Starting phenix.real_space_refine on Thu May 22 08:52:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dum_47170/05_2025/9dum_47170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dum_47170/05_2025/9dum_47170.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dum_47170/05_2025/9dum_47170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dum_47170/05_2025/9dum_47170.map" model { file = "/net/cci-nas-00/data/ceres_data/9dum_47170/05_2025/9dum_47170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dum_47170/05_2025/9dum_47170.cif" } resolution = 3.56 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= 0.001 sd= 0.052 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 140 5.16 5 C 14497 2.51 5 N 3937 2.21 5 O 4088 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.08s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 22662 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 358, 2718 Classifications: {'peptide': 358} Link IDs: {'PTRANS': 16, 'TRANS': 341} Chain breaks: 3 Chain: "B" Number of atoms: 2872 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2872 Classifications: {'peptide': 376} Link IDs: {'PTRANS': 19, 'TRANS': 356} Chain breaks: 1 Chain: "C" Number of atoms: 3655 Number of conformers: 1 Conformer: "" Number of residues, atoms: 481, 3655 Classifications: {'peptide': 481} Link IDs: {'PTRANS': 30, 'TRANS': 450} Chain breaks: 6 Chain: "D" Number of atoms: 3683 Number of conformers: 1 Conformer: "" Number of residues, atoms: 485, 3683 Classifications: {'peptide': 485} Link IDs: {'PTRANS': 29, 'TRANS': 455} Chain breaks: 6 Chain: "H" Number of atoms: 5690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 710, 5690 Classifications: {'peptide': 710} Link IDs: {'PTRANS': 27, 'TRANS': 682} Chain breaks: 10 Chain: "G" Number of atoms: 4044 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4044 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 18, 'TRANS': 486} Chain breaks: 3 Time building chain proxies: 12.55, per 1000 atoms: 0.55 Number of scatterers: 22662 At special positions: 0 Unit cell: (145.122, 133.209, 155.952, 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 140 16.00 O 4088 8.00 N 3937 7.00 C 14497 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: 5.27 Conformation dependent library (CDL) restraints added in 2.9 seconds 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5484 Finding SS restraints... Secondary structure from input PDB file: 131 helices and 19 sheets defined 56.6% alpha, 6.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.43 Creating SS restraints... Processing helix chain 'A' and resid 149 through 155 removed outlier: 3.839A pdb=" N LEU A 154 " --> pdb=" O LEU A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 376 Processing helix chain 'A' and resid 376 through 388 Processing helix chain 'B' and resid 255 through 259 Processing helix chain 'B' and resid 322 through 327 removed outlier: 3.700A pdb=" N LEU B 326 " --> pdb=" O PRO B 322 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 388 Processing helix chain 'C' and resid 65 through 76 Processing helix chain 'C' and resid 97 through 101 removed outlier: 3.670A pdb=" N SER C 100 " --> pdb=" O ALA C 97 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N SER C 101 " --> pdb=" O ARG C 98 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 97 through 101' Processing helix chain 'C' and resid 104 through 118 removed outlier: 4.090A pdb=" N LEU C 111 " --> pdb=" O GLU C 107 " (cutoff:3.500A) Processing helix chain 'C' and resid 120 through 139 removed outlier: 5.974A pdb=" N VAL C 129 " --> pdb=" O GLN C 125 " (cutoff:3.500A) removed outlier: 5.352A pdb=" N SER C 130 " --> pdb=" O GLN C 126 " (cutoff:3.500A) Processing helix chain 'C' and resid 144 through 163 removed outlier: 3.652A pdb=" N ASP C 157 " --> pdb=" O ALA C 153 " (cutoff:3.500A) Processing helix chain 'C' and resid 165 through 176 Processing helix chain 'C' and resid 176 through 186 Processing helix chain 'C' and resid 191 through 206 removed outlier: 3.553A pdb=" N ALA C 201 " --> pdb=" O GLU C 197 " (cutoff:3.500A) Processing helix chain 'C' and resid 207 through 212 removed outlier: 3.716A pdb=" N CYS C 210 " --> pdb=" O PRO C 207 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N GLY C 211 " --> pdb=" O ARG C 208 " (cutoff:3.500A) removed outlier: 4.447A pdb=" N SER C 212 " --> pdb=" O ALA C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 207 through 212' Processing helix chain 'C' and resid 213 through 224 Processing helix chain 'C' and resid 229 through 241 Processing helix chain 'C' and resid 242 through 246 removed outlier: 3.579A pdb=" N LEU C 246 " --> pdb=" O LEU C 243 " (cutoff:3.500A) Processing helix chain 'C' and resid 257 through 275 removed outlier: 3.559A pdb=" N GLU C 263 " --> pdb=" O SER C 259 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N SER C 266 " --> pdb=" O GLN C 262 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N ALA C 269 " --> pdb=" O HIS C 265 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) Processing helix chain 'C' and resid 306 through 327 removed outlier: 3.792A pdb=" N GLN C 313 " --> pdb=" O LEU C 309 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N LEU C 322 " --> pdb=" O LEU C 318 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N SER C 327 " --> pdb=" O GLY C 323 " (cutoff:3.500A) Processing helix chain 'C' and resid 337 through 349 Processing helix chain 'C' and resid 361 through 368 Processing helix chain 'C' and resid 368 through 388 removed outlier: 3.729A pdb=" N ILE C 372 " --> pdb=" O LEU C 368 " (cutoff:3.500A) Processing helix chain 'C' and resid 394 through 409 removed outlier: 3.739A pdb=" N LEU C 402 " --> pdb=" O ILE C 398 " (cutoff:3.500A) Proline residue: C 403 - end of helix Processing helix chain 'C' and resid 426 through 443 Processing helix chain 'C' and resid 452 through 464 Processing helix chain 'C' and resid 520 through 536 removed outlier: 3.689A pdb=" N LEU C 526 " --> pdb=" O CYS C 522 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N ARG C 531 " --> pdb=" O ARG C 527 " (cutoff:3.500A) Processing helix chain 'C' and resid 541 through 557 removed outlier: 3.699A pdb=" N HIS C 545 " --> pdb=" O LYS C 541 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N LEU C 551 " --> pdb=" O ARG C 547 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N LEU C 553 " --> pdb=" O HIS C 549 " (cutoff:3.500A) Proline residue: C 554 - end of helix removed outlier: 3.644A pdb=" N MET C 557 " --> pdb=" O LEU C 553 " (cutoff:3.500A) Processing helix chain 'C' and resid 568 through 572 removed outlier: 3.854A pdb=" N SER C 572 " --> pdb=" O PRO C 569 " (cutoff:3.500A) Processing helix chain 'C' and resid 573 through 589 removed outlier: 3.576A pdb=" N GLU C 578 " --> pdb=" O ARG C 574 " (cutoff:3.500A) removed outlier: 4.154A pdb=" N LEU C 579 " --> pdb=" O CYS C 575 " (cutoff:3.500A) Processing helix chain 'C' and resid 597 through 609 removed outlier: 3.621A pdb=" N GLN C 603 " --> pdb=" O ALA C 599 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ALA C 604 " --> pdb=" O CYS C 600 " (cutoff:3.500A) Processing helix chain 'C' and resid 615 through 632 removed outlier: 3.900A pdb=" N SER C 621 " --> pdb=" O SER C 617 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N LEU C 624 " --> pdb=" O CYS C 620 " (cutoff:3.500A) removed outlier: 4.041A pdb=" N VAL C 625 " --> pdb=" O SER C 621 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N THR C 626 " --> pdb=" O GLU C 622 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ALA C 629 " --> pdb=" O VAL C 625 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N LEU C 630 " --> pdb=" O THR C 626 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N THR C 631 " --> pdb=" O CYS C 627 " (cutoff:3.500A) Processing helix chain 'D' and resid 62 through 64 No H-bonds generated for 'chain 'D' and resid 62 through 64' Processing helix chain 'D' and resid 65 through 77 removed outlier: 3.530A pdb=" N GLY D 77 " --> pdb=" O LEU D 73 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 98 Processing helix chain 'D' and resid 104 through 118 removed outlier: 3.578A pdb=" N GLY D 117 " --> pdb=" O SER D 113 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 139 removed outlier: 6.060A pdb=" N VAL D 129 " --> pdb=" O GLN D 125 " (cutoff:3.500A) removed outlier: 5.576A pdb=" N SER D 130 " --> pdb=" O GLN D 126 " (cutoff:3.500A) Processing helix chain 'D' and resid 144 through 162 removed outlier: 3.695A pdb=" N MET D 148 " --> pdb=" O PRO D 144 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N ASP D 157 " --> pdb=" O ALA D 153 " (cutoff:3.500A) Processing helix chain 'D' and resid 165 through 176 Processing helix chain 'D' and resid 176 through 186 Processing helix chain 'D' and resid 191 through 205 removed outlier: 3.945A pdb=" N ALA D 195 " --> pdb=" O CYS D 191 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N TYR D 205 " --> pdb=" O ALA D 201 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 224 removed outlier: 3.539A pdb=" N SER D 223 " --> pdb=" O SER D 219 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG D 224 " --> pdb=" O PHE D 220 " (cutoff:3.500A) Processing helix chain 'D' and resid 229 through 241 Processing helix chain 'D' and resid 255 through 279 Processing helix chain 'D' and resid 307 through 327 removed outlier: 3.758A pdb=" N GLN D 313 " --> pdb=" O LEU D 309 " (cutoff:3.500A) Processing helix chain 'D' and resid 337 through 349 removed outlier: 3.774A pdb=" N ILE D 341 " --> pdb=" O PRO D 337 " (cutoff:3.500A) Processing helix chain 'D' and resid 361 through 368 Processing helix chain 'D' and resid 368 through 388 Processing helix chain 'D' and resid 389 through 393 removed outlier: 3.745A pdb=" N LEU D 392 " --> pdb=" O SER D 389 " (cutoff:3.500A) removed outlier: 4.309A pdb=" N ARG D 393 " --> pdb=" O ARG D 390 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 389 through 393' Processing helix chain 'D' and resid 394 through 406 removed outlier: 3.949A pdb=" N ILE D 398 " --> pdb=" O PHE D 394 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N LEU D 402 " --> pdb=" O ILE D 398 " (cutoff:3.500A) Proline residue: D 403 - end of helix Processing helix chain 'D' and resid 424 through 443 removed outlier: 3.788A pdb=" N ARG D 428 " --> pdb=" O TYR D 424 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N TYR D 432 " --> pdb=" O ARG D 428 " (cutoff:3.500A) Processing helix chain 'D' and resid 458 through 464 Processing helix chain 'D' and resid 520 through 536 removed outlier: 3.969A pdb=" N LEU D 526 " --> pdb=" O CYS D 522 " (cutoff:3.500A) Processing helix chain 'D' and resid 541 through 557 removed outlier: 3.627A pdb=" N HIS D 545 " --> pdb=" O LYS D 541 " (cutoff:3.500A) Proline residue: D 554 - end of helix removed outlier: 3.804A pdb=" N MET D 557 " --> pdb=" O LEU D 553 " (cutoff:3.500A) Processing helix chain 'D' and resid 576 through 589 Processing helix chain 'D' and resid 597 through 607 removed outlier: 3.866A pdb=" N LEU D 602 " --> pdb=" O LEU D 598 " (cutoff:3.500A) removed outlier: 3.992A pdb=" N GLN D 603 " --> pdb=" O ALA D 599 " (cutoff:3.500A) Processing helix chain 'D' and resid 614 through 627 removed outlier: 3.927A pdb=" N SER D 621 " --> pdb=" O SER D 617 " (cutoff:3.500A) removed outlier: 4.253A pdb=" N VAL D 625 " --> pdb=" O SER D 621 