Starting phenix.real_space_refine on Fri Sep 19 03:12:47 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dum_47170/09_2025/9dum_47170.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dum_47170/09_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_47170/09_2025/9dum_47170.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dum_47170/09_2025/9dum_47170.map" model { file = "/net/cci-nas-00/data/ceres_data/9dum_47170/09_2025/9dum_47170.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dum_47170/09_2025/9dum_47170.cif" } resolution = 3.56 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.02s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 4.67, per 1000 atoms: 0.21 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: 1.92 Conformation dependent library (CDL) restraints added in 869.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.80 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: 3.78 Time building geometry restraints manager: 2.53 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: 1.620 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: 0.010 Extract box with map and model: 0.280 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 19.450 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 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: 0.000 Load rotamer database and sin/cos tables:1.270 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.070 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.010 0.000 ARG D 224 TYR 0.019 0.001 TYR H 914 PHE 0.015 0.001 PHE A 136 TRP 0.028 0.001 TRP G 903 HIS 0.005 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00314 (23108) covalent geometry : angle 0.61769 (31358) hydrogen bonds : bond 0.21224 ( 1055) hydrogen bonds : angle 6.31633 ( 3102) *********************** 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 : 0.812 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: 0.1687 time to fit residues: 117.9758 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 : 0.851 ------------------------------------------------------------------------------- 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 197 optimal weight: 0.8980 chunk 215 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 132 optimal weight: 4.9990 chunk 261 optimal weight: 1.9990 chunk 248 optimal weight: 3.9990 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 20.0000 chunk 183 optimal weight: 10.0000 chunk 111 optimal weight: 2.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 122 GLN A 342 HIS B 56 GLN B 155 GLN B 196 GLN ** B 315 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4118 r_free = 0.4118 target = 0.185274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.134453 restraints weight = 26683.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.131095 restraints weight = 23528.534| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133540 restraints weight = 25281.124| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.133750 restraints weight = 15572.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3578 r_free = 0.3578 target = 0.134967 restraints weight = 14212.965| |-----------------------------------------------------------------------------| r_work (final): 0.3608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7755 moved from start: 0.1407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23108 Z= 0.168 Angle : 0.631 9.457 31358 Z= 0.315 Chirality : 0.042 0.228 3725 Planarity : 0.005 0.058 3926 Dihedral : 7.339 57.924 3246 Min Nonbonded Distance : 2.547 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.11 % Allowed : 6.43 % Favored : 93.46 % Rotamer: Outliers : 5.82 % Allowed : 27.86 % Favored : 66.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.86 (0.16), residues: 2845 helix: 0.78 (0.14), residues: 1579 sheet: -2.40 (0.31), residues: 268 loop : -2.23 (0.18), residues: 998 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 461 TYR 0.029 0.002 TYR G 802 PHE 0.021 0.002 PHE H 807 TRP 0.018 0.001 TRP G 487 HIS 0.010 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00405 (23108) covalent geometry : angle 0.63143 (31358) hydrogen bonds : bond 0.05217 ( 1055) hydrogen bonds : angle 4.59146 ( 3102) *********************** 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: 148 poor density : 255 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 269 ARG cc_start: 0.7802 (ptm-80) cc_final: 0.7560 (ptp-110) REVERT: B 12 ASP cc_start: 0.7506 (OUTLIER) cc_final: 0.7243 (p0) REVERT: B 129 PHE cc_start: 0.8761 (OUTLIER) cc_final: 0.7316 (t80) REVERT: B 227 GLU cc_start: 0.8131 (OUTLIER) cc_final: 0.7716 (mt-10) REVERT: B 252 GLU cc_start: 0.8194 (OUTLIER) cc_final: 0.7155 (mt-10) REVERT: B 258 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.6012 (tm-30) REVERT: C 137 GLN cc_start: 0.7134 (OUTLIER) cc_final: 0.6499 (mp10) REVERT: C 149 GLU cc_start: 0.6455 (tp30) cc_final: 0.6169 (tp30) REVERT: C 180 LEU cc_start: 0.7463 (OUTLIER) cc_final: 0.7189 (mp) REVERT: C 262 GLN cc_start: 0.8155 (tp-100) cc_final: 0.7841 (tt0) REVERT: C 511 ARG cc_start: 0.6306 (tpt90) cc_final: 0.5757 (ttp-170) REVERT: C 518 ASN cc_start: 0.7559 (OUTLIER) cc_final: 0.7132 (p0) REVERT: D 235 LEU cc_start: 0.7427 (OUTLIER) cc_final: 0.7028 (tt) REVERT: D 379 LEU cc_start: 0.7913 (OUTLIER) cc_final: 0.7601 (tt) REVERT: D 546 ARG cc_start: 0.8128 (OUTLIER) cc_final: 0.7893 (mtm-85) REVERT: D 561 GLN cc_start: 0.7614 (OUTLIER) cc_final: 0.7001 (pp30) REVERT: D 614 LEU cc_start: 0.8486 (OUTLIER) cc_final: 0.8232 (tt) REVERT: H 181 ILE cc_start: 0.7738 (OUTLIER) cc_final: 0.7472 (mp) REVERT: H 364 SER cc_start: 0.8820 (t) cc_final: 0.8573 (p) REVERT: H 544 ARG cc_start: 0.6792 (ptp90) cc_final: 0.5324 (mmt180) REVERT: H 648 SER cc_start: 