a 584 PHE cc_start: 0.8704 (m-80) cc_final: 0.8193 (m-80) REVERT: a 651 MET cc_start: 0.8066 (mtm) cc_final: 0.7493 (mpp) REVERT: a 745 LEU cc_start: 0.9077 (mp) cc_final: 0.8779 (mp) REVERT: a 804 LEU cc_start: 0.9087 (mt) cc_final: 0.8801 (mt) REVERT: b 90 ASN cc_start: 0.7597 (m110) cc_final: 0.7323 (m110) REVERT: b 137 MET cc_start: 0.4920 (ppp) cc_final: 0.4493 (ppp) REVERT: b 149 LEU cc_start: 0.8272 (tt) cc_final: 0.7881 (tt) REVERT: d 86 MET cc_start: 0.7548 (mmp) cc_final: 0.6528 (mmm) REVERT: d 153 ASN cc_start: 0.8814 (m-40) cc_final: 0.8553 (p0) REVERT: g 61 MET cc_start: 0.8521 (mmt) cc_final: 0.7737 (mmt) REVERT: g 68 TYR cc_start: 0.8346 (m-10) cc_final: 0.8135 (m-80) REVERT: h 47 MET cc_start: 0.8327 (ppp) cc_final: 0.7559 (pmm) REVERT: h 132 ILE cc_start: 0.8478 (mm) cc_final: 0.8157 (mm) REVERT: i 44 MET cc_start: 0.5284 (ptp) cc_final: 0.4769 (ptp) REVERT: i 131 MET cc_start: 0.6910 (ppp) cc_final: 0.6637 (ppp) REVERT: j 44 MET cc_start: 0.5606 (ptm) cc_final: 0.5343 (ptm) REVERT: j 53 MET cc_start: 0.7666 (mmp) cc_final: 0.7082 (mmt) REVERT: j 61 MET cc_start: 0.5900 (ppp) cc_final: 0.5669 (ppp) REVERT: j 131 MET cc_start: 0.7727 (ppp) cc_final: 0.7317 (ppp) REVERT: k 28 MET cc_start: 0.8270 (mmp) cc_final: 0.7566 (mmm) REVERT: k 44 MET cc_start: 0.7687 (mmm) cc_final: 0.6947 (mmm) REVERT: k 57 ILE cc_start: 0.8654 (mt) cc_final: 0.8434 (mt) REVERT: l 28 MET cc_start: 0.8964 (mmp) cc_final: 0.8598 (mmm) REVERT: l 131 MET cc_start: 0.8608 (ptp) cc_final: 0.8297 (mpp) REVERT: m 28 MET cc_start: 0.8363 (mmp) cc_final: 0.7820 (mmp) REVERT: n 44 MET cc_start: 0.6490 (ptp) cc_final: 0.6097 (ptp) REVERT: n 61 MET cc_start: 0.6303 (ttm) cc_final: 0.5973 (ttt) REVERT: o 37 SER cc_start: 0.7753 (m) cc_final: 0.7232 (p) REVERT: p 615 LEU cc_start: 0.7657 (pp) cc_final: 0.7365 (tt) REVERT: c 274 ASP cc_start: 0.9046 (m-30) cc_final: 0.8843 (m-30) REVERT: c 336 MET cc_start: 0.6381 (tpt) cc_final: 0.5868 (tpp) REVERT: c 365 CYS cc_start: 0.9331 (m) cc_final: 0.8530 (t) REVERT: f 24 ILE cc_start: 0.8816 (mt) cc_final: 0.8461 (mt) REVERT: f 26 LEU cc_start: 0.7167 (tt) cc_final: 0.6580 (tt) REVERT: f 28 MET cc_start: 0.8494 (mpp) cc_final: 0.8191 (mpp) REVERT: s 32 LEU cc_start: 0.6119 (mt) cc_final: 0.5864 (pp) REVERT: e 9 PRO cc_start: 0.7967 (Cg_exo) cc_final: 0.7304 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7877 (m-10) cc_final: 0.7420 (m-10) REVERT: e 40 MET cc_start: 0.6409 (ppp) cc_final: 0.6172 (ppp) REVERT: e 57 LEU cc_start: 0.7625 (pp) cc_final: 0.7406 (pp) outliers start: 1 outliers final: 0 residues processed: 876 average time/residue: 0.5950 time to fit residues: 910.2965 Evaluate side-chains 700 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 700 time to evaluate : 5.712 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 498 optimal weight: 8.9990 chunk 802 optimal weight: 0.6980 chunk 489 optimal weight: 7.9990 chunk 380 optimal weight: 6.9990 chunk 557 optimal weight: 9.9990 chunk 841 optimal weight: 5.9990 chunk 774 optimal weight: 5.9990 chunk 670 optimal weight: 5.9990 chunk 69 optimal weight: 6.9990 chunk 517 optimal weight: 3.9990 chunk 411 optimal weight: 9.