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR D 626 " --> pdb=" O GLU D 622 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 630 No H-bonds generated for 'chain 'D' and resid 628 through 630' Processing helix chain 'H' and resid 59 through 67 removed outlier: 3.505A pdb=" N HIS H 67 " --> pdb=" O LEU H 63 " (cutoff:3.500A) Processing helix chain 'H' and resid 70 through 88 removed outlier: 3.881A pdb=" N LYS H 74 " --> pdb=" O ASN H 70 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N GLN H 75 " --> pdb=" O ALA H 71 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N SER H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA H 77 " --> pdb=" O VAL H 73 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LEU H 79 " --> pdb=" O GLN H 75 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N ASP H 83 " --> pdb=" O LEU H 79 " (cutoff:3.500A) Processing helix chain 'H' and resid 89 through 95 removed outlier: 4.289A pdb=" N ASP H 93 " --> pdb=" O PRO H 89 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N ALA H 94 " --> pdb=" O PHE H 90 " (cutoff:3.500A) removed outlier: 4.035A pdb=" N HIS H 95 " --> pdb=" O ILE H 91 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 89 through 95' Processing helix chain 'H' and resid 95 through 104 Processing helix chain 'H' and resid 111 through 126 removed outlier: 3.988A pdb=" N ARG H 115 " --> pdb=" O ASP H 111 " (cutoff:3.500A) Processing helix chain 'H' and resid 134 through 136 No H-bonds generated for 'chain 'H' and resid 134 through 136' Processing helix chain 'H' and resid 137 through 150 Processing helix chain 'H' and resid 153 through 171 removed outlier: 3.531A pdb=" N GLN H 157 " --> pdb=" O THR H 153 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ASP H 165 " --> pdb=" O LEU H 161 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU H 169 " --> pdb=" O ASP H 165 " (cutoff:3.500A) removed outlier: 4.134A pdb=" N GLN H 170 " --> pdb=" O ILE H 166 " (cutoff:3.500A) Processing helix chain 'H' and resid 171 through 176 removed outlier: 3.635A pdb=" N ILE H 175 " --> pdb=" O TYR H 171 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N THR H 176 " --> pdb=" O PRO H 172 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 171 through 176' Processing helix chain 'H' and resid 180 through 191 removed outlier: 4.321A pdb=" N LYS H 184 " --> pdb=" O SER H 180 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N VAL H 187 " --> pdb=" O LEU H 183 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ILE H 190 " --> pdb=" O PHE H 186 " (cutoff:3.500A) Processing helix chain 'H' and resid 222 through 244 removed outlier: 4.159A pdb=" N ARG H 230 " --> pdb=" O LYS H 226 " (cutoff:3.500A) removed outlier: 3.818A pdb=" N LYS H 233 " --> pdb=" O VAL H 229 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N LEU H 238 " --> pdb=" O PHE H 234 " (cutoff:3.500A) Processing helix chain 'H' and resid 313 through 336 removed outlier: 3.627A pdb=" N GLU H 322 " --> pdb=" O LYS H 318 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ILE H 323 " --> pdb=" O GLY H 319 " (cutoff:3.500A) removed outlier: 3.612A pdb=" N ILE H 325 " --> pdb=" O ILE H 321 " (cutoff:3.500A) Proline residue: H 326 - end of helix removed outlier: 3.846A pdb=" N VAL H 336 " --> pdb=" O TRP H 332 " (cutoff:3.500A) Processing helix chain 'H' and resid 353 through 371 removed outlier: 4.633A pdb=" N GLN H 357 " --> pdb=" O LEU H 353 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N ILE H 363 " --> pdb=" O VAL H 359 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N SER H 364 " --> pdb=" O LEU H 360 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LYS H 371 " --> pdb=" O TRP H 367 " (cutoff:3.500A) Processing helix chain 'H' and resid 377 through 394 removed outlier: 5.839A pdb=" N ILE H 389 " --> pdb=" O LYS H 385 " (cutoff:3.500A) removed outlier: 5.651A pdb=" N ASP H 390 " --> pdb=" O ASN H 386 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N HIS H 393 " --> pdb=" O ILE H 389 " (cutoff:3.500A) Processing helix chain 'H' and resid 431 through 444 removed outlier: 3.681A pdb=" N LEU H 437 " --> pdb=" O LEU H 433 " (cutoff:3.500A) Processing helix chain 'H' and resid 453 through 470 removed outlier: 3.540A pdb=" N ASP H 470 " --> pdb=" O GLU H 466 " (cutoff:3.500A) Processing helix chain 'H' and resid 475 through 493 Processing helix chain 'H' and resid 495 through 511 removed outlier: 4.194A pdb=" N THR H 501 " --> pdb=" O GLU H 497 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N LEU H 502 " --> pdb=" O ASP H 498 " (cutoff:3.500A) Processing helix chain 'H' and resid 516 through 532 Processing helix chain 'H' and resid 545 through 554 removed outlier: 3.589A pdb=" N TRP H 551 " --> pdb=" O VAL H 547 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU H 552 " --> pdb=" O LEU H 548 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ALA H 553 " --> pdb=" O SER H 549 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N GLY H 554 " --> pdb=" O ARG H 550 " (cutoff:3.500A) Processing helix chain 'H' and resid 554 through 562 removed outlier: 3.505A pdb=" N GLN H 558 " --> pdb=" O GLY H 554 " (cutoff:3.500A) Processing helix chain 'H' and resid 566 through 582 Processing helix chain 'H' and resid 585 through 600 removed outlier: 4.014A pdb=" N LYS H 590 " --> pdb=" O LYS H 586 " (cutoff:3.500A) removed outlier: 4.886A pdb=" N SER H 591 " --> pdb=" O GLU H 587 " (cutoff:3.500A) removed outlier: 4.847A pdb=" N LEU H 597 " --> pdb=" O GLN H 593 " (cutoff:3.500A) removed outlier: 5.473A pdb=" N ARG H 598 " --> pdb=" O ALA H 594 " (cutoff:3.500A) Processing helix chain 'H' and resid 613 through 621 removed outlier: 4.163A pdb=" N ARG H 617 " --> pdb=" O ASP H 613 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LEU H 618 " --> pdb=" O SER H 614 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N VAL H 619 " --> pdb=" O GLN H 615 " (cutoff:3.500A) Processing helix chain 'H' and resid 622 through 625 Processing helix chain 'H' and resid 629 through 642 removed outlier: 3.549A pdb=" N CYS H 639 " --> pdb=" O ARG H 635 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N MET H 642 " --> pdb=" O ARG H 638 " (cutoff:3.500A) Processing helix chain 'H' and resid 647 through 660 removed outlier: 3.863A pdb=" N ALA H 651 " --> pdb=" O SER H 647 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N MET H 652 " --> pdb=" O SER H 648 " (cutoff:3.500A) removed outlier: 4.955A pdb=" N LEU H 653 " --> pdb=" O LEU H 649 " (cutoff:3.500A) Processing helix chain 'H' and resid 677 through 689 Processing helix chain 'H' and resid 692 through 702 Processing helix chain 'H' and resid 722 through 732 Processing helix chain 'H' and resid 732 through 742 removed outlier: 3.908A pdb=" N VAL H 736 " --> pdb=" O VAL H 732 " (cutoff:3.500A) Processing helix chain 'H' and resid 745 through 761 removed outlier: 3.631A pdb=" N ASN H 749 " --> pdb=" O ALA H 745 " (cutoff:3.500A) Processing helix chain 'H' and resid 770 through 782 removed outlier: 4.155A pdb=" N PHE H 776 " --> pdb=" O ALA H 772 " (cutoff:3.500A) Processing helix chain 'H' and resid 793 through 810 Processing helix chain 'H' and resid 822 through 836 Processing helix chain 'H' and resid 836 through 846 removed outlier: 4.089A pdb=" N LEU H 840 " --> pdb=" O LEU H 836 " (cutoff:3.500A) Processing helix chain 'H' and resid 853 through 855 No H-bonds generated for 'chain 'H' and resid 853 through 855' Processing helix chain 'H' and resid 856 through 870 removed outlier: 3.530A pdb=" N VAL H 860 " --> pdb=" O GLU H 856 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY H 861 " --> pdb=" O LEU H 857 " (cutoff:3.500A) Processing helix chain 'H' and resid 874 through 879 removed outlier: 4.012A pdb=" N THR H 879 " --> pdb=" O THR H 875 " (cutoff:3.500A) Processing helix chain 'H' and resid 881 through 893 Processing helix chain 'H' and resid 904 through 910 Processing helix chain 'G' and resid 269 through 274 Processing helix chain 'G' and resid 430 through 438 removed outlier: 4.132A pdb=" N ASN G 434 " --> pdb=" O HIS G 430 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N THR G 436 " --> pdb=" O LEU G 432 " (cutoff:3.500A) Processing helix chain 'G' and resid 439 through 443 removed outlier: 3.510A pdb=" N SER G 443 " --> pdb=" O ILE G 440 " (cutoff:3.500A) Processing helix chain 'G' and resid 459 through 471 removed outlier: 3.610A pdb=" N VAL G 464 " --> pdb=" O ILE G 460 " (cutoff:3.500A) removed outlier: 4.072A pdb=" N THR G 465 " --> pdb=" O ARG G 461 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N GLU G 466 " --> pdb=" O LYS G 462 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ASP G 470 " --> pdb=" O GLU G 466 " (cutoff:3.500A) Processing helix chain 'G' and resid 475 through 493 removed outlier: 3.735A pdb=" N ARG G 488 " --> pdb=" O GLY G 484 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N LEU G 489 " --> pdb=" O VAL G 485 " (cutoff:3.500A) Processing helix chain 'G' and resid 495 through 498 Processing helix chain 'G' and resid 499 through 512 removed outlier: 3.606A pdb=" N ILE G 503 " --> pdb=" O THR G 499 " (cutoff:3.500A) Processing helix chain 'G' and resid 516 through 532 removed outlier: 3.925A pdb=" N LEU G 522 " --> pdb=" O PRO G 518 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N ILE G 530 " --> pdb=" O PHE G 526 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N TYR G 531 " --> pdb=" O PHE G 527 " (cutoff:3.500A) Processing helix chain 'G' and resid 545 through 554 removed outlier: 3.671A pdb=" N GLY G 554 " --> pdb=" O ARG G 550 " (cutoff:3.500A) Processing helix chain 'G' and resid 554 through 562 removed outlier: 3.567A pdb=" N ALA G 560 " --> pdb=" O PRO G 556 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N HIS G 561 " --> pdb=" O LEU G 557 " (cutoff:3.500A) Processing helix chain 'G' and resid 566 through 573 Processing helix chain 'G' and resid 574 through 582 Processing helix chain 'G' and resid 587 through 595 Processing helix chain 'G' and resid 595 through 600 Processing helix chain 'G' and resid 613 through 620 removed outlier: 3.842A pdb=" N ARG G 617 " --> pdb=" O ASP G 613 " (cutoff:3.500A) Processing helix chain 'G' and resid 629 through 642 removed outlier: 3.969A pdb=" N CYS G 640 " --> pdb=" O LEU G 636 " (cutoff:3.500A) removed outlier: 3.950A pdb=" N ILE G 641 " --> pdb=" O SER G 637 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N MET G 642 " --> pdb=" O ARG G 638 " (cutoff:3.500A) Processing helix chain 'G' and resid 646 through 651 removed outlier: 3.565A pdb=" N ALA G 651 " --> pdb=" O SER G 647 " (cutoff:3.500A) Processing helix chain 'G' and resid 652 through 660 Processing helix chain 'G' and resid 676 through 689 removed outlier: 4.098A pdb=" N PHE G 681 " --> pdb=" O ASP G 677 " (cutoff:3.500A) removed outlier: 4.522A pdb=" N SER G 682 " --> pdb=" O VAL G 678 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N SER G 686 " --> pdb=" O SER G 682 " (cutoff:3.500A) Processing helix chain 'G' and resid 692 through 700 removed outlier: 3.531A pdb=" N LEU G 696 " --> pdb=" O SER G 692 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N TRP G 698 " --> pdb=" O GLU G 694 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N GLN G 700 " --> pdb=" O LEU G 696 " (cutoff:3.500A) Processing helix chain 'G' and resid 732 through 743 removed outlier: 3.882A pdb=" N VAL G 736 " --> pdb=" O VAL G 732 