0.8418 (t) cc_final: 0.7984 (m) REVERT: H 720 LEU cc_start: 0.7395 (mp) cc_final: 0.7085 (mp) REVERT: H 732 VAL cc_start: 0.8770 (OUTLIER) cc_final: 0.8447 (t) REVERT: H 867 LEU cc_start: 0.6517 (tt) cc_final: 0.6053 (tt) REVERT: G 525 LYS cc_start: 0.8219 (ttpt) cc_final: 0.7725 (ttmm) REVERT: G 527 PHE cc_start: 0.7816 (OUTLIER) cc_final: 0.7605 (m-80) REVERT: G 620 GLN cc_start: 0.8566 (OUTLIER) cc_final: 0.7060 (mt0) REVERT: G 682 SER cc_start: 0.8576 (OUTLIER) cc_final: 0.8269 (t) REVERT: G 685 PHE cc_start: 0.8534 (t80) cc_final: 0.8331 (t80) REVERT: G 697 THR cc_start: 0.8654 (m) cc_final: 0.8442 (m) REVERT: G 707 HIS cc_start: 0.5880 (m170) cc_final: 0.5325 (m90) REVERT: G 724 ASP cc_start: 0.8055 (m-30) cc_final: 0.7584 (m-30) REVERT: G 731 ASP cc_start: 0.8081 (m-30) cc_final: 0.7255 (t0) REVERT: G 817 GLU cc_start: 0.6349 (mm-30) cc_final: 0.5984 (pt0) outliers start: 148 outliers final: 77 residues processed: 388 average time/residue: 0.1622 time to fit residues: 97.3544 Evaluate side-chains 323 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 95 poor density : 228 time to evaluate : 0.845 ------------------------------------------------------------------------------- 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 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 89 SER 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 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 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 371 SER 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 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 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 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 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 830 VAL Chi-restraints excluded: chain G residue 842 LEU Chi-restraints excluded: chain G residue 849 VAL Chi-restraints excluded: chain G residue 860 VAL Chi-restraints excluded: chain G residue 863 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 132 optimal weight: 0.9990 chunk 242 optimal weight: 5.9990 chunk 171 optimal weight: 10.0000 chunk 286 optimal weight: 0.9980 chunk 126 optimal weight: 0.8980 chunk 94 optimal weight: 5.9990 chunk 167 optimal weight: 0.7980 chunk 90 optimal weight: 2.9990 chunk 84 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 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 = 0.4129 r_free = 0.4129 target = 0.186493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.135260 restraints weight = 26586.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3547 r_free = 0.3547 target = 0.131667 restraints weight = 22773.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3569 r_free = 0.3569 target = 0.134146 restraints weight = 24623.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.134509 restraints weight = 14192.723| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3585 r_free = 0.3585 target = 0.135996 restraints weight = 12649.542| |-----------------------------------------------------------------------------| r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7772 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 23108 Z= 0.130 Angle : 0.569 7.927 31358 Z= 0.284 Chirality : 0.040 0.211 3725 Planarity : 0.004 0.053 3926 Dihedral : 6.029 59.167 3153 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.11 % Allowed : 5.66 % Favored : 94.24 % Rotamer: Outliers : 4.95 % Allowed : 27.78 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.65 (0.16), residues: 2845 helix: 0.91 (0.14), residues: 1591 sheet: -2.23 (0.31), residues: 268 loop : -2.13 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 224 TYR 0.019 0.002 TYR H 668 PHE 0.017 0.001 PHE A 136 TRP 0.018 0.001 TRP G 487 HIS 0.007 0.001 HIS H 144 Details of bonding type rmsd covalent geometry : bond 0.00304 (23108) covalent geometry : angle 0.56923 (31358) hydrogen bonds : bond 0.04221 ( 1055) hydrogen bonds : angle 4.21684 ( 3102) *********************** 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 360 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 126 poor density : 234 time to evaluate : 1.012 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 219 MET cc_start: 0.8482 (mmm) cc_final: 0.8110 (mmm) REVERT: B 129 PHE cc_start: 0.8754 (OUTLIER) cc_final: 0.7268 (t80) REVERT: B 227 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7686 (mt-10) REVERT: B 252 GLU cc_start: 0.8161 (OUTLIER) cc_final: 0.7120 (mt-10) REVERT: B 258 GLU cc_start: 0.8018 (OUTLIER) cc_final: 0.5868 (tm-30) REVERT: B 266 LYS cc_start: 0.8247 (ptpp) cc_final: 0.7990 (tptt) REVERT: C 137 GLN cc_start: 0.7110 (OUTLIER) cc_final: 0.6496 (mp10) REVERT: C 149 GLU cc_start: 0.6406 (tp30) cc_final: 0.6122 (tp30) REVERT: C 180 LEU cc_start: 0.7341 (OUTLIER) cc_final: 0.7064 (mp) REVERT: C 374 LEU cc_start: 0.7763 (OUTLIER) cc_final: 0.7400 (mt) REVERT: C 511 ARG cc_start: 0.6375 (tpt90) cc_final: 0.5808 (ttp-170) REVERT: C 518 ASN cc_start: 0.7384 (OUTLIER) cc_final: 0.6924 (p0) REVERT: D 99 LEU cc_start: 0.7458 (OUTLIER) cc_final: 0.6908 (mp) REVERT: D 235 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.7073 (tt) REVERT: D 379 LEU cc_start: 0.7938 (OUTLIER) cc_final: 0.7657 (tt) REVERT: D 546 ARG cc_start: 0.8189 (OUTLIER) cc_final: 0.7966 (mtm-85) REVERT: D 561 GLN cc_start: 0.7636 (OUTLIER) cc_final: 0.7174 (pp30) REVERT: D 614 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8237 (tt) REVERT: H 149 MET cc_start: 0.5578 (ptp) cc_final: 0.4882 (ttp) REVERT: H 364 SER cc_start: 0.8773 (t) cc_final: 0.8512 (p) REVERT: H 459 MET cc_start: 0.7753 (ptp) cc_final: 0.7382 (ptp) REVERT: H 544 ARG cc_start: 0.7035 (ptp90) cc_final: 0.5431 (mmt180) REVERT: H 867 LEU cc_start: 0.6731 (tt) cc_final: 0.5969 (tt) REVERT: G 441 MET cc_start: 0.4208 (ptp) cc_final: 0.2871 (tpt) REVERT: G 527 PHE cc_start: 0.7914 (OUTLIER) cc_final: 0.7656 (m-80) REVERT: G 620 GLN cc_start: 0.8439 (OUTLIER) cc_final: 0.7581 (mt0) REVERT: G 682 SER cc_start: 0.8438 (m) cc_final: 0.8189 (t) REVERT: G 685 PHE cc_start: 0.8556 (t80) cc_final: 0.8340 (t80) REVERT: G 707 HIS cc_start: 0.5892 (m170) cc_final: 0.5327 (m90) REVERT: G 724 ASP cc_start: 0.8092 (m-30) cc_final: 0.7644 (m-30) REVERT: G 731 ASP cc_start: 0.8066 (m-30) cc_final: 0.7286 (t0) REVERT: G 817 GLU cc_start: 0.6391 (mm-30) cc_final: 0.5989 (pt0) outliers start: 126 outliers final: 71 residues processed: 344 average time/residue: 0.1526 time to fit residues: 82.2440 Evaluate side-chains 297 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 87 poor density : 210 time to evaluate : 0.870 ------------------------------------------------------------------------------- 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 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 314 THR 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 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 117 LEU Chi-restraints excluded: chain B residue 129 PHE Chi-restraints excluded: chain B residue 176 THR 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 114 LEU 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 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 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 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 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 614 LEU Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 115 ARG 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 682 SER Chi-restraints excluded: chain H residue 684 LEU 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 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 275 optimal weight: 0.7980 chunk 140 optimal weight: 6.9990 chunk 85 optimal weight: 0.0020 chunk 47 optimal weight: 2.9990 chunk 245 optimal weight: 9.9990 chunk 244 optimal weight: 9.9990 chunk 232 optimal weight: 2.9990 chunk 151 optimal weight: 0.1980 chunk 258 optimal weight: 0.0670 chunk 274 optimal weight: 10.0000 chunk 214 optimal weight: 2.9990 overall best weight: 0.8128 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 342 HIS C 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4130 r_free = 0.4130 target = 0.186711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.136379 restraints weight = 26776.880| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.132945 restraints weight = 24177.722| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3584 r_free = 0.3584 target = 0.135186 restraints weight = 25909.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.135846 restraints weight = 15432.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.139117 restraints weight = 13791.062| |-----------------------------------------------------------------------------| r_work (final): 0.3596 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1972 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 23108 Z= 0.122 Angle : 0.560 9.356 31358 Z= 0.277 Chirality : 0.039 0.186 3725 Planarity : 0.004 0.049 3926 Dihedral : 5.729 59.505 3143 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 4.72 % Allowed : 27.47 % Favored : 67.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.16), residues: 2845 helix: 0.99 (0.14), residues: 1595 sheet: -2.11 (0.31), residues: 268 loop : -2.14 (0.19), residues: 982 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG D 224 TYR 0.016 0.001 TYR H 387 PHE 0.016 0.001 PHE A 136 TRP 0.014 0.001 TRP G 487 HIS 0.009 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00287 (23108) covalent geometry : angle 0.56036 (31358) hydrogen bonds : bond 0.03840 ( 1055) hydrogen bonds : angle 4.07061 ( 3102) *********************** 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 339 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 120 poor density : 219 time to evaluate : 0.724 Fit side-chains revert: symmetry clash REVERT: A 219 MET cc_start: 0.8525 (mmm) cc_final: 0.8106 (mmm) REVERT: A 286 SER cc_start: 0.8775 (OUTLIER) cc_final: 0.8536 (p) REVERT: B 227 GLU cc_start: 0.8228 (OUTLIER) cc_final: 0.7806 (mt-10) REVERT: B 252 GLU cc_start: 0.8209 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: B 258 GLU cc_start: 0.7984 (OUTLIER) cc_final: 0.5832 (tm-30) REVERT: B 266 LYS cc_start: 0.8290 (ptpp) cc_final: 0.8000 (tptt) REVERT: B 274 CYS cc_start: 0.8246 (OUTLIER) cc_final: 0.8044 (m) REVERT: C 137 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6406 (mp10) REVERT: C 180 LEU cc_start: 0.7236 (mp) cc_final: 0.6980 (mp) REVERT: C 374 LEU cc_start: 0.7717 (OUTLIER) cc_final: 0.7372 (mt) REVERT: C 511 ARG cc_start: 0.6358 (tpt90) cc_final: 0.5770 (ttp-170) REVERT: D 99 LEU cc_start: 0.7381 (OUTLIER) cc_final: 0.6824 (mp) REVERT: D 235 LEU cc_start: 0.7342 (OUTLIER) cc_final: 0.6930 (tt) REVERT: D 379 LEU cc_start: 0.7877 (OUTLIER) cc_final: 0.7597 (tt) REVERT: D 546 ARG cc_start: 0.8097 (OUTLIER) cc_final: 0.7864 (mtm-85) REVERT: D 561 GLN cc_start: 0.7612 (OUTLIER) cc_final: 0.7148 (pp30) REVERT: D 614 LEU cc_start: 0.8375 (OUTLIER) cc_final: 0.8108 (tt) REVERT: H 149 MET cc_start: 0.4583 (ptp) cc_final: 0.4308 (ttp) REVERT: H 230 ARG cc_start: 0.8130 (OUTLIER) cc_final: 0.7907 (mpp-170) REVERT: H 364 SER cc_start: 0.8858 (t) cc_final: 0.8573 (p) REVERT: H 459 MET cc_start: 0.7803 (ptp) cc_final: 0.7437 (ptp) REVERT: H 544 ARG cc_start: 0.7039 (ptp90) cc_final: 0.5417 (mmt180) REVERT: H 672 ASP cc_start: 0.3778 (p0) cc_final: 0.3309 (m-30) REVERT: H 867 LEU cc_start: 0.6732 (tt) cc_final: 0.6418 (tt) REVERT: G 441 MET cc_start: 0.4285 (ptp) cc_final: 