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Q 14 HIS V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 0 103 GLN 1 468 HIS ** 1 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 543 ASN 3 251 ASN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 4 171 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 HIS 6 287 ASN 7 113 HIS ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** d 85 HIS d 89 HIS ** d 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** d 339 GLN ** d 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.3210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 68114 Z= 0.295 Angle : 0.691 10.805 92059 Z= 0.363 Chirality : 0.044 0.425 10442 Planarity : 0.005 0.089 11782 Dihedral : 4.774 27.351 9259 Min Nonbonded Distance : 2.335 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 0.00 % Allowed : 0.35 % Favored : 99.65 % 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: 0.40 (0.09), residues: 8466 helix: 1.13 (0.07), residues: 4812 sheet: -0.12 (0.20), residues: 733 loop : -1.04 (0.12), residues: 2921 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.063 0.002 TRP 6 20 HIS 0.017 0.001 HIS 6 337 PHE 0.041 0.002 PHE p 605 TYR 0.054 0.002 TYR f 62 ARG 0.010 0.001 ARG a 805 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 16932 Ramachandran restraints generated. 8466 Oldfield, 0 Emsley, 8466 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 858 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 858 time to evaluate : 5.745 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: 8 72 MET cc_start: 0.9072 (tpt) cc_final: 0.8497 (tpt) REVERT: 8 76 MET cc_start: 0.9496 (mmm) cc_final: 0.9057 (mmm) REVERT: 8 93 ASP cc_start: 0.8984 (m-30) cc_final: 0.8738 (m-30) REVERT: 8 132 MET cc_start: 0.9014 (mtp) cc_final: 0.8720 (mtt) REVERT: 8 208 MET cc_start: 0.8960 (ttt) cc_final: 0.8421 (mpp) REVERT: 9 54 MET cc_start: 0.9035 (mmp) cc_final: 0.8786 (mmp) REVERT: 9 89 ASP cc_start: 0.9068 (m-30) cc_final: 0.8866 (m-30) REVERT: T 63 MET cc_start: 0.8868 (tpt) cc_final: 0.8269 (mtt) REVERT: T 84 MET cc_start: 0.8591 (tpt) cc_final: 0.8343 (tpp) REVERT: Q 207 MET cc_start: 0.9061 (tpt) cc_final: 0.8626 (tpp) REVERT: V 33 LEU cc_start: 0.6885 (mt) cc_final: 0.6023 (tp) REVERT: 0 284 MET cc_start: 0.8917 (mmm) cc_final: 0.8550 (mmm) REVERT: 0 340 MET cc_start: 0.8573 (ttm) cc_final: 0.7917 (ttm) REVERT: 0 458 MET cc_start: 0.9269 (mmm) cc_final: 0.7953 (mmt) REVERT: 1 167 MET cc_start: 0.9022 (pmm) cc_final: 0.8764 (pmm) REVERT: 1 246 THR cc_start: 0.9150 (t) cc_final: 0.8840 (m) REVERT: 1 340 MET cc_start: 0.8724 (tpp) cc_final: 0.8418 (tpp) REVERT: 1 368 MET cc_start: 0.9404 (tpp) cc_final: 0.9087 (tpp) REVERT: 1 485 GLU cc_start: 0.9115 (tm-30) cc_final: 0.8477 (tm-30) REVERT: 1 489 LEU cc_start: 0.9394 (mt) cc_final: 0.9116 (mt) REVERT: 1 550 MET cc_start: 0.9290 (tpt) cc_final: 0.9060 (tpp) REVERT: 1 584 MET cc_start: 0.8038 (ttp) cc_final: 0.7777 (ttp) REVERT: 2 34 MET cc_start: 0.9162 (mmm) cc_final: 0.8916 (mmm) REVERT: 2 205 MET cc_start: 0.8543 (ptp) cc_final: 0.8213 (pmm) REVERT: 2 318 MET cc_start: 0.8992 (mmm) cc_final: 0.8539 (mmm) REVERT: 2 510 GLU cc_start: 0.8431 (mp0) cc_final: 0.8159 (mp0) REVERT: 2 525 TYR cc_start: 0.6512 (p90) cc_final: 0.6265 (p90) REVERT: 2 544 MET cc_start: 0.9034 (mtt) cc_final: 0.8743 (mtt) REVERT: 2 576 GLU cc_start: 0.9098 (tt0) cc_final: 0.8481 (tp30) REVERT: 3 270 GLU cc_start: 0.9509 (mt-10) cc_final: 0.9065 (tp30) REVERT: 3 435 MET cc_start: 0.9377 (ttp) cc_final: 0.9070 (ttp) REVERT: 3 450 LEU cc_start: 0.8772 (tp) cc_final: 0.8220 (tp) REVERT: 3 453 GLU cc_start: 0.8679 (pp20) cc_final: 0.8381 (pp20) REVERT: 3 478 ASP cc_start: 0.9202 (m-30) cc_final: 0.8838 (m-30) REVERT: 4 127 MET cc_start: 0.9553 (mtp) cc_final: 0.9127 (mtp) REVERT: 4 169 MET cc_start: 0.9098 (tmm) cc_final: 0.8738 (tmm) REVERT: 4 283 GLU cc_start: 0.9255 (tt0) cc_final: 0.8816 (tm-30) REVERT: 4 309 GLU cc_start: 0.9217 (tm-30) cc_final: 0.8978 (tm-30) REVERT: 