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N LEU G 741 " --> pdb=" O PHE G 737 " (cutoff:3.500A) removed outlier: 4.232A pdb=" N ILE G 743 " --> pdb=" O SER G 739 " (cutoff:3.500A) Processing helix chain 'G' and resid 745 through 761 Processing helix chain 'G' and resid 770 through 781 removed outlier: 3.733A pdb=" N PHE G 776 " --> pdb=" O ALA G 772 " (cutoff:3.500A) Processing helix chain 'G' and resid 793 through 810 Processing helix chain 'G' and resid 816 through 820 removed outlier: 3.708A pdb=" N LEU G 819 " --> pdb=" O ALA G 816 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ARG G 820 " --> pdb=" O GLU G 817 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 816 through 820' Processing helix chain 'G' and resid 822 through 836 removed outlier: 3.519A pdb=" N ILE G 832 " --> pdb=" O VAL G 828 " (cutoff:3.500A) removed outlier: 4.151A pdb=" N LEU G 833 " --> pdb=" O CYS G 829 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA G 834 " --> pdb=" O VAL G 830 " (cutoff:3.500A) Processing helix chain 'G' and resid 836 through 845 removed outlier: 3.913A pdb=" N LEU G 840 " --> pdb=" O LEU G 836 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N ARG G 841 " --> pdb=" O PRO G 837 " (cutoff:3.500A) Processing helix chain 'G' and resid 856 through 868 removed outlier: 3.574A pdb=" N LEU G 868 " --> pdb=" O LEU G 864 " (cutoff:3.500A) Processing helix chain 'G' and resid 870 through 872 No H-bonds generated for 'chain 'G' and resid 870 through 872' Processing helix chain 'G' and resid 873 through 880 removed outlier: 3.805A pdb=" N MET G 877 " --> pdb=" O LEU G 873 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ASN G 880 " --> pdb=" O HIS G 876 " (cutoff:3.500A) Processing helix chain 'G' and resid 880 through 895 removed outlier: 3.547A pdb=" N LEU G 894 " --> pdb=" O ASN G 890 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS G 895 " --> pdb=" O ILE G 891 " (cutoff:3.500A) Processing helix chain 'G' and resid 901 through 915 removed outlier: 3.567A pdb=" N LEU G 907 " --> pdb=" O TRP G 903 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N TYR G 909 " --> pdb=" O THR G 905 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ILE G 915 " --> pdb=" O PHE G 911 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 30 through 34 removed outlier: 6.846A pdb=" N ASN A 30 " --> pdb=" O GLU A 24 " (cutoff:3.500A) removed outlier: 6.576A pdb=" N GLU A 24 " --> pdb=" O ASN A 30 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N CYS A 10 " --> pdb=" O ILE A 21 " (cutoff:3.500A) removed outlier: 3.959A pdb=" N TRP A 23 " --> pdb=" O ALA A 8 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 39 through 47 removed outlier: 6.078A pdb=" N ALA A 55 " --> pdb=" O GLY A 40 " (cutoff:3.500A) removed outlier: 9.971A pdb=" N ARG A 42 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 10.812A pdb=" N LEU A 53 " --> pdb=" O ARG A 42 " (cutoff:3.500A) removed outlier: 10.353A pdb=" N LEU A 44 " --> pdb=" O TYR A 51 " (cutoff:3.500A) removed outlier: 11.923A pdb=" N TYR A 51 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N TYR A 61 " --> pdb=" O GLN A 56 " (cutoff:3.500A) removed outlier: 4.124A pdb=" N ALA A 64 " --> pdb=" O GLN A 75 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N GLN A 75 " --> pdb=" O ALA A 64 " (cutoff:3.500A) removed outlier: 8.088A pdb=" N GLU A 66 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 7.890A pdb=" N LEU A 73 " --> pdb=" O GLU A 66 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 87 through 88 Processing sheet with id=AA4, first strand: chain 'A' and resid 103 through 106 removed outlier: 3.948A pdb=" N VAL A 115 " --> pdb=" O LEU A 105 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 124 through 129 Processing sheet with id=AA6, first strand: chain 'A' and resid 175 through 177 removed outlier: 7.100A pdb=" N SER A 192 " --> pdb=" O THR A 176 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU A 210 " --> pdb=" O LEU A 200 " (cutoff:3.500A) removed outlier: 3.857A pdb=" N ILE G 267 " --> pdb=" O SER A 211 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 221 through 223 removed outlier: 3.553A pdb=" N THR A 222 " --> pdb=" O PHE A 231 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 272 through 277 Processing sheet with id=AA9, first strand: chain 'A' and resid 293 through 296 removed outlier: 3.937A pdb=" N ARG A 305 " --> pdb=" O LEU A 295 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 30 through 32 removed outlier: 6.797A pdb=" N VAL B 22 " --> pdb=" O LEU B 31 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N TRP B 23 " --> pdb=" O ALA B 8 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASN B 315 " --> pdb=" O THR B 11 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 44 through 47 Processing sheet with id=AB3, first strand: chain 'B' and resid 83 through 88 removed outlier: 3.835A pdb=" N CYS B 85 " --> pdb=" O GLY B 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 105 through 106 removed outlier: 3.947A pdb=" N VAL B 115 " --> pdb=" O LEU B 105 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 124 through 129 Processing sheet with id=AB6, first strand: chain 'B' and resid 175 through 177 removed outlier: 7.107A pdb=" N SER B 192 " --> pdb=" O THR B 176 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 188 through 189 removed outlier: 3.630A pdb=" N LEU B 210 " --> pdb=" O LEU B 200 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N GLU B 202 " --> pdb=" O LEU B 208 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N LEU B 208 " --> pdb=" O GLU B 202 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 221 through 223 Processing sheet with id=AB9, first strand: chain 'B' and resid 275 through 277 removed outlier: 4.046A pdb=" N ARG B 305 " --> pdb=" O LEU B 295 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'H' and resid 708 through 709 removed outlier: 3.543A pdb=" N LEU H 718 " --> pdb=" O ILE H 709 " (cutoff:3.500A) removed outlier: 6.266A pdb=" N LEU H 717 " --> pdb=" O ILE H 767 " (cutoff:3.500A) 1055 hydrogen bonds defined for protein. 3102 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: 6.97 Time building geometry restraints manager: 6.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 5639 1.33 - 1.45: 4146 1.45 - 1.58: 13127 1.58 - 1.70: 0 1.70 - 1.82: 196 Bond restraints: 23108 Sorted by residual: bond pdb=" N ILE H 530 " pdb=" CA ILE H 530 " ideal model delta sigma weight residual 1.459 1.492 -0.033 9.10e-03 1.21e+04 1.31e+01 bond pdb=" N ASP A 290 " pdb=" CA ASP A 290 " ideal model delta sigma weight residual 1.457 1.494 -0.036 1.10e-02 8.26e+03 1.09e+01 bond pdb=" CA SER A 118 " pdb=" CB SER A 118 " ideal model delta sigma weight residual 1.523 1.482 0.041 1.35e-02 5.49e+03 9.28e+00 bond pdb=" CA SER H 528 " pdb=" CB SER H 528 " ideal model delta sigma weight residual 1.530 1.485 0.044 1.56e-02 4.11e+03 8.03e+00 bond pdb=" N GLN G 532 " pdb=" CA GLN G 532 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.48e+00 ... (remaining 23103 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.86: 30706 1.86 - 3.71: 515 3.71 - 5.57: 110 5.57 - 7.42: 22 7.42 - 9.28: 5 Bond angle restraints: 31358 Sorted by residual: angle pdb=" N ILE H 530 " pdb=" CA ILE H 530 " pdb=" C ILE H 530 " ideal model delta sigma weight residual 113.47 104.68 8.79 1.01e+00 9.80e-01 7.57e+01 angle pdb=" CA ASP A 195 " pdb=" CB ASP A 195 " pdb=" CG ASP A 195 " ideal model delta sigma weight residual 112.60 119.27 -6.67 1.00e+00 1.00e+00 4.45e+01 angle pdb=" CA ASP B 195 " pdb=" CB ASP B 195 " pdb=" CG ASP B 195 " ideal model delta sigma weight residual 112.60 118.72 -6.12 1.00e+00 1.00e+00 3.75e+01 angle pdb=" CA ASP A 290 " pdb=" CB ASP A 290 " pdb=" CG ASP A 290 " ideal model delta sigma weight residual 112.60 118.22 -5.62 1.00e+00 1.00e+00 3.16e+01 angle pdb=" N SER H 364 " pdb=" CA SER H 364 " pdb=" C SER H 364 " ideal model delta sigma weight residual 111.36 106.47 4.89 1.09e+00 8.42e-01 2.02e+01 ... (remaining 31353 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 11689 17.94 - 35.88: 1662 35.88 - 53.82: 478 53.82 - 71.76: 90 71.76 - 89.69: 25 Dihedral angle restraints: 13944 sinusoidal: 5521 harmonic: 8423 Sorted by residual: dihedral pdb=" CA VAL A 298 " pdb=" C VAL A 298 " pdb=" N GLN A 299 " pdb=" CA GLN A 299 " ideal model delta harmonic sigma weight residual 180.00 151.01 28.99 0 5.00e+00 4.00e-02 3.36e+01 dihedral pdb=" CA ASP B 297 " pdb=" C ASP B 297 " pdb=" N VAL B 298 " pdb=" CA VAL B 298 " ideal model delta harmonic sigma weight residual 180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA SER G 692 " pdb=" C SER G 692 " pdb=" N LYS G 693 " pdb=" CA LYS G 693 " ideal model delta harmonic sigma weight residual -180.00 -160.65 -19.35 0 5.00e+00 4.00e-02 1.50e+01 ... (remaining 13941 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 3053 0.050 - 0.100: 568 0.100 - 0.150: 98 0.150 - 0.200: 5 0.200 - 0.250: 1 Chirality restraints: 3725 Sorted by residual: chirality pdb=" CA GLU G 535 " pdb=" N GLU G 535 " pdb=" C GLU G 535 " pdb=" CB GLU G 535 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CA VAL H 705 " pdb=" N VAL H 705 " pdb=" C VAL H 705 " pdb=" CB VAL H 705 " both_signs ideal model delta sigma weight residual False 2.44 2.63 -0.19 2.00e-01 2.50e+01 9.30e-01 chirality pdb=" CA ILE H 530 " pdb=" N ILE H 530 " pdb=" C ILE H 530 " pdb=" CB ILE H 530 " both_signs ideal model delta sigma weight residual False 2.43 2.61 -0.18 2.00e-01 2.50e+01 8.12e-01 ... (remaining 3722 not shown) Planarity restraints: 3926 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 116 " -0.012 2.00e-02 2.50e+03 2.36e-02 5.58e+00 pdb=" C ILE B 116 " 0.041 2.00e-02 2.50e+03 pdb=" O ILE B 116 " -0.015 2.00e-02 2.50e+03 pdb=" N LEU B 117 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 119 " -0.201 9.50e-02 1.11e+02 9.02e-02 4.99e+00 pdb=" NE ARG A 119 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG A 119 " 0.002 2.00e-02 2.50e+03 pdb=" NH1 ARG A 119 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 119 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 119 " -0.182 9.50e-02 1.11e+02 8.17e-02 4.13e+00 pdb=" NE ARG B 119 " 0.012 2.00e-02 2.50e+03 pdb=" CZ ARG B 119 " -0.001 2.00e-02 2.50e+03 pdb=" NH1 ARG B 119 " 0.003 2.00e-02 2.50e+03 pdb=" NH2 ARG B 119 " -0.005 2.00e-02 2.50e+03 ... (remaining 3923 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1768 2.74 - 3.28: 21938 3.28 - 3.82: 35987 3.82 - 4.36: 40608 4.36 - 4.90: 72246 Nonbonded interactions: 172547 Sorted by model distance: nonbonded pdb=" OE2 GLU A 6 " pdb=" OG1 THR A 279 " model vdw 2.198 3.040 nonbonded pdb=" O ILE D 466 " pdb=" OH TYR D 570 " model vdw 2.216 3.040 nonbonded pdb=" O LEU G 482 " pdb=" OG SER G 486 " model vdw 2.216 3.040 nonbonded pdb=" OH TYR C 432 " pdb=" OD2 ASP C 465 " model vdw 2.226 3.040 nonbonded pdb=" NE2 GLN H 700 " pdb=" O VAL H 766 " model vdw 2.244 3.120 ... (remaining 172542 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 3 through 157 or resid 161 through 246 or resid 262 throug \ h 388)) } ncs_group { reference = (chain 'C' and (resid 62 through 79 or resid 96 through 282 or resid 305 through \ 636)) selection = (chain 'D' and (resid 62 through 79 or resid 96 through 247 or resid 256 through \ 411 or resid 420 through 469 or resid 511 through 562 or resid 567 through 636) \ ) } 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: 1.340 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.910 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.310 Find NCS groups from input model: 0.630 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7246 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 : 0.003 0.044 23108 Z= 0.166 Angle : 0.618 9.276 31358 Z= 0.345 Chirality : 0.040 0.250 3725 Planarity : 0.005 0.090 3926 Dihedral : 18.324 89.694 8460 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 7.