0.2907 (tpt) REVERT: G 527 PHE cc_start: 0.8098 (OUTLIER) cc_final: 0.7829 (m-80) REVERT: G 620 GLN cc_start: 0.8518 (OUTLIER) cc_final: 0.7663 (mt0) REVERT: G 682 SER cc_start: 0.8392 (m) cc_final: 0.8141 (t) REVERT: G 685 PHE cc_start: 0.8464 (t80) cc_final: 0.8196 (t80) REVERT: G 707 HIS cc_start: 0.5862 (m170) cc_final: 0.5263 (m90) REVERT: G 724 ASP cc_start: 0.8038 (m-30) cc_final: 0.7543 (m-30) REVERT: G 731 ASP cc_start: 0.8118 (m-30) cc_final: 0.7284 (t0) REVERT: G 817 GLU cc_start: 0.6300 (mm-30) cc_final: 0.5975 (pt0) outliers start: 120 outliers final: 75 residues processed: 324 average time/residue: 0.1592 time to fit residues: 81.5555 Evaluate side-chains 298 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 91 poor density : 207 time to evaluate : 0.939 ------------------------------------------------------------------------------- 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 286 SER 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 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 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 B residue 383 LEU Chi-restraints excluded: chain C residue 114 LEU Chi-restraints excluded: chain C residue 137 GLN Chi-restraints excluded: chain C residue 225 VAL 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 516 ASN 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 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 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 H residue 95 HIS Chi-restraints excluded: chain H residue 108 THR Chi-restraints excluded: chain H residue 230 ARG 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 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 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 842 LEU Chi-restraints excluded: chain G residue 849 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 74 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 152 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 250 optimal weight: 0.9990 chunk 105 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 190 optimal weight: 20.0000 chunk 144 optimal weight: 1.9990 chunk 173 optimal weight: 8.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- 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 ** C 516 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 516 ASN H 185 ASN H 386 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN ** G 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4109 r_free = 0.4109 target = 0.184509 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3596 r_free = 0.3596 target = 0.133971 restraints weight = 26662.135| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.131039 restraints weight = 23707.970| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.133148 restraints weight = 25821.748| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133705 restraints weight = 15640.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.136944 restraints weight = 14102.431| |-----------------------------------------------------------------------------| r_work (final): 0.3578 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7708 moved from start: 0.2155 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= 0.152 Angle : 0.570 6.869 31358 Z= 0.283 Chirality : 0.040 0.179 3725 Planarity : 0.004 0.063 3926 Dihedral : 5.760 59.682 3141 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.12 % Favored : 93.81 % Rotamer: Outliers : 5.46 % Allowed : 26.92 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.56 (0.16), residues: 2845 helix: 1.00 (0.14), residues: 1589 sheet: -2.01 (0.31), residues: 268 loop : -2.18 (0.18), residues: 988 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 224 TYR 0.015 0.002 TYR G 510 PHE 0.048 0.002 PHE H 391 TRP 0.015 0.001 TRP H 903 HIS 0.007 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00372 (23108) covalent geometry : angle 0.56997 (31358) hydrogen bonds : bond 0.03883 ( 1055) hydrogen bonds : angle 4.04573 ( 3102) *********************** 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 360 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 139 poor density : 221 time to evaluate : 0.905 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 286 SER cc_start: 0.8806 (OUTLIER) cc_final: 0.8538 (p) REVERT: B 227 GLU cc_start: 0.8283 (OUTLIER) cc_final: 0.7888 (mt-10) REVERT: B 252 GLU cc_start: 0.8272 (OUTLIER) cc_final: 0.7245 (mt-10) REVERT: B 258 GLU cc_start: 0.8015 (OUTLIER) cc_final: 0.5806 (tm-30) REVERT: C 137 GLN cc_start: 0.7075 (OUTLIER) cc_final: 0.6410 (mp10) REVERT: C 149 GLU cc_start: 0.6448 (tp30) cc_final: 0.6155 (tp30) REVERT: C 180 LEU cc_start: 0.7303 (OUTLIER) cc_final: 0.6990 (mp) REVERT: C 235 LEU cc_start: 0.7569 (OUTLIER) cc_final: 0.7294 (mt) REVERT: C 374 LEU cc_start: 0.7744 (OUTLIER) cc_final: 0.7380 (mt) REVERT: C 511 ARG cc_start: 0.6381 (tpt90) cc_final: 0.5785 (ttp-170) REVERT: C 518 ASN cc_start: 0.7287 (OUTLIER) cc_final: 0.6831 (p0) REVERT: D 99 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.6898 (mp) REVERT: D 235 LEU cc_start: 0.7355 (OUTLIER) cc_final: 0.7007 (tt) REVERT: D 379 LEU cc_start: 0.7864 (OUTLIER) cc_final: 0.7585 (tt) REVERT: D 546 ARG cc_start: 0.8134 (OUTLIER) cc_final: 0.7886 (mtm-85) REVERT: D 561 GLN cc_start: 0.7620 (OUTLIER) cc_final: 0.7154 (pp30) REVERT: D 614 LEU cc_start: 0.8467 (OUTLIER) cc_final: 0.8196 (tt) REVERT: H 149 MET cc_start: 0.4567 (OUTLIER) cc_final: 0.4359 (ttp) REVERT: H 183 LEU cc_start: 0.7178 (OUTLIER) cc_final: 0.6622 (mt) REVERT: H 238 LEU cc_start: 0.8235 (OUTLIER) cc_final: 0.7842 (tt) REVERT: H 396 MET cc_start: 0.5072 (ttt) cc_final: 0.4711 (ttt) REVERT: H 481 ARG cc_start: 0.7871 (ptm160) cc_final: 0.7358 (ptp90) REVERT: H 544 ARG