4 351 ILE cc_start: 0.9609 (mt) cc_final: 0.9273 (tp) REVERT: 4 410 MET cc_start: 0.8959 (mpp) cc_final: 0.8462 (mpp) REVERT: 4 425 CYS cc_start: 0.9530 (m) cc_final: 0.9205 (m) REVERT: 5 127 MET cc_start: 0.8534 (mtt) cc_final: 0.8312 (mtt) REVERT: 5 234 MET cc_start: 0.8448 (mmm) cc_final: 0.7910 (mmt) REVERT: 5 270 GLU cc_start: 0.8704 (tp30) cc_final: 0.8460 (tp30) REVERT: 5 299 ASP cc_start: 0.8238 (t0) cc_final: 0.7824 (t0) REVERT: 5 300 MET cc_start: 0.9065 (mmm) cc_final: 0.8695 (mmm) REVERT: 5 402 MET cc_start: 0.8516 (ttt) cc_final: 0.7778 (tmm) REVERT: 5 420 ASN cc_start: 0.9707 (m110) cc_final: 0.9489 (m-40) REVERT: 5 431 ASP cc_start: 0.9564 (t0) cc_final: 0.9006 (t0) REVERT: 6 163 LEU cc_start: 0.7938 (mm) cc_final: 0.6959 (tp) REVERT: 6 259 MET cc_start: 0.6039 (mtm) cc_final: 0.5593 (mtt) REVERT: 7 79 PHE cc_start: 0.9357 (p90) cc_final: 0.9149 (p90) REVERT: U 97 MET cc_start: 0.5253 (tpp) cc_final: 0.4174 (ptt) REVERT: U 112 MET cc_start: 0.6637 (pmm) cc_final: 0.6363 (pmm) REVERT: U 156 MET cc_start: 0.8007 (pmm) cc_final: 0.7747 (pmm) REVERT: U 181 PHE cc_start: 0.7479 (m-10) cc_final: 0.7136 (m-80) REVERT: X 98 GLU cc_start: 0.7823 (mp0) cc_final: 0.7528 (mp0) REVERT: a 186 MET cc_start: 0.8767 (mtm) cc_final: 0.8406 (mtp) REVERT: a 423 MET cc_start: 0.8742 (mpp) cc_final: 0.8409 (mpp) REVERT: a 484 MET cc_start: 0.6153 (tmm) cc_final: 0.5557 (tmm) REVERT: a 584 PHE cc_start: 0.8728 (m-80) cc_final: 0.8235 (m-80) REVERT: a 651 MET cc_start: 0.8013 (mtm) cc_final: 0.7458 (mpp) REVERT: a 745 LEU cc_start: 0.9064 (mp) cc_final: 0.8635 (mp) REVERT: a 804 LEU cc_start: 0.9108 (mt) cc_final: 0.8758 (mt) REVERT: b 90 ASN cc_start: 0.7598 (m110) cc_final: 0.7303 (m110) REVERT: b 137 MET cc_start: 0.4964 (ppp) cc_final: 0.4467 (ppp) REVERT: b 149 LEU cc_start: 0.8233 (tt) cc_final: 0.7818 (tt) REVERT: d 86 MET cc_start: 0.7720 (mmp) cc_final: 0.6362 (mmm) REVERT: g 53 MET cc_start: 0.7865 (mmm) cc_final: 0.6648 (ppp) REVERT: g 61 MET cc_start: 0.8515 (mmt) cc_final: 0.7729 (mmt) REVERT: g 68 TYR cc_start: 0.8317 (m-10) cc_final: 0.8051 (m-80) REVERT: h 47 MET cc_start: 0.8469 (ppp) cc_final: 0.7733 (pmm) REVERT: h 128 PHE cc_start: 0.6181 (t80) cc_final: 0.5917 (t80) REVERT: h 132 ILE cc_start: 0.8433 (mm) cc_final: 0.8216 (mm) REVERT: i 44 MET cc_start: 0.5539 (ptp) cc_final: 0.4978 (ptp) REVERT: i 131 MET cc_start: 0.6904 (ppp) cc_final: 0.6635 (ppp) REVERT: j 53 MET cc_start: 0.7660 (mmp) cc_final: 0.7197 (tpp) REVERT: j 61 MET cc_start: 0.6127 (ppp) cc_final: 0.5887 (ppp) REVERT: j 131 MET cc_start: 0.7723 (ppp) cc_final: 0.7321 (ppp) REVERT: k 28 MET cc_start: 0.8254 (mmp) cc_final: 0.7570 (mmm) REVERT: k 44 MET cc_start: 0.7672 (mmm) cc_final: 0.7039 (mmm) REVERT: l 28 MET cc_start: 0.8982 (mmp) cc_final: 0.8600 (mmm) REVERT: l 131 MET cc_start: 0.8640 (ptp) cc_final: 0.8299 (mpp) REVERT: m 28 MET cc_start: 0.8353 (mmp) cc_final: 0.7848 (mmp) REVERT: n 44 MET cc_start: 0.6551 (ptp) cc_final: 0.6149 (ptp) REVERT: n 61 MET cc_start: 0.6576 (ttm) cc_final: 0.6224 (ttm) REVERT: o 37 SER cc_start: 0.7627 (m) cc_final: 0.7042 (p) REVERT: p 615 LEU cc_start: 0.7545 (pp) cc_final: 0.7310 (tt) REVERT: c 336 MET cc_start: 0.6343 (tpt) cc_final: 0.5784 (tpp) REVERT: c 365 CYS cc_start: 0.9317 (m) cc_final: 0.8651 (t) REVERT: f 24 ILE cc_start: 0.8837 (mt) cc_final: 0.8478 (mt) REVERT: f 26 LEU cc_start: 0.7040 (tt) cc_final: 0.6747 (tt) REVERT: f 28 MET cc_start: 0.8667 (mpp) cc_final: 0.8288 (mpp) REVERT: s 32 LEU cc_start: 0.6201 (mt) cc_final: 0.5965 (pp) REVERT: s 120 MET cc_start: 0.4141 (mtp) cc_final: 0.3755 (mtp) REVERT: s 142 MET cc_start: 0.4901 (mmt) cc_final: 0.4180 (mmt) REVERT: e 9 PRO cc_start: 0.7929 (Cg_exo) cc_final: 0.7232 (Cg_endo) REVERT: e 13 PHE cc_start: 0.7890 (m-10) cc_final: 0.7424 (m-10) REVERT: e 57 LEU cc_start: 0.7669 (pp) cc_final: 0.7458 (pp) outliers start: 0 outliers final: 0 residues processed: 858 average time/residue: 0.6054 time to fit residues: 914.6478 Evaluate side-chains 684 residues out of total 7193 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 684 time to evaluate : 5.791 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 845 random chunks: chunk 532 optimal weight: 20.0000 chunk 714 optimal weight: 10.0000 chunk 205 optimal weight: 3.9990 chunk 618 optimal weight: 9.9990 chunk 98 optimal weight: 0.8980 chunk 186 optimal weight: 0.4980 chunk 671 optimal weight: 8.9990 chunk 280 optimal weight: 7.9990 chunk 689 optimal weight: 7.9990 chunk 85 optimal weight: 10.0000 chunk 123 optimal weight: 8.9990 overall best weight: 4.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 13 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 ASN ** 9 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** V 41 GLN ** V 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 468 HIS ** 1 522 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** 1 543 ASN ** 3 237 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 3 251 ASN ** 4 159 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 288 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 5 415 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** 6 195 HIS 6 287 ASN U 99 HIS ** U 272 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** U 276 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 51 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 148 ASN d 85 HIS ** d 264 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** d 341 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** g 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** h 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** i 124 GLN ** j 124 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** m 123 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** o 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** s 33 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 67 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.077224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.056229 restraints weight = 434954.271| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.056879 restraints weight = 276472.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3206 r_free = 0.3206 target = 0.057902 restraints weight = 167706.635| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.3318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 68114 Z= 0.286 Angle : 0.689 10.824 92059 Z= 0.360 Chirality : 0.044 0.257 10442 Planarity : 0.005 0.087 11782 Dihedral : 4.789 27.835 9259 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 15.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 0.00 % Allowed : 0.49 % Favored : 99.51 % 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: 0.38 (0.09), residues: 8466 helix: 1.12 (0.07), residues: 4807 sheet: -0.16 (0.20), residues: 733 loop : -1.04 (0.12), residues: 2926 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.062 0.002 TRP 6 20 HIS 0.015 0.001 HIS 6 337 PHE 0.033 0.002 PHE a 579 TYR 0.053 0.002 TYR f 62 ARG 0.010 0.001 ARG a 805 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 15771.53 seconds wall clock time: 274 minutes 4.14 seconds (16444.14 seconds total)