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 5.62 % Favored : 94.20 % Rotamer: Outliers : 4.95 % Allowed : 30.84 % Favored : 64.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.16), residues: 2845 helix: 0.77 (0.14), residues: 1535 sheet: -2.75 (0.31), residues: 265 loop : -2.18 (0.18), residues: 1045 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP G 903 HIS 0.005 0.001 HIS A 135 PHE 0.015 0.001 PHE A 136 TYR 0.019 0.001 TYR H 914 ARG 0.010 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.21224 ( 1055) hydrogen bonds : angle 6.31633 ( 3102) covalent geometry : bond 0.00314 (23108) covalent geometry : angle 0.61769 (31358) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 347 time to evaluate : 2.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8540 (OUTLIER) cc_final: 0.7845 (m110) REVERT: A 119 ARG cc_start: 0.7806 (OUTLIER) cc_final: 0.7511 (tpt-90) REVERT: A 269 ARG cc_start: 0.8057 (OUTLIER) cc_final: 0.7779 (ptm-80) REVERT: A 291 GLU cc_start: 0.8142 (OUTLIER) cc_final: 0.7746 (mp0) REVERT: B 146 LEU cc_start: 0.8506 (OUTLIER) cc_final: 0.8255 (mp) REVERT: B 252 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7136 (mt-10) REVERT: B 258 GLU cc_start: 0.7351 (OUTLIER) cc_final: 0.5175 (tm-30) REVERT: B 385 SER cc_start: 0.7472 (OUTLIER) cc_final: 0.7219 (m) REVERT: C 210 CYS cc_start: 0.7139 (m) cc_final: 0.6798 (t) REVERT: C 222 LEU cc_start: 0.6883 (OUTLIER) cc_final: 0.6528 (tt) REVERT: C 262 GLN cc_start: 0.8367 (tp-100) cc_final: 0.7969 (tt0) REVERT: C 361 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7210 (t0) REVERT: C 374 LEU cc_start: 0.7163 (OUTLIER) cc_final: 0.6749 (mp) REVERT: C 375 GLU cc_start: 0.7287 (OUTLIER) cc_final: 0.6629 (mp0) REVERT: C 516 ASN cc_start: 0.8617 (p0) cc_final: 0.8398 (p0) REVERT: C 518 ASN cc_start: 0.7246 (OUTLIER) cc_final: 0.6870 (p0) REVERT: D 235 LEU cc_start: 0.6467 (OUTLIER) cc_final: 0.6035 (tt) REVERT: D 379 LEU cc_start: 0.7084 (OUTLIER) cc_final: 0.6792 (tt) REVERT: D 561 GLN cc_start: 0.6931 (OUTLIER) cc_final: 0.6336 (pp30) REVERT: H 149 MET cc_start: 0.6433 (mtp) cc_final: 0.6128 (ptp) REVERT: H 364 SER cc_start: 0.9282 (t) cc_final: 0.9080 (p) REVERT: H 449 THR cc_start: 0.6633 (OUTLIER) cc_final: 0.6328 (m) REVERT: H 544 ARG cc_start: 0.6806 (ptp90) cc_final: 0.5302 (mmt180) REVERT: H 631 ASP cc_start: 0.7776 (OUTLIER) cc_final: 0.7491 (m-30) REVERT: H 648 SER cc_start: 0.8379 (t) cc_final: 0.7911 (m) REVERT: H 843 MET cc_start: 0.7210 (ttp) cc_final: 0.6946 (ttm) REVERT: H 867 LEU cc_start: 0.6515 (tt) cc_final: 0.5838 (tt) REVERT: G 517 LEU cc_start: 0.4234 (OUTLIER) cc_final: 0.3818 (tm) REVERT: G 564 SER cc_start: 0.8485 (t) cc_final: 0.8212 (p) REVERT: G 682 SER cc_start: 0.8696 (m) cc_final: 0.8462 (t) REVERT: G 707 HIS cc_start: 0.5984 (m170) cc_final: 0.5595 (m90) REVERT: G 724 ASP cc_start: 0.7992 (m-30) cc_final: 0.7550 (m-30) REVERT: G 731 ASP cc_start: 0.7821 (m-30) cc_final: 0.7202 (t0) REVERT: G 817 GLU cc_start: 0.6341 (mm-30) cc_final: 0.6054 (pt0) outliers start: 126 outliers final: 63 residues processed: 455 average time/residue: 0.3379 time to fit residues: 237.0432 Evaluate side-chains 329 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 82 poor density : 247 time to evaluate : 2.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 11 THR Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 57 LEU Chi-restraints excluded: chain A residue 60 ASN Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 118 SER Chi-restraints excluded: chain A residue 119 ARG Chi-restraints excluded: chain A residue 134 SER Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 217 SER Chi-restraints excluded: chain A residue 269 ARG Chi-restraints excluded: chain A residue 288 SER Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 291 GLU Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 119 ARG Chi-restraints excluded: chain B residue 146 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 385 SER Chi-restraints excluded: chain C residue 175 ASN Chi-restraints excluded: chain C residue 183 SER Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 225 VAL Chi-restraints excluded: chain C residue 259 SER Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 316 SER Chi-restraints excluded: chain C residue 346 CYS Chi-restraints excluded: chain C residue 361 ASP Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 375 GLU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 574 ARG Chi-restraints excluded: chain C residue 618 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 350 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 408 SER Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 293 SER Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 449 THR Chi-restraints excluded: chain H residue 587 GLU Chi-restraints excluded: chain H residue 631 ASP Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 786 THR Chi-restraints excluded: chain H residue 842 LEU Chi-restraints excluded: chain H residue 866 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 555 LEU Chi-restraints excluded: chain G residue 585 ASN Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 859 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 244 optimal weight: 20.0000 chunk 219 optimal weight: 10.0000 chunk 121 optimal weight: 6.9990 chunk 74 optimal weight: 0.0270 chunk 147 optimal weight: 1.9990 chunk 117 optimal weight: 2.9990 chunk 226 optimal weight: 2.9990 chunk 87 optimal weight: 0.5980 chunk 137 optimal weight: 0.2980 chunk 168 optimal weight: 8.9990 chunk 262 optimal weight: 7.9990 overall best weight: 1.1842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 122 GLN A 342 HIS B 56 GLN B 155 GLN B 196 GLN C 175 ASN D 450 GLN H 354 GLN H 478 GLN ** G 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 700 GLN G 862 GLN G 880 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4124 r_free = 0.4124 target = 0.185872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135186 restraints weight = 26522.610| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3561 r_free = 0.3561 target = 0.132198 restraints weight = 23271.117| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.134368 restraints weight = 25582.895| |-----------------------------------------------------------------------------| r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1433 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 23108 Z= 0.160 Angle : 0.627 9.613 31358 Z= 0.312 Chirality : 0.042 0.232 3725 Planarity : 0.005 0.057 3926 Dihedral : 7.281 58.036 3246 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.47 % Favored : 93.43 % Rotamer: Outliers : 5.85 % Allowed : 27.70 % Favored : 66.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.87 (0.16), residues: 2845 helix: 0.76 (0.14), residues: 1581 sheet: -2.38 (0.31), residues: 268 loop : -2.22 (0.18), residues: 996 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP G 487 HIS 0.010 0.001 HIS H 144 PHE 0.022 0.002 PHE H 807 TYR 0.030 0.002 TYR G 802 ARG 0.007 0.000 ARG G 461 Details of bonding type rmsd hydrogen bonds : bond 0.04899 ( 1055) hydrogen bonds : angle 4.54089 ( 3102) covalent geometry : bond 0.00379 (23108) covalent geometry : angle 0.62658 (31358) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 403 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 149 poor density : 254 time to evaluate : 2.312 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7383 (OUTLIER) cc_final: 0.7161 (p0) REVERT: B 129 PHE cc_start: 0.8707 (OUTLIER) cc_final: 0.7318 (t80) REVERT: B 227 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7683 (mt-10) REVERT: B 252 GLU cc_start: 0.8177 (OUTLIER) cc_final: 0.7165 (mt-10) REVERT: B 258 GLU cc_start: 0.8173 (OUTLIER) cc_final: 0.6056 (tm-30) REVERT: B 266 LYS cc_start: 0.8264 (ptpp) cc_final: 0.8045 (tptt) REVERT: C 137 GLN cc_start: 0.7213 (OUTLIER) cc_final: 0.6620 (mp10) REVERT: C 149 GLU cc_start: 0.6506 (tp30) cc_final: 0.6212 (tp30) REVERT: C 180 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7396 (mp) REVERT: C 262 GLN cc_start: 0.8116 (tp-100) cc_final: 0.7834 (tt0) REVERT: C 511 ARG cc_start: 0.6399 (tpt90) cc_final: 0.5843 (ttp-170) REVERT: C 518 ASN cc_start: 0.7504 (OUTLIER) cc_final: 0.7083 (p0) REVERT: D 99 LEU cc_start: 0.7466 (OUTLIER) cc_final: 0.6858 (mp) REVERT: D 235 LEU cc_start: 0.7562 (OUTLIER) cc_final: 0.7175 (tt) REVERT: D 379 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7741 (tt) REVERT: D 546 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.8009 (mtm-85) REVERT: D 561 GLN cc_start: 0.7674 (OUTLIER) cc_final: 0.7217 (pp30) REVERT: D 614 LEU cc_start: 0.8582 (OUTLIER) cc_final: 0.8343 (tt) REVERT: H 181 ILE cc_start: 0.7681 (OUTLIER) cc_final: 0.7401 (mp) REVERT: H 544 ARG cc_start: 0.6938 (ptp90) cc_final: 0.5377 (mmt180) REVERT: H 648 SER cc_start: 0.8431 (t) cc_final: 0.8022 (m) REVERT: H 720 LEU cc_start: 0.7370 (mp) cc_final: 0.7102 (mp) REVERT: H 732 VAL cc_start: 0.8807 (OUTLIER) cc_final: 0.8463 (t) REVERT: H 867 LEU cc_start: 0.6564 (tt) cc_final: 0.6139 (tt) REVERT: G 525 LYS cc_start: 0.8321 (ttpt) cc_final: 0.7818 (ttmm) REVERT: G 527 PHE cc_start: 0.7860 (OUTLIER) cc_final: 0.7612 (m-10) REVERT: G 620 GLN cc_start: 0.8590 (OUTLIER) cc_final: 0.7089 (mt0) REVERT: G 652 MET cc_start: 0.8061 (OUTLIER) cc_final: 0.7620 (ptt) REVERT: G 682 SER cc_start: 0.8534 (OUTLIER) cc_final: 0.8243 (t) REVERT: G 697 THR cc_start: 0.8627 (m) cc_final: 0.8418 (m) REVERT: G 707 HIS cc_start: 0.5946 (m170) cc_final: 0.5442 (m90) REVERT: G 724 ASP cc_start: 0.8078 (m-30) cc_final: 0.7637 (m-30) REVERT: G 731 ASP cc_start: 0.7998 (m-30) cc_final: 0.7271 (t0) REVERT: G 817 GLU cc_start: 0.6329 (mm-30) cc_final: 0.6011 (pt0) outliers start: 149 outliers final: 69 residues processed: 386 average time/residue: 0.3383 time to fit residues: 201.7661 Evaluate side-chains 320 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 231 time to evaluate : 2.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 89 SER Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 181 ILE Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 521 THR Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 755 SER Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 842 LEU Chi-restraints excluded: chain H residue 844 LEU Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 527 PHE Chi-restraints excluded: chain G residue 529 LYS Chi-restraints excluded: chain G residue 549 SER Chi-restraints excluded: chain G residue 585 ASN Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 682 SER Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 860 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 1 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 241 optimal weight: 0.0270 chunk 130 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 131 optimal weight: 0.0770 chunk 253 optimal weight: 2.9990 chunk 149 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 overall best weight: 1.3600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 342 HIS D 516 ASN H 151 HIS ** H 475 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.184868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3599 r_free = 0.3599 target = 0.134105 restraints weight = 26568.