cc_start: 0.7067 (ptp90) cc_final: 0.5365 (mmt180) REVERT: H 672 ASP cc_start: 0.3862 (p0) cc_final: 0.3353 (m-30) REVERT: H 732 VAL cc_start: 0.8832 (OUTLIER) cc_final: 0.8627 (t) REVERT: G 527 PHE cc_start: 0.8107 (OUTLIER) cc_final: 0.7824 (m-80) REVERT: G 620 GLN cc_start: 0.8565 (OUTLIER) cc_final: 0.7693 (mt0) REVERT: G 682 SER cc_start: 0.8347 (m) cc_final: 0.8115 (t) REVERT: G 707 HIS cc_start: 0.5872 (m170) cc_final: 0.5246 (m90) REVERT: G 724 ASP cc_start: 0.8100 (m-30) cc_final: 0.7613 (m-30) REVERT: G 731 ASP cc_start: 0.8122 (m-30) cc_final: 0.7323 (t0) REVERT: G 817 GLU cc_start: 0.6363 (mm-30) cc_final: 0.6015 (pt0) outliers start: 139 outliers final: 89 residues processed: 341 average time/residue: 0.1604 time to fit residues: 86.0793 Evaluate side-chains 321 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 211 time to evaluate : 0.997 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 21 ILE 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 286 SER 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 75 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 176 THR Chi-restraints excluded: chain B residue 178 LEU Chi-restraints excluded: chain B residue 192 SER 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 284 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 383 LEU 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 278 LEU Chi-restraints excluded: chain C residue 307 VAL 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 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 203 MET Chi-restraints excluded: chain D residue 216 LYS Chi-restraints excluded: chain D residue 228 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 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 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 149 MET 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 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 682 SER Chi-restraints excluded: chain H residue 684 LEU Chi-restraints excluded: chain H residue 732 VAL Chi-restraints excluded: chain H residue 753 LEU 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 459 MET 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 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 842 LEU Chi-restraints excluded: chain G residue 849 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 289 random chunks: chunk 241 optimal weight: 0.0170 chunk 23 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 38 optimal weight: 0.0770 chunk 134 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 92 optimal weight: 0.8980 chunk 254 optimal weight: 1.9990 chunk 180 optimal weight: 10.0000 overall best weight: 0.7778 ------------------------------------------------------------------------------- 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 C 516 ASN D 510 HIS D 516 ASN ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 566 ASN G 754 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4103 r_free = 0.4103 target = 0.183367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3588 r_free = 0.3588 target = 0.132663 restraints weight = 26233.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.127365 restraints weight = 25338.741| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3530 r_free = 0.3530 target = 0.130589 restraints weight = 22935.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.130604 restraints weight = 13796.284| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3540 r_free = 0.3540 target = 0.131819 restraints weight = 12550.122| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2276 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= 0.117 Angle : 0.550 12.276 31358 Z= 0.271 Chirality : 0.039 0.179 3725 Planarity : 0.004 0.061 3926 Dihedral : 5.544 59.399 3137 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.69 % Favored : 94.24 % Rotamer: Outliers : 4.99 % Allowed : 27.43 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.42 (0.16), residues: 2845 helix: 1.10 (0.14), residues: 1590 sheet: -1.96 (0.31), residues: 276 loop : -2.09 (0.19), residues: 979 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 224 TYR 0.018 0.001 TYR H 802 PHE 0.017 0.001 PHE A 330 TRP 0.013 0.001 TRP H 903 HIS 0.005 0.001 HIS D 510 Details of bonding type rmsd covalent geometry : bond 0.00276 (23108) covalent geometry : angle 0.54993 (31358) hydrogen bonds : bond 0.03527 ( 1055) hydrogen bonds : angle 3.94370 ( 3102) *********************** 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 341 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 127 poor density : 214 time to evaluate : 0.808 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8769 (m-40) cc_final: 0.8302 (m110) REVERT: A 286 SER cc_start: 0.8760 (OUTLIER) cc_final: 0.8559 (p) REVERT: B 227 GLU cc_start: 0.8246 (OUTLIER) cc_final: 0.7846 (mt-10) REVERT: B 252 GLU cc_start: 0.8208 (OUTLIER) cc_final: 0.7173 (mt-10) REVERT: B 258 GLU cc_start: 0.8026 (OUTLIER) cc_final: 0.5838 (tm-30) REVERT: C 137 GLN cc_start: 0.7086 (OUTLIER) cc_final: 0.6442 (mp10) REVERT: C 149 GLU cc_start: 0.6453 (tp30) cc_final: 0.6172 (tp30) REVERT: C 180 LEU cc_start: 0.7424 (OUTLIER) cc_final: 0.7114 (mp) REVERT: C 222 LEU cc_start: 0.7674 (OUTLIER) cc_final: 0.7269 (tt) REVERT: C 235 LEU cc_start: 0.7666 (OUTLIER) cc_final: 0.7416 (mt) REVERT: C 374 LEU cc_start: 0.7750 (OUTLIER) cc_final: 0.7325 (mp) REVERT: C 511 ARG cc_start: 0.6421 (tpt90) cc_final: 0.5848 (ttp-170) REVERT: C 518 ASN cc_start: 0.7337 (OUTLIER) cc_final: 0.6941 (p0) REVERT: D 99 LEU cc_start: 0.7450 (OUTLIER) cc_final: 0.6896 (mp) REVERT: D 235 LEU cc_start: 0.7436 (OUTLIER) cc_final: 0.7080 (tt) REVERT: D 379 LEU cc_start: 0.7942 (OUTLIER) cc_final: 0.7685 (tt) REVERT: D 546 ARG cc_start: 0.8172 (OUTLIER) cc_final: 0.7946 (mtm-85) REVERT: D 561 GLN cc_start: 0.7579 (OUTLIER) cc_final: 0.7120 (pp30) REVERT: D 614 LEU cc_start: 0.8519 (OUTLIER) cc_final: 0.8276 (tt) REVERT: H 149 MET cc_start: 0.4735 (OUTLIER) cc_final: 0.4524 (ttp) REVERT: H 183 LEU cc_start: 0.7116 (OUTLIER) cc_final: 0.6540 (mt) REVERT: H 396 MET cc_start: 0.4897 (ttt) cc_final: 0.4534 (ttt) REVERT: H 459 MET cc_start: 0.7736 (ptp) cc_final: 0.7344 (ptp) REVERT: H 544 ARG cc_start: 0.7036 (ptp90) cc_final: 0.5331 (mmt180) REVERT: H 672 ASP cc_start: 0.3591 (p0) cc_final: 0.3200 (m-30) REVERT: G 527 PHE cc_start: 0.8126 (OUTLIER) cc_final: 0.7854 (m-80) REVERT: G 620 GLN cc_start: 0.8498 (OUTLIER) cc_final: 0.7668 (mt0) REVERT: G 682 SER cc_start: 0.8299 (m) cc_final: 0.8088 (t) REVERT: G 685 PHE cc_start: 0.8429 (t80) cc_final: 0.7918 (t80) REVERT: G 707 HIS cc_start: 0.5835 (m170) cc_final: 0.5210 (m90) REVERT: G 724 ASP cc_start: 0.8033 (m-30) cc_final: 0.7564 (m-30) REVERT: G 731 ASP cc_start: 0.8056 (m-30) cc_final: 0.7351 (t0) REVERT: G 787 CYS cc_start: 0.6939 (OUTLIER) cc_final: 0.6370 (m) REVERT: G 817 GLU cc_start: 0.6293 (mm-30) cc_final: 0.5944 (pt0) outliers start: 127 outliers final: 91 residues processed: 324 average time/residue: 0.1538 time to fit residues: 78.8470 Evaluate side-chains 317 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 112 poor density : 205 time to evaluate : 0.909 ------------------------------------------------------------------------------- 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 286 SER 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 75 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 117 LEU 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 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 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 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 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 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 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 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 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 149 MET 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 609 VAL 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 755 SER Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS 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 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 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 787 CYS Chi-restraints excluded: chain G residue 815 GLU 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 103 optimal weight: 0.0980 chunk 203 optimal weight: 0.8980 chunk 209 optimal weight: 0.7980 chunk 123 optimal weight: 3.9990 chunk 142 optimal weight: 1.9990 chunk 53 optimal weight: 0.0050 chunk 171 optimal weight: 0.8980 chunk 230 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 74 optimal weight: 0.0270 chunk 219 optimal weight: 9.9990 overall best weight: 0.3652 ------------------------------------------------------------------------------- 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 D 272 HIS ** H 478 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 = 0.4143 r_free = 0.4143 target = 0.188145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.137672 restraints weight = 26614.326| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135198 restraints weight = 23666.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.137437 restraints weight = 25224.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137446 restraints weight = 15061.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.138816 restraints weight = 13634.621| |-----------------------------------------------------------------------------| r_work (final): 0.3605 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2410 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= 0.098 Angle : 0.528 10.459 31358 Z= 0.261 Chirality : 0.038 0.179 3725 Planarity : 0.004 0.057 3926 Dihedral : 5.353 59.270 3135 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.45 % Favored : 94.48 % Rotamer: Outliers : 4.17 % Allowed : 28.09 % Favored : 67.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.26 (0.17), residues: 2845 helix: 1.20 (0.14), residues: 1592 sheet: -1.75 (0.32), residues: 267 loop : -2.03 (0.19), residues: 986 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 224 TYR 0.016 0.001 TYR H 387 PHE 0.043 0.001 PHE H 391 TRP 0.014 0.001 TRP H 903 HIS 0.005 0.000 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00222 (23108) covalent geometry : angle 0.52808 (31358) hydrogen bonds : bond 0.03150 ( 1055) hydrogen bonds : angle 3.79945 ( 3102) *********************** 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 333 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 227 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8712 (m-40) cc_final: 0.8269 (m110) REVERT: B 227 GLU cc_start: 0.8191 (OUTLIER) cc_final: 0.7801 (mt-10) REVERT: B 252 GLU cc_start: 0.8140 (OUTLIER) cc_final: 0.7156 (mt-10) REVERT: B 258 GLU cc_start: 0.8031 (OUTLIER) cc_final: 0.5846 (tm-30) REVERT: C 137 GLN cc_start: 0.7094 (OUTLIER) cc_final: 0.6470 (mp10) REVERT: C 149 GLU cc_start: 0.6407 (tp30) cc_final: 0.6131 (tp30) REVERT: C 180 LEU cc_start: 0.7492 (OUTLIER) cc_final: 0.7188 (mp) REVERT: C 222 LEU cc_start: 0.7646 (OUTLIER) cc_final: 0.7228 (tt) REVERT: C 374 LEU cc_start: 0.7633 (OUTLIER) cc_final: 0.7267 (mp) REVERT: C 511 ARG cc_start: 0.6410 (tpt90) cc_final: 0.5837 (ttp-170) REVERT: D 99 LEU cc_start: 0.7519 (OUTLIER) cc_final: 0.6975 (mp) REVERT: D 118 GLU cc_start: 0.7241 (mp0) cc_final: 0.6953 (mp0) REVERT: D 379 LEU cc_start: 0.8001 (OUTLIER) cc_final: 0.7754 (tt) REVERT: D 546 ARG cc_start: 0.8162 (OUTLIER) cc_final: 0.7945 (mtm-85) REVERT: D 561 GLN cc_start: 0.7578 (OUTLIER) cc_final: 0.7108 (pp30) REVERT: D 614 LEU cc_start: 0.8502 (OUTLIER) cc_final: 0.8288 (tt) REVERT: H 183 LEU cc_start: 0.6974 (OUTLIER) cc_final: 0.6422 (mt) REVERT: H 396 MET cc_start: 0.5144 (ttt) cc_final: 0.4829 (ttt) REVERT: H 459 MET cc_start: 0.7584 (ptp) cc_final: 0.7185 (ptp) REVERT: H 529 LYS cc_start: 0.8778 (mmtt) cc_final: 0.8450 (ttpt) REVERT: H 544 ARG cc_start: 0.7093 (ptp90) cc_final: 0.5340 (mmt180) REVERT: H 672 ASP cc_start: 0.3514 (p0) cc_final: 0.3214 (m-30) REVERT: G 620 GLN cc_start: 0.8389 (OUTLIER) cc_final: 0.7245 (mt0) REVERT: G 685 PHE cc_start: 0.8371 (t80) cc_final: 0.7909 (t80) REVERT: G 707 HIS cc_start: 0.5852 (m170) cc_final: 0.5233 (m90) REVERT: G 724 ASP cc_start: 0.8127 (m-30) cc_final: 0.7637 (m-30) REVERT: G 731 ASP cc_start: 0.7968 (m-30) cc_final: 0.7340 (t0) REVERT: G 787 CYS cc_start: 0.6774 (OUTLIER) cc_final: 0.6312 (m) REVERT: G 817 GLU cc_start: 0.6242 (mm-30) cc_final: 0.5971 (pt0) outliers start: 106 outliers final: 74 residues processed: 317 average time/residue: 0.1535 time to fit residues: 77.5010 Evaluate side-chains 298 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 89 poor density : 209 time to evaluate : 0.856 ------------------------------------------------------------------------------- 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 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 44 LEU Chi-restraints excluded: chain B residue 75 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 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 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 137 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 533 ILE Chi-restraints excluded: chain D residue 66 LEU 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 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 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 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 867 LEU 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 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 787 CYS Chi-restraints excluded: chain G residue 815 GLU 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 251 optimal weight: 0.8980 chunk 107 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 198 optimal weight: 3.9990 chunk 241 optimal weight: 2.9990 chunk 137 optimal weight: 7.9990 chunk 60 optimal weight: 5.9990 chunk 200 optimal weight: 0.0170 chunk 115 optimal weight: 0.8980 chunk 143 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- 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 D 272 HIS ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 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 = 0.4140 r_free = 0.4140 target = 0.187657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.137421 restraints weight = 26511.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.135073 restraints weight = 25138.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.137163 restraints weight = 26187.657| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.137203 restraints weight = 15616.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3618 r_free = 0.3618 target = 0.138165 restraints weight = 14371.189| |-----------------------------------------------------------------------------| r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2494 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 23108 Z= 0.107 Angle : 0.531 9.861 31358 Z= 0.261 Chirality : 0.038 0.179 3725 Planarity : 0.004 0.080 3926 Dihedral : 5.270 59.792 3131 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.34 % Favored : 94.59 % Rotamer: Outliers : 4.32 % Allowed : 28.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.17), residues: 2845 helix: 1.27 (0.14), residues: 1588 sheet: -1.66 (0.32), residues: 266 loop : -1.97 (0.19), residues: 991 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 224 TYR 0.016 0.001 TYR H 387 PHE 0.018 0.001 PHE A 330 TRP 0.014 0.001 TRP H 367 HIS 0.008 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00253 (23108) covalent geometry : angle 0.53145 (31358) hydrogen bonds : bond 0.03167 ( 1055) hydrogen bonds : angle 3.76494 ( 3102) *********************** 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 329 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 110 poor density : 219 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 ASN cc_start: 0.8697 (m-40) cc_final: 0.8248 (m110) REVERT: B 227 GLU cc_start: 0.8202 (OUTLIER) cc_final: 0.7818 (mt-10) REVERT: B 252 GLU cc_start: 0.8139 (OUTLIER) cc_final: 0.7153 (mt-10) REVERT: B 258 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.5824 (tm-30) REVERT: C 137 GLN cc_start: 0.7072 (OUTLIER) cc_final: 0.6449 (mp10) REVERT: C 180 LEU cc_start: 0.7496 (OUTLIER) cc_final: 0.7194 (mp) REVERT: C 222 LEU cc_start: 0.7639 (OUTLIER) cc_final: 0.7221 (tt) REVERT: C 235 LEU cc_start: 0.7735 (OUTLIER) cc_final: 0.7499 (mt) REVERT: C 374 LEU cc_start: 0.7648 (OUTLIER) cc_final: 0.7273 (mp) REVERT: C 511 ARG cc_start: 0.6430 (tpt90) cc_final: 0.5852 (ttp-170) REVERT: D 99 LEU cc_start: 0.7524 (OUTLIER) cc_final: 0.6963 (mp) REVERT: D 118 GLU cc_start: 0.7504 (mp0) cc_final: 0.7228 (mp0) REVERT: D 546 ARG cc_start: 0.8174 (OUTLIER) cc_final: 0.7959 (mtm-85) REVERT: D 561 GLN cc_start: 0.7568 (OUTLIER) cc_final: 0.7107 (pp30) REVERT: D 614 LEU cc_start: 0.8525 (OUTLIER) cc_final: 0.8301 (tt) REVERT: H 183 LEU cc_start: 0.6965 (OUTLIER) cc_final: 0.6372 (mt) REVERT: H 396 MET cc_start: 0.5189 (ttt) cc_final: 0.4880 (ttt) REVERT: H 459 MET cc_start: 0.7553 (ptp) cc_final: 0.7155 (ptp) REVERT: H 481 ARG cc_start: 0.7795 (ptm160) cc_final: 