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130464 restraints weight = 24023.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.132625 restraints weight = 26407.023| |-----------------------------------------------------------------------------| r_work (final): 0.3532 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 23108 Z= 0.162 Angle : 0.598 7.959 31358 Z= 0.298 Chirality : 0.041 0.241 3725 Planarity : 0.005 0.053 3926 Dihedral : 6.013 59.923 3148 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.12 % Favored : 93.78 % Rotamer: Outliers : 5.30 % Allowed : 27.70 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.16), residues: 2845 helix: 0.82 (0.14), residues: 1591 sheet: -2.29 (0.30), residues: 269 loop : -2.21 (0.18), residues: 985 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP G 487 HIS 0.007 0.001 HIS A 135 PHE 0.019 0.002 PHE A 136 TYR 0.022 0.002 TYR H 668 ARG 0.008 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.04544 ( 1055) hydrogen bonds : angle 4.27985 ( 3102) covalent geometry : bond 0.00396 (23108) covalent geometry : angle 0.59808 (31358) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 236 time to evaluate : 2.284 Fit side-chains revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7462 (OUTLIER) cc_final: 0.7207 (p0) REVERT: B 129 PHE cc_start: 0.8735 (OUTLIER) cc_final: 0.7282 (t80) REVERT: B 227 GLU cc_start: 0.8126 (OUTLIER) cc_final: 0.7725 (mt-10) REVERT: B 252 GLU cc_start: 0.8213 (OUTLIER) cc_final: 0.7190 (mt-10) REVERT: B 258 GLU cc_start: 0.8115 (OUTLIER) cc_final: 0.5979 (tm-30) REVERT: C 137 GLN cc_start: 0.7131 (OUTLIER) cc_final: 0.6518 (mp10) REVERT: C 149 GLU cc_start: 0.6492 (tp30) cc_final: 0.6209 (tp30) REVERT: C 180 LEU cc_start: 0.7474 (OUTLIER) cc_final: 0.7149 (mp) REVERT: C 374 LEU cc_start: 0.7894 (OUTLIER) cc_final: 0.7520 (mt) REVERT: C 511 ARG cc_start: 0.6410 (tpt90) cc_final: 0.5834 (ttp-170) REVERT: C 518 ASN cc_start: 0.7462 (OUTLIER) cc_final: 0.6989 (p0) REVERT: D 235 LEU cc_start: 0.7512 (OUTLIER) cc_final: 0.7144 (tt) REVERT: D 379 LEU cc_start: 0.8037 (OUTLIER) cc_final: 0.7769 (tt) REVERT: D 546 ARG cc_start: 0.8243 (OUTLIER) cc_final: 0.8003 (mtm-85) REVERT: D 561 GLN cc_start: 0.7644 (OUTLIER) cc_final: 0.7243 (pp30) REVERT: D 614 LEU cc_start: 0.8539 (OUTLIER) cc_final: 0.8292 (tt) REVERT: H 149 MET cc_start: 0.5418 (ptp) cc_final: 0.4818 (ttp) REVERT: H 364 SER cc_start: 0.8789 (t) cc_final: 0.8583 (p) REVERT: H 367 TRP cc_start: 0.6531 (t60) cc_final: 0.6196 (t60) REVERT: H 459 MET cc_start: 0.7763 (ptp) cc_final: 0.7382 (ptp) REVERT: H 544 ARG cc_start: 0.7100 (ptp90) cc_final: 0.5438 (mmt180) REVERT: H 732 VAL cc_start: 0.8904 (OUTLIER) cc_final: 0.8630 (t) REVERT: H 867 LEU cc_start: 0.6905 (tt) cc_final: 0.6068 (tt) REVERT: G 441 MET cc_start: 0.4221 (ptp) cc_final: 0.2893 (tpt) REVERT: G 527 PHE cc_start: 0.7950 (OUTLIER) cc_final: 0.7662 (m-80) REVERT: G 620 GLN cc_start: 0.8655 (OUTLIER) cc_final: 0.7801 (mt0) REVERT: G 682 SER cc_start: 0.8454 (m) cc_final: 0.8227 (t) REVERT: G 685 PHE cc_start: 0.8069 (t80) cc_final: 0.7796 (t80) REVERT: G 707 HIS cc_start: 0.5861 (m170) cc_final: 0.5299 (m90) REVERT: G 724 ASP cc_start: 0.8172 (m-30) cc_final: 0.7705 (m-30) REVERT: G 731 ASP cc_start: 0.8119 (m-30) cc_final: 0.7342 (t0) REVERT: G 817 GLU cc_start: 0.6398 (mm-30) cc_final: 0.6064 (pt0) outliers start: 135 outliers final: 80 residues processed: 355 average time/residue: 0.3171 time to fit residues: 176.9629 Evaluate side-chains 318 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 221 time to evaluate : 2.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain C residue 101 SER Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 755 SER Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 842 LEU Chi-restraints excluded: chain H residue 844 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 527 PHE Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 857 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 223 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 233 optimal weight: 6.9990 chunk 164 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 126 optimal weight: 0.8980 chunk 68 optimal weight: 0.0670 chunk 124 optimal weight: 3.9990 chunk 105 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 145 optimal weight: 10.0000 overall best weight: 1.1922 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS D 272 HIS D 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 566 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.184440 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.134217 restraints weight = 26896.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130197 restraints weight = 24688.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.132537 restraints weight = 26806.663| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 23108 Z= 0.148 Angle : 0.578 9.745 31358 Z= 0.287 Chirality : 0.040 0.187 3725 Planarity : 0.004 0.049 3926 Dihedral : 5.735 59.903 3139 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.29 % Favored : 93.64 % Rotamer: Outliers : 5.30 % Allowed : 27.35 % Favored : 67.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.16), residues: 2845 helix: 0.88 (0.14), residues: 1593 sheet: -2.21 (0.30), residues: 268 loop : -2.21 (0.18), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 487 HIS 0.007 0.001 HIS H 144 PHE 0.036 0.002 PHE H 391 TYR 0.020 0.002 TYR H 387 ARG 0.008 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.04042 ( 1055) hydrogen bonds : angle 4.13106 ( 3102) covalent geometry : bond 0.00359 (23108) covalent geometry : angle 0.57830 (31358) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 135 poor density : 218 time to evaluate : 2.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7435 (OUTLIER) cc_final: 0.7067 (p0) REVERT: B 227 GLU cc_start: 0.8130 (OUTLIER) cc_final: 0.7741 (mt-10) REVERT: B 252 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7201 (mt-10) REVERT: B 258 GLU cc_start: 0.8064 (OUTLIER) cc_final: 0.5893 (tm-30) REVERT: B 274 CYS cc_start: 0.8229 (OUTLIER) cc_final: 0.7978 (m) REVERT: C 137 GLN cc_start: 0.7154 (OUTLIER) cc_final: 0.6507 (mp10) REVERT: C 149 GLU cc_start: 0.6540 (tp30) cc_final: 0.6248 (tp30) REVERT: C 180 LEU cc_start: 0.7530 (OUTLIER) cc_final: 0.7227 (mp) REVERT: C 235 LEU cc_start: 0.7662 (OUTLIER) cc_final: 0.7382 (mt) REVERT: C 374 LEU cc_start: 0.7917 (OUTLIER) cc_final: 0.7533 (mt) REVERT: C 511 ARG cc_start: 0.6420 (tpt90) cc_final: 0.5847 (ttp-170) REVERT: C 518 ASN cc_start: 0.7404 (OUTLIER) cc_final: 0.6912 (p0) REVERT: D 99 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.6895 (mp) REVERT: D 235 LEU cc_start: 0.7510 (OUTLIER) cc_final: 0.7139 (tt) REVERT: D 379 LEU cc_start: 0.8048 (OUTLIER) cc_final: 0.7783 (tt) REVERT: D 546 ARG cc_start: 0.8240 (OUTLIER) cc_final: 0.7996 (mtm-85) REVERT: D 561 GLN cc_start: 0.7658 (OUTLIER) cc_final: 0.7211 (pp30) REVERT: D 614 LEU cc_start: 0.8528 (OUTLIER) cc_final: 0.8280 (tt) REVERT: H 149 MET cc_start: 0.5593 (ptp) cc_final: 0.4906 (ttp) REVERT: H 238 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7458 (tp) REVERT: H 459 MET cc_start: 0.7603 (ptp) cc_final: 0.7328 (ptp) REVERT: H 544 ARG cc_start: 0.7102 (ptp90) cc_final: 0.5421 (mmt180) REVERT: H 732 VAL cc_start: 0.8915 (OUTLIER) cc_final: 0.8680 (t) REVERT: H 867 LEU cc_start: 0.6793 (tt) cc_final: 0.6522 (tt) REVERT: G 441 MET cc_start: 0.4389 (ptp) cc_final: 0.3072 (tpt) REVERT: G 527 PHE cc_start: 0.8000 (OUTLIER) cc_final: 0.7677 (m-80) REVERT: G 620 GLN cc_start: 0.8725 (OUTLIER) cc_final: 0.7902 (mt0) REVERT: G 682 SER cc_start: 0.8400 (m) cc_final: 0.8145 (t) REVERT: G 685 PHE cc_start: 0.8176 (t80) cc_final: 0.7863 (t80) REVERT: G 707 HIS cc_start: 0.5930 (m170) cc_final: 0.5311 (m90) REVERT: G 724 ASP cc_start: 0.8105 (m-30) cc_final: 0.7698 (m-30) REVERT: G 731 ASP cc_start: 0.8086 (m-30) cc_final: 0.7364 (t0) REVERT: G 817 GLU cc_start: 0.6389 (mm-30) cc_final: 0.6037 (pt0) outliers start: 135 outliers final: 86 residues processed: 337 average time/residue: 0.3330 time to fit residues: 178.5263 Evaluate side-chains 314 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 208 time to evaluate : 2.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 117 LEU Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 272 HIS Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 609 VAL Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 707 HIS Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 808 LEU Chi-restraints excluded: chain H residue 842 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 527 PHE Chi-restraints excluded: chain G residue 609 VAL Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 901 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 37 optimal weight: 0.8980 chunk 131 optimal weight: 1.9990 chunk 151 optimal weight: 0.6980 chunk 278 optimal weight: 2.9990 chunk 103 optimal weight: 0.4980 chunk 162 optimal weight: 0.6980 chunk 184 optimal weight: 0.5980 chunk 172 optimal weight: 8.9990 chunk 246 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN D 272 HIS H 185 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.135847 restraints weight = 26726.659| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3557 r_free = 0.3557 target = 0.132347 restraints weight = 24121.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3576 r_free = 0.3576 target = 0.134597 restraints weight = 25708.727| |-----------------------------------------------------------------------------| r_work (final): 0.3604 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.2197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 23108 Z= 0.110 Angle : 0.541 7.242 31358 Z= 0.268 Chirality : 0.039 0.176 3725 Planarity : 0.004 0.060 3926 Dihedral : 5.595 59.232 3139 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.80 % Favored : 94.13 % Rotamer: Outliers : 5.07 % Allowed : 27.35 % Favored : 67.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.53 (0.16), residues: 2845 helix: 1.01 (0.14), residues: 1596 sheet: -2.00 (0.31), residues: 268 loop : -2.15 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 487 HIS 0.019 0.001 HIS D 272 PHE 0.017 0.001 PHE H 391 TYR 0.018 0.001 TYR H 668 ARG 0.009 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03573 ( 1055) hydrogen bonds : angle 3.97448 ( 3102) covalent geometry : bond 0.00255 (23108) covalent geometry : angle 0.54107 (31358) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 129 poor density : 226 time to evaluate : 2.521 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 227 GLU cc_start: 0.8204 (OUTLIER) cc_final: 0.7805 (mt-10) REVERT: B 252 GLU cc_start: 0.8210 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: B 258 GLU cc_start: 0.8070 (OUTLIER) cc_final: 0.5854 (tm-30) REVERT: B 266 LYS cc_start: 0.8225 (ptpp) cc_final: 0.8020 (tptt) REVERT: B 274 CYS cc_start: 0.8196 (OUTLIER) cc_final: 0.7881 (m) REVERT: C 137 GLN cc_start: 0.7144 (OUTLIER) cc_final: 0.6517 (mp10) REVERT: C 149 GLU cc_start: 0.6496 (tp30) cc_final: 0.6202 (tp30) REVERT: C 180 LEU cc_start: 0.7528 (OUTLIER) cc_final: 0.7239 (mp) REVERT: C 235 LEU cc_start: 0.7742 (OUTLIER) cc_final: 0.7494 (mt) REVERT: C 374 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7375 (mp) REVERT: C 511 ARG cc_start: 0.6443 (tpt90) cc_final: 0.5877 (ttp-170) REVERT: D 99 LEU cc_start: 0.7499 (OUTLIER) cc_final: 0.6929 (mp) REVERT: D 148 MET cc_start: 0.7816 (mmt) cc_final: 0.7615 (mmt) REVERT: D 235 LEU cc_start: 0.7516 (OUTLIER) cc_final: 0.7169 (tt) REVERT: D 379 LEU cc_start: 0.8054 (OUTLIER) cc_final: 0.7806 (tt) REVERT: D 546 ARG cc_start: 0.8228 (OUTLIER) cc_final: 0.8006 (mtm-85) REVERT: D 561 GLN cc_start: 0.7605 (OUTLIER) cc_final: 0.7172 (pp30) REVERT: D 614 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8307 (tt) REVERT: H 149 MET cc_start: 0.5382 (ptp) cc_final: 0.4783 (ttp) REVERT: H 183 LEU cc_start: 0.7062 (OUTLIER) cc_final: 0.6496 (mt) REVERT: H 238 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7429 (tp) REVERT: H 396 MET cc_start: 0.5047 (ttt) cc_final: 0.4719 (ttt) REVERT: H 459 MET cc_start: 0.7685 (ptp) cc_final: 0.7306 (ptp) REVERT: H 544 ARG cc_start: 0.7060 (ptp90) cc_final: 0.5362 (mmt180) REVERT: H 672 ASP cc_start: 0.3512 (OUTLIER) cc_final: 0.3153 (m-30) REVERT: H 802 TYR cc_start: 0.8333 (t80) cc_final: 0.8112 (t80) REVERT: G 527 PHE cc_start: 0.8164 (OUTLIER) cc_final: 0.7892 (m-80) REVERT: G 620 GLN cc_start: 0.8509 (OUTLIER) cc_final: 0.7729 (mt0) REVERT: G 685 PHE cc_start: 0.8141 (t80) cc_final: 0.7825 (t80) REVERT: G 707 HIS cc_start: 0.5905 (m170) cc_final: 0.5319 (m90) REVERT: G 724 ASP cc_start: 0.8147 (m-30) cc_final: 0.7675 (m-30) REVERT: G 731 ASP cc_start: 0.8010 (m-30) cc_final: 0.7367 (t0) REVERT: G 817 GLU cc_start: 0.6351 (mm-30) cc_final: 0.6006 (pt0) outliers start: 129 outliers final: 85 residues processed: 336 average time/residue: 0.3191 time to fit residues: 170.2552 Evaluate side-chains 314 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 104 poor density : 210 time to evaluate : 2.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 274 CYS Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 371 SER Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 516 ASN Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 203 MET Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 385 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 115 ARG Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 238 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 468 LEU Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 609 VAL Chi-restraints excluded: chain H residue 631 ASP Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 707 HIS Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 842 LEU Chi-restraints excluded: chain H residue 844 LEU Chi-restraints excluded: chain G residue 527 PHE Chi-restraints excluded: chain G residue 566 ASN Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 857 LEU Chi-restraints excluded: chain G residue 901 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 251 optimal weight: 0.7980 chunk 288 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 199 optimal weight: 0.9980 chunk 136 optimal weight: 4.9990 chunk 245 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 282 optimal weight: 2.9990 chunk 159 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 315 ASN A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN D 510 HIS D 516 ASN H 386 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4127 r_free = 0.4127 target = 0.184597 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.133854 restraints weight = 26706.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.128611 restraints weight = 28643.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131483 restraints weight = 25045.423| |-----------------------------------------------------------------------------| r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7892 moved from start: 0.2373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 23108 Z= 0.202 Angle : 0.618 11.493 31358 Z= 0.306 Chirality : 0.042 0.181 3725 Planarity : 0.005 0.064 3926 Dihedral : 5.731 59.561 3135 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.78 % Favored : 93.15 % Rotamer: Outliers : 5.62 % Allowed : 27.39 % Favored : 66.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.16), residues: 2845 helix: 0.92 (0.14), residues: 1590 sheet: -2.14 (0.30), residues: 275 loop : -2.26 (0.18), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 487 HIS 0.009 0.001 HIS A 135 PHE 0.041 0.002 PHE H 391 TYR 0.018 0.002 TYR B 61 ARG 0.008 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.04200 ( 1055) hydrogen bonds : angle 4.10271 ( 3102) covalent geometry : bond 0.00507 (23108) covalent geometry : angle 0.61799 (31358) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 361 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 143 poor density : 218 time to evaluate : 2.337 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 12 ASP cc_start: 0.7438 (OUTLIER) cc_final: 0.7077 (p0) REVERT: B 227 GLU cc_start: 0.8300 (OUTLIER) cc_final: 0.7911 (mt-10) REVERT: B 252 GLU cc_start: 0.8248 (OUTLIER) cc_final: 0.7241 (mt-10) REVERT: B 258 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.5909 (tm-30) REVERT: C 137 GLN cc_start: 0.7034 (OUTLIER) cc_final: 0.6484 (mp10) REVERT: C 149 GLU cc_start: 0.6613 (tp30) cc_final: 0.6298 (tp30) REVERT: C 180 LEU cc_start: 0.7550 (OUTLIER) cc_final: 0.7206 (mp) REVERT: C 222 LEU cc_start: 0.7620 (OUTLIER) cc_final: 0.7183 (tt) REVERT: C 235 LEU cc_start: 0.7741 (OUTLIER) cc_final: 0.7445 (mt) REVERT: C 374 LEU cc_start: 0.7943 (OUTLIER) cc_final: 0.7530 (mt) REVERT: C 511 ARG cc_start: 0.6480 (tpt90) cc_final: 0.5887 (ttp-170) REVERT: C 518 ASN cc_start: 0.7584 (OUTLIER) cc_final: 0.7190 (p0) REVERT: D 99 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.6832 (mp) REVERT: D 235 LEU cc_start: 0.7508 (OUTLIER) cc_final: 0.7176 (tt) REVERT: D 379 LEU cc_start: 0.8186 (OUTLIER) cc_final: 0.7920 (tt) REVERT: D 546 ARG cc_start: 0.8283 (OUTLIER) cc_final: 0.8042 (mtm-85) REVERT: D 561 GLN cc_start: 0.7677 (OUTLIER) cc_final: 0.7194 (pp30) REVERT: D 614 LEU cc_start: 0.8617 (OUTLIER) cc_final: 0.8382 (tt) REVERT: H 149 MET cc_start: 0.5550 (ptp) cc_final: 0.4798 (ttp) REVERT: H 183 LEU cc_start: 0.7097 (OUTLIER) cc_final: 0.6478 (mt) REVERT: H 396 MET cc_start: 0.4937 (ttt) cc_final: 0.4644 (ttt) REVERT: H 459 MET cc_start: 0.7585 (ptp) cc_final: 0.7301 (ptp) REVERT: H 481 ARG cc_start: 0.7864 (ptm160) cc_final: 0.7184 (ptp90) REVERT: H 544 ARG cc_start: 0.7373 (ptp90) cc_final: 0.5471 (mmt180) REVERT: H 572 GLN cc_start: 0.7683 (mm-40) cc_final: 0.7460 (mt0) REVERT: H 672 ASP cc_start: 0.3770 (OUTLIER) cc_final: 0.3321 (m-30) REVERT: H 732 VAL cc_start: 0.8990 (OUTLIER) cc_final: 0.8746 (t) REVERT: G 527 PHE cc_start: 0.8147 (OUTLIER) cc_final: 0.7755 (m-80) REVERT: G 590 LYS cc_start: 0.8296 (OUTLIER) cc_final: 0.8081 (ttpp) REVERT: G 620 GLN cc_start: 0.8802 (OUTLIER) cc_final: 0.8012 (mt0) REVERT: G 685 PHE cc_start: 0.8231 (t80) cc_final: 0.7805 (t80) REVERT: G 707 HIS cc_start: 0.5990 (m170) cc_final: 0.5298 (m90) REVERT: G 731 ASP cc_start: 0.8145 (m-30) cc_final: 0.7422 (t0) REVERT: G 817 GLU cc_start: 0.6419 (mm-30) cc_final: 0.6034 (pt0) outliers start: 143 outliers final: 96 residues processed: 340 average time/residue: 0.3205 time to fit residues: 171.6815 Evaluate side-chains 329 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 118 poor density : 211 time to evaluate : 2.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 127 LEU Chi-restraints excluded: chain A residue 141 LYS Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 225 LEU Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 225 LEU Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 129 VAL Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 532 THR Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain C residue 572 SER Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 225 VAL Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain D residue 631 THR Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 395 PHE Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 468 LEU Chi-restraints excluded: chain H residue 579 THR Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 609 VAL Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 707 HIS Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 842 LEU Chi-restraints excluded: chain H residue 844 LEU Chi-restraints excluded: chain H residue 866 LEU Chi-restraints excluded: chain H residue 867 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 527 PHE Chi-restraints excluded: chain G residue 590 LYS Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 833 LEU Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 245 optimal weight: 7.9990 chunk 140 optimal weight: 1.9990 chunk 174 optimal weight: 10.0000 chunk 261 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 171 optimal weight: 4.9990 chunk 181 optimal weight: 0.0060 chunk 160 optimal weight: 0.4980 chunk 154 optimal weight: 4.9990 chunk 182 optimal weight: 4.9990 chunk 42 optimal weight: 2.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN D 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.182022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.131112 restraints weight = 26243.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3516 r_free = 0.3516 target = 0.128542 restraints weight = 22104.448| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3533 r_free = 0.3533 target = 0.130488 restraints weight = 24036.890| |-----------------------------------------------------------------------------| r_work (final): 0.3554 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 23108 Z= 0.117 Angle : 0.549 10.564 31358 Z= 0.273 Chirality : 0.039 0.180 3725 Planarity : 0.004 0.060 3926 Dihedral : 5.577 59.121 3135 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.41 % Favored : 94.52 % Rotamer: Outliers : 4.68 % Allowed : 28.17 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.16), residues: 2845 helix: 1.07 (0.14), residues: 1592 sheet: -1.98 (0.31), residues: 276 loop : -2.14 (0.19), residues: 977 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP G 487 HIS 0.004 0.001 HIS A 135 PHE 0.017 0.001 PHE A 330 TYR 0.022 0.001 TYR H 802 ARG 0.009 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03478 ( 1055) hydrogen bonds : angle 3.92243 ( 3102) covalent geometry : bond 0.00278 (23108) covalent geometry : angle 0.54877 (31358) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 336 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 119 poor density : 217 time to evaluate : 2.618 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8102 (tpp) cc_final: 0.7296 (tpp) REVERT: A 24 GLU cc_start: 0.7612 (mt-10) cc_final: 0.7256 (mt-10) REVERT: B 12 ASP cc_start: 0.7434 (OUTLIER) cc_final: 0.7214 (p0) REVERT: B 227 GLU cc_start: 0.8239 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: B 252 GLU cc_start: 0.8268 (OUTLIER) cc_final: 0.7250 (mt-10) REVERT: B 258 GLU cc_start: 0.8022 (OUTLIER) cc_final: 0.5841 (tm-30) REVERT: C 137 GLN cc_start: 0.7112 (OUTLIER) cc_final: 0.6473 (mp10) REVERT: C 149 GLU cc_start: 0.6597 (tp30) cc_final: 0.6317 (tp30) REVERT: C 180 LEU cc_start: 0.7549 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 222 LEU cc_start: 0.7649 (OUTLIER) cc_final: 0.7254 (tt) REVERT: C 235 LEU cc_start: 0.7683 (OUTLIER) cc_final: 0.7425 (mt) REVERT: C 374 LEU cc_start: 0.7767 (OUTLIER) cc_final: 0.7330 (mp) REVERT: C 511 ARG cc_start: 0.6467 (tpt90) cc_final: 0.5890 (ttp-170) REVERT: C 518 ASN cc_start: 0.7257 (OUTLIER) cc_final: 0.6829 (p0) REVERT: D 99 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6893 (mp) REVERT: D 235 LEU cc_start: 0.7471 (OUTLIER) cc_final: 0.7127 (tt) REVERT: D 379 LEU cc_start: 0.8073 (OUTLIER) cc_final: 0.7818 (tt) REVERT: D 546 ARG cc_start: 0.8206 (OUTLIER) cc_final: 0.7970 (mtm-85) REVERT: D 561 GLN cc_start: 0.7567 (OUTLIER) cc_final: 0.7120 (pp30) REVERT: D 614 LEU cc_start: 0.8526 (OUTLIER) cc_final: 0.8280 (tt) REVERT: H 149 MET cc_start: 0.5153 (ptp) cc_final: 0.4894 (mtt) REVERT: H 183 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6371 (mt) REVERT: H 396 MET cc_start: 0.5200 (ttt) cc_final: 0.4957 (ttt) REVERT: H 459 MET cc_start: 0.7373 (ptp) cc_final: 0.7078 (ptp) REVERT: H 481 ARG cc_start: 0.7798 (ptm160) cc_final: 0.7237 (ptm160) REVERT: H 544 ARG cc_start: 0.7460 (ptp90) cc_final: 0.5459 (mmt180) REVERT: H 672 ASP cc_start: 0.3495 (OUTLIER) cc_final: 0.3176 (m-30) REVERT: G 527 PHE cc_start: 0.8180 (OUTLIER) cc_final: 0.7964 (m-80) REVERT: G 620 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7736 (mt0) REVERT: G 685 PHE cc_start: 0.8158 (t80) cc_final: 0.7734 (t80) REVERT: G 724 ASP cc_start: 0.8402 (m-30) cc_final: 0.7943 (m-30) REVERT: G 731 ASP cc_start: 0.8098 (m-30) cc_final: 0.7374 (t0) REVERT: G 817 GLU cc_start: 0.6391 (mm-30) cc_final: 0.6009 (pt0) outliers start: 119 outliers final: 89 residues processed: 318 average time/residue: 0.3293 time to fit residues: 165.6529 Evaluate side-chains 317 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 109 poor density : 208 time to evaluate : 2.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 319 LEU Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 516 ASN Chi-restraints excluded: chain C residue 518 ASN Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 432 LEU Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 609 VAL Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 707 HIS Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain H residue 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 844 LEU Chi-restraints excluded: chain H residue 867 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 527 PHE Chi-restraints excluded: chain G residue 566 ASN Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 682 SER Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 833 LEU Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 236 optimal weight: 7.9990 chunk 127 optimal weight: 1.9990 chunk 165 optimal weight: 2.9990 chunk 211 optimal weight: 0.1980 chunk 161 optimal weight: 1.9990 chunk 107 optimal weight: 0.0000 chunk 113 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 4.9990 chunk 42 optimal weight: 1.9990 chunk 140 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.186678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3624 r_free = 0.3624 target = 0.136244 restraints weight = 26661.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.132905 restraints weight = 25434.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135431 restraints weight = 25310.768| |-----------------------------------------------------------------------------| r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7813 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 23108 Z= 0.106 Angle : 0.535 10.116 31358 Z= 0.265 Chirality : 0.038 0.180 3725 Planarity : 0.004 0.063 3926 Dihedral : 5.418 59.957 3133 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.55 % Favored : 94.38 % Rotamer: Outliers : 4.44 % Allowed : 28.41 % Favored : 67.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.32 (0.17), residues: 2845 helix: 1.17 (0.14), residues: 1591 sheet: -1.83 (0.31), residues: 276 loop : -2.05 (0.19), residues: 978 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 903 HIS 0.004 0.001 HIS D 632 PHE 0.042 0.001 PHE H 391 TYR 0.018 0.001 TYR H 802 ARG 0.009 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03252 ( 1055) hydrogen bonds : angle 3.82881 ( 3102) covalent geometry : bond 0.00244 (23108) covalent geometry : angle 0.53458 (31358) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 331 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 113 poor density : 218 time to evaluate : 2.598 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8003 (tpp) cc_final: 0.7384 (tpp) REVERT: A 24 GLU cc_start: 0.7685 (mt-10) cc_final: 0.7314 (mt-10) REVERT: A 60 ASN cc_start: 0.8757 (m-40) cc_final: 0.8319 (m110) REVERT: B 227 GLU cc_start: 0.8207 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: B 252 GLU cc_start: 0.8230 (OUTLIER) cc_final: 0.7205 (mt-10) REVERT: B 258 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.5873 (tm-30) REVERT: C 137 GLN cc_start: 0.7089 (OUTLIER) cc_final: 0.6478 (mp10) REVERT: C 149 GLU cc_start: 0.6563 (tp30) cc_final: 0.6280 (tp30) REVERT: C 180 LEU cc_start: 0.7614 (OUTLIER) cc_final: 0.7285 (mp) REVERT: C 222 LEU cc_start: 0.7604 (OUTLIER) cc_final: 0.7199 (tt) REVERT: C 374 LEU cc_start: 0.7740 (OUTLIER) cc_final: 0.7338 (mp) REVERT: C 511 ARG cc_start: 0.6489 (tpt90) cc_final: 0.5924 (ttp-170) REVERT: C 516 ASN cc_start: 0.8534 (p0) cc_final: 0.8331 (p0) REVERT: D 99 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6939 (mp) REVERT: D 379 LEU cc_start: 0.8119 (OUTLIER) cc_final: 0.7881 (tt) REVERT: D 546 ARG cc_start: 0.8224 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: D 561 GLN cc_start: 0.7594 (OUTLIER) cc_final: 0.7132 (pp30) REVERT: D 614 LEU cc_start: 0.8530 (OUTLIER) cc_final: 0.8308 (tt) REVERT: H 183 LEU cc_start: 0.6942 (OUTLIER) cc_final: 0.6366 (mt) REVERT: H 396 MET cc_start: 0.5211 (ttt) cc_final: 0.4995 (ttt) REVERT: H 459 MET cc_start: 0.7650 (ptp) cc_final: 0.7246 (ptp) REVERT: H 481 ARG cc_start: 0.7782 (ptm160) cc_final: 0.7230 (ptm160) REVERT: H 544 ARG cc_start: 0.7441 (ptp90) cc_final: 0.5485 (mmt180) REVERT: H 672 ASP cc_start: 0.3417 (OUTLIER) cc_final: 0.3172 (m-30) REVERT: G 620 GLN cc_start: 0.8569 (OUTLIER) cc_final: 0.7812 (mt0) REVERT: G 674 LEU cc_start: 0.7561 (tp) cc_final: 0.7026 (tt) REVERT: G 685 PHE cc_start: 0.8124 (t80) cc_final: 0.7699 (t80) REVERT: G 724 ASP cc_start: 0.8287 (m-30) cc_final: 0.7853 (m-30) REVERT: G 731 ASP cc_start: 0.8029 (m-30) cc_final: 0.7414 (t0) REVERT: G 787 CYS cc_start: 0.6886 (OUTLIER) cc_final: 0.6315 (m) REVERT: G 817 GLU cc_start: 0.6372 (mm-30) cc_final: 0.6011 (pt0) outliers start: 113 outliers final: 89 residues processed: 313 average time/residue: 0.3238 time to fit residues: 160.7822 Evaluate side-chains 312 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 105 poor density : 207 time to evaluate : 2.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 12 ASP Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 374 LEU Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 516 ASN Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 395 PHE Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 468 LEU Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 672 ASP Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 707 HIS Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 867 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 566 ASN Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 682 SER Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 718 LEU Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 787 CYS Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 833 LEU Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 857 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 149 optimal weight: 0.8980 chunk 99 optimal weight: 3.9990 chunk 95 optimal weight: 0.7980 chunk 34 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 132 optimal weight: 4.9990 chunk 231 optimal weight: 2.9990 chunk 187 optimal weight: 20.0000 chunk 154 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4116 r_free = 0.4116 target = 0.185324 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.134956 restraints weight = 26680.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.131244 restraints weight = 24662.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133315 restraints weight = 27169.627| |-----------------------------------------------------------------------------| r_work (final): 0.3547 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 23108 Z= 0.129 Angle : 0.547 9.738 31358 Z= 0.270 Chirality : 0.039 0.180 3725 Planarity : 0.004 0.084 3926 Dihedral : 5.425 59.814 3133 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 4.48 % Allowed : 28.25 % Favored : 67.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.16), residues: 2845 helix: 1.18 (0.14), residues: 1589 sheet: -1.81 (0.31), residues: 276 loop : -2.06 (0.19), residues: 980 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP H 367 HIS 0.006 0.001 HIS A 135 PHE 0.020 0.001 PHE A 330 TYR 0.014 0.001 TYR H 387 ARG 0.009 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03393 ( 1055) hydrogen bonds : angle 3.83447 ( 3102) covalent geometry : bond 0.00314 (23108) covalent geometry : angle 0.54713 (31358) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 114 poor density : 219 time to evaluate : 2.394 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 24 GLU cc_start: 0.7678 (mt-10) cc_final: 0.7323 (mt-10) REVERT: A 60 ASN cc_start: 0.8758 (m-40) cc_final: 0.8311 (m110) REVERT: B 227 GLU cc_start: 0.8231 (OUTLIER) cc_final: 0.7853 (mt-10) REVERT: B 252 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7234 (mt-10) REVERT: B 258 GLU cc_start: 0.8010 (OUTLIER) cc_final: 0.5800 (tm-30) REVERT: C 137 GLN cc_start: 0.7011 (OUTLIER) cc_final: 0.6406 (mp10) REVERT: C 149 GLU cc_start: 0.6607 (tp30) cc_final: 0.6315 (tp30) REVERT: C 180 LEU cc_start: 0.7572 (OUTLIER) cc_final: 0.7221 (mp) REVERT: C 210 CYS cc_start: 0.7073 (t) cc_final: 0.6457 (t) REVERT: C 222 LEU cc_start: 0.7601 (OUTLIER) cc_final: 0.7196 (tt) REVERT: C 235 LEU cc_start: 0.7681 (OUTLIER) cc_final: 0.7403 (mt) REVERT: C 374 LEU cc_start: 0.7756 (OUTLIER) cc_final: 0.7359 (mp) REVERT: C 511 ARG cc_start: 0.6395 (tpt90) cc_final: 0.5855 (ttp-170) REVERT: D 99 LEU cc_start: 0.7413 (OUTLIER) cc_final: 0.6848 (mp) REVERT: D 235 LEU cc_start: 0.7475 (OUTLIER) cc_final: 0.7164 (tt) REVERT: D 379 LEU cc_start: 0.8171 (OUTLIER) cc_final: 0.7931 (tt) REVERT: D 546 ARG cc_start: 0.8221 (OUTLIER) cc_final: 0.8001 (mtm-85) REVERT: D 561 GLN cc_start: 0.7587 (OUTLIER) cc_final: 0.7132 (pp30) REVERT: D 614 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8353 (tt) REVERT: H 183 LEU cc_start: 0.7008 (OUTLIER) cc_final: 0.6404 (mt) REVERT: H 459 MET cc_start: 0.7487 (ptp) cc_final: 0.7194 (ptp) REVERT: H 481 ARG cc_start: 0.7849 (ptm160) cc_final: 0.7304 (ptm160) REVERT: H 544 ARG cc_start: 0.7411 (ptp90) cc_final: 0.5416 (mmt180) REVERT: H 672 ASP cc_start: 0.3464 (p0) cc_final: 0.3231 (m-30) REVERT: G 620 GLN cc_start: 0.8589 (OUTLIER) cc_final: 0.7373 (mt0) REVERT: G 674 LEU cc_start: 0.7630 (tp) cc_final: 0.7058 (tt) REVERT: G 685 PHE cc_start: 0.8141 (t80) cc_final: 0.7713 (t80) REVERT: G 724 ASP cc_start: 0.8359 (m-30) cc_final: 0.7873 (m-30) REVERT: G 731 ASP cc_start: 0.8082 (m-30) cc_final: 0.7431 (t0) REVERT: G 817 GLU cc_start: 0.6407 (mm-30) cc_final: 0.5984 (pt0) outliers start: 114 outliers final: 91 residues processed: 316 average time/residue: 0.3228 time to fit residues: 161.5654 Evaluate side-chains 320 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 107 poor density : 213 time to evaluate : 2.345 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 197 THR Chi-restraints excluded: chain A residue 232 CYS Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 57 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 250 GLN Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 284 LEU Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 180 LEU Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 308 LEU Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 464 SER Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain D residue 66 LEU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 379 LEU Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 514 ASP Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 573 SER Chi-restraints excluded: chain D residue 598 LEU Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 395 PHE Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 468 LEU Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 707 HIS Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 866 LEU Chi-restraints excluded: chain H residue 867 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 682 SER Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 833 LEU Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 193 optimal weight: 5.9990 chunk 195 optimal weight: 0.7980 chunk 236 optimal weight: 9.9990 chunk 12 optimal weight: 0.9990 chunk 66 optimal weight: 0.9990 chunk 175 optimal weight: 0.4980 chunk 5 optimal weight: 0.4980 chunk 221 optimal weight: 2.9990 chunk 285 optimal weight: 5.9990 chunk 232 optimal weight: 0.0170 chunk 71 optimal weight: 7.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 493 GLN G 558 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.188720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.138698 restraints weight = 26864.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.133901 restraints weight = 27215.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.136726 restraints weight = 24876.136| |-----------------------------------------------------------------------------| r_work (final): 0.3511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 23108 Z= 0.103 Angle : 0.530 9.375 31358 Z= 0.262 Chirality : 0.038 0.178 3725 Planarity : 0.004 0.074 3926 Dihedral : 5.224 59.058 3131 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.24 % Favored : 94.69 % Rotamer: Outliers : 4.01 % Allowed : 28.88 % Favored : 67.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.17 (0.17), residues: 2845 helix: 1.27 (0.14), residues: 1589 sheet: -1.64 (0.32), residues: 273 loop : -1.99 (0.19), residues: 983 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP G 487 HIS 0.004 0.001 HIS A 135 PHE 0.044 0.001 PHE H 391 TYR 0.013 0.001 TYR H 171 ARG 0.010 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03117 ( 1055) hydrogen bonds : angle 3.72439 ( 3102) covalent geometry : bond 0.00241 (23108) covalent geometry : angle 0.53018 (31358) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5690 Ramachandran restraints generated. 2845 Oldfield, 0 Emsley, 2845 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 325 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 223 time to evaluate : 2.712 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8040 (tpp) cc_final: 0.7279 (tpp) REVERT: A 24 GLU cc_start: 0.7646 (mt-10) cc_final: 0.7276 (mt-10) REVERT: A 60 ASN cc_start: 0.8716 (m-40) cc_final: 0.8285 (m110) REVERT: B 227 GLU cc_start: 0.8212 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: B 252 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7142 (mt-10) REVERT: B 258 GLU cc_start: 0.7882 (OUTLIER) cc_final: 0.5696 (tm-30) REVERT: C 137 GLN cc_start: 0.6947 (OUTLIER) cc_final: 0.6328 (mp10) REVERT: C 149 GLU cc_start: 0.6536 (tp30) cc_final: 0.6260 (tp30) REVERT: C 210 CYS cc_start: 0.7182 (t) cc_final: 0.6647 (t) REVERT: C 222 LEU cc_start: 0.7586 (OUTLIER) cc_final: 0.7172 (tt) REVERT: C 235 LEU cc_start: 0.7661 (OUTLIER) cc_final: 0.7406 (mt) REVERT: C 374 LEU cc_start: 0.7715 (OUTLIER) cc_final: 0.7339 (mp) REVERT: C 511 ARG cc_start: 0.6386 (tpt90) cc_final: 0.5853 (ttp-170) REVERT: D 99 LEU cc_start: 0.7356 (OUTLIER) cc_final: 0.6794 (mp) REVERT: D 546 ARG cc_start: 0.8184 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: D 561 GLN cc_start: 0.7510 (OUTLIER) cc_final: 0.7057 (pp30) REVERT: D 614 LEU cc_start: 0.8431 (OUTLIER) cc_final: 0.8207 (tt) REVERT: H 183 LEU cc_start: 0.7095 (OUTLIER) cc_final: 0.6533 (mt) REVERT: H 459 MET cc_start: 0.7595 (ptp) cc_final: 0.7188 (ptp) REVERT: H 481 ARG cc_start: 0.7822 (ptm160) cc_final: 0.7286 (ptm160) REVERT: H 529 LYS cc_start: 0.8826 (mmtt) cc_final: 0.8558 (ttpt) REVERT: H 544 ARG cc_start: 0.7324 (ptp90) cc_final: 0.5326 (mmt180) REVERT: G 512 GLN cc_start: 0.7453 (tm-30) cc_final: 0.7249 (tm-30) REVERT: G 620 GLN cc_start: 0.8459 (OUTLIER) cc_final: 0.7696 (mt0) REVERT: G 674 LEU cc_start: 0.7595 (tp) cc_final: 0.7036 (tt) REVERT: G 685 PHE cc_start: 0.8047 (t80) cc_final: 0.7617 (t80) REVERT: G 724 ASP cc_start: 0.8204 (m-30) cc_final: 0.7775 (m-30) REVERT: G 731 ASP cc_start: 0.8051 (m-30) cc_final: 0.7399 (t0) REVERT: G 817 GLU cc_start: 0.6415 (mm-30) cc_final: 0.5893 (pt0) outliers start: 102 outliers final: 78 residues processed: 309 average time/residue: 0.3337 time to fit residues: 163.5538 Evaluate side-chains 301 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 210 time to evaluate : 2.397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 SER Chi-restraints excluded: chain A residue 21 ILE Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 157 ASP Chi-restraints excluded: chain A residue 289 HIS Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 323 VAL Chi-restraints excluded: chain A residue 340 ASN Chi-restraints excluded: chain A residue 343 LEU Chi-restraints excluded: chain B residue 12 ASP Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 84 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 91 ASN Chi-restraints excluded: chain B residue 96 LEU Chi-restraints excluded: chain B residue 110 THR Chi-restraints excluded: chain B residue 176 THR Chi-restraints excluded: chain B residue 192 SER Chi-restraints excluded: chain B residue 227 GLU Chi-restraints excluded: chain B residue 252 GLU Chi-restraints excluded: chain B residue 258 GLU Chi-restraints excluded: chain B residue 276 SER Chi-restraints excluded: chain B residue 283 VAL Chi-restraints excluded: chain B residue 285 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 142 GLN Chi-restraints excluded: chain C residue 222 LEU Chi-restraints excluded: chain C residue 235 LEU Chi-restraints excluded: chain C residue 278 LEU Chi-restraints excluded: chain C residue 307 VAL Chi-restraints excluded: chain C residue 374 LEU Chi-restraints excluded: chain C residue 397 LEU Chi-restraints excluded: chain C residue 411 ILE Chi-restraints excluded: chain C residue 445 SER Chi-restraints excluded: chain C residue 516 ASN Chi-restraints excluded: chain C residue 533 ILE Chi-restraints excluded: chain D residue 99 LEU Chi-restraints excluded: chain D residue 101 SER Chi-restraints excluded: chain D residue 116 VAL Chi-restraints excluded: chain D residue 184 LEU Chi-restraints excluded: chain D residue 235 LEU Chi-restraints excluded: chain D residue 245 SER Chi-restraints excluded: chain D residue 328 SER Chi-restraints excluded: chain D residue 352 SER Chi-restraints excluded: chain D residue 396 ILE Chi-restraints excluded: chain D residue 518 ASN Chi-restraints excluded: chain D residue 541 LYS Chi-restraints excluded: chain D residue 546 ARG Chi-restraints excluded: chain D residue 553 LEU Chi-restraints excluded: chain D residue 561 GLN Chi-restraints excluded: chain D residue 614 LEU Chi-restraints excluded: chain D residue 617 SER Chi-restraints excluded: chain H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 183 LEU Chi-restraints excluded: chain H residue 356 MET Chi-restraints excluded: chain H residue 395 PHE Chi-restraints excluded: chain H residue 401 TYR Chi-restraints excluded: chain H residue 468 LEU Chi-restraints excluded: chain H residue 589 LEU Chi-restraints excluded: chain H residue 639 CYS Chi-restraints excluded: chain H residue 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 718 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS Chi-restraints excluded: chain H residue 829 CYS Chi-restraints excluded: chain H residue 866 LEU Chi-restraints excluded: chain H residue 867 LEU Chi-restraints excluded: chain G residue 519 VAL Chi-restraints excluded: chain G residue 620 GLN Chi-restraints excluded: chain G residue 622 VAL Chi-restraints excluded: chain G residue 634 SER Chi-restraints excluded: chain G residue 641 ILE Chi-restraints excluded: chain G residue 642 MET Chi-restraints excluded: chain G residue 652 MET Chi-restraints excluded: chain G residue 682 SER Chi-restraints excluded: chain G residue 714 SER Chi-restraints excluded: chain G residue 727 LEU Chi-restraints excluded: chain G residue 766 VAL Chi-restraints excluded: chain G residue 782 LEU Chi-restraints excluded: chain G residue 815 GLU Chi-restraints excluded: chain G residue 830 VAL Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 857 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 55 optimal weight: 3.9990 chunk 76 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 189 optimal weight: 6.9990 chunk 31 optimal weight: 0.1980 chunk 50 optimal weight: 0.0870 chunk 205 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 148 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 229 optimal weight: 7.9990 overall best weight: 1.1762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS ** B 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 558 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.183989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.133072 restraints weight = 26934.457| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.128855 restraints weight = 24309.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.131355 restraints weight = 25305.773| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 23108 Z= 0.142 Angle : 0.565 10.955 31358 Z= 0.278 Chirality : 0.040 0.251 3725 Planarity : 0.004 0.077 3926 Dihedral : 5.089 58.619 3124 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.98 % Favored : 93.95 % Rotamer: Outliers : 4.13 % Allowed : 28.96 % Favored : 66.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.16), residues: 2845 helix: 1.23 (0.14), residues: 1588 sheet: -1.71 (0.32), residues: 276 loop : -2.04 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 487 HIS 0.006 0.001 HIS A 135 PHE 0.021 0.001 PHE A 330 TYR 0.013 0.001 TYR B 61 ARG 0.010 0.000 ARG D 224 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 1055) hydrogen bonds : angle 3.79753 ( 3102) covalent geometry : bond 0.00350 (23108) covalent geometry : angle 0.56512 (31358) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6402.67 seconds wall clock time: 113 minutes 9.53 seconds (6789.53 seconds total)