0.7022 (ptp90) REVERT: H 529 LYS cc_start: 0.8801 (mmtt) cc_final: 0.8522 (ttpt) REVERT: H 544 ARG cc_start: 0.7074 (ptp90) cc_final: 0.5347 (mmt180) REVERT: H 672 ASP cc_start: 0.3463 (p0) cc_final: 0.3172 (m-30) REVERT: G 620 GLN cc_start: 0.8490 (OUTLIER) cc_final: 0.7323 (mt0) REVERT: G 685 PHE cc_start: 0.8348 (t80) cc_final: 0.7932 (t80) REVERT: G 707 HIS cc_start: 0.5833 (m170) cc_final: 0.5235 (m90) REVERT: G 724 ASP cc_start: 0.7976 (m-30) cc_final: 0.7532 (m-30) REVERT: G 731 ASP cc_start: 0.7971 (m-30) cc_final: 0.7359 (t0) REVERT: G 787 CYS cc_start: 0.6815 (OUTLIER) cc_final: 0.6341 (m) REVERT: G 817 GLU cc_start: 0.6199 (mm-30) cc_final: 0.5927 (pt0) outliers start: 110 outliers final: 84 residues processed: 313 average time/residue: 0.1525 time to fit residues: 75.7025 Evaluate side-chains 309 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 99 poor density : 210 time to evaluate : 0.846 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 314 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 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 75 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 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 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 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 307 VAL 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 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 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 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 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 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS 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 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 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 56 optimal weight: 0.6980 chunk 226 optimal weight: 0.9980 chunk 42 optimal weight: 4.9990 chunk 251 optimal weight: 2.9990 chunk 120 optimal weight: 3.9990 chunk 37 optimal weight: 0.0050 chunk 207 optimal weight: 0.8980 chunk 261 optimal weight: 0.9990 chunk 234 optimal weight: 5.9990 chunk 132 optimal weight: 4.9990 chunk 51 optimal weight: 3.9990 overall best weight: 0.7196 ------------------------------------------------------------------------------- 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 ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.187422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.136831 restraints weight = 26666.313| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.133405 restraints weight = 25030.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.136000 restraints weight = 25720.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3595 r_free = 0.3595 target = 0.136036 restraints weight = 15769.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.140064 restraints weight = 14218.896| |-----------------------------------------------------------------------------| r_work (final): 0.3615 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 23108 Z= 0.109 Angle : 0.527 9.688 31358 Z= 0.259 Chirality : 0.038 0.179 3725 Planarity : 0.004 0.070 3926 Dihedral : 5.167 59.622 3127 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.48 % Favored : 94.45 % Rotamer: Outliers : 4.17 % Allowed : 28.21 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.17), residues: 2845 helix: 1.33 (0.14), residues: 1588 sheet: -1.66 (0.32), residues: 273 loop : -1.94 (0.19), residues: 984 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 224 TYR 0.014 0.001 TYR H 387 PHE 0.040 0.001 PHE H 391 TRP 0.015 0.001 TRP H 367 HIS 0.007 0.001 HIS B 338 Details of bonding type rmsd covalent geometry : bond 0.00260 (23108) covalent geometry : angle 0.52666 (31358) hydrogen bonds : bond 0.03144 ( 1055) hydrogen bonds : angle 3.70971 ( 3102) *********************** 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 323 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 106 poor density : 217 time to evaluate : 0.818 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.8031 (tpp) cc_final: 0.7356 (tpp) REVERT: A 24 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7208 (mt-10) REVERT: A 60 ASN cc_start: 0.8738 (m-40) cc_final: 0.8291 (m110) REVERT: B 227 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7843 (mt-10) REVERT: B 252 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7185 (mt-10) REVERT: B 258 GLU cc_start: 0.7926 (OUTLIER) cc_final: 0.5737 (tm-30) REVERT: C 137 GLN cc_start: 0.6992 (OUTLIER) cc_final: 0.6334 (mp10) REVERT: C 149 GLU cc_start: 0.6380 (tp30) cc_final: 0.6103 (tp30) REVERT: C 180 LEU cc_start: 0.7263 (OUTLIER) cc_final: 0.6981 (mp) REVERT: C 222 LEU cc_start: 0.7534 (OUTLIER) cc_final: 0.7113 (tt) REVERT: C 235 LEU cc_start: 0.7619 (OUTLIER) cc_final: 0.7382 (mt) REVERT: C 374 LEU cc_start: 0.7561 (OUTLIER) cc_final: 0.7177 (mp) REVERT: C 511 ARG cc_start: 0.6408 (tpt90) cc_final: 0.5803 (ttp-170) REVERT: D 99 LEU cc_start: 0.7328 (OUTLIER) cc_final: 0.6790 (mp) REVERT: D 118 GLU cc_start: 0.7316 (mp0) cc_final: 0.7023 (mp0) REVERT: D 379 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7593 (tt) REVERT: D 546 ARG cc_start: 0.8099 (OUTLIER) cc_final: 0.7873 (mtm-85) REVERT: D 561 GLN cc_start: 0.7541 (OUTLIER) cc_final: 0.7061 (pp30) REVERT: D 614 LEU cc_start: 0.8444 (OUTLIER) cc_final: 0.8201 (tt) REVERT: H 149 MET cc_start: 0.5310 (mmt) cc_final: 0.4969 (ttt) REVERT: H 183 LEU cc_start: 0.7098 (OUTLIER) cc_final: 0.6502 (mt) REVERT: H 396 MET cc_start: 0.4952 (ttt) cc_final: 0.4705 (ttt) REVERT: H 459 MET cc_start: 0.7668 (ptp) cc_final: 0.7316 (ptp) REVERT: H 529 LYS cc_start: 0.8840 (mmtt) cc_final: 0.8386 (ttpt) REVERT: H 544 ARG cc_start: 0.7044 (ptp90) cc_final: 0.5321 (mmt180) REVERT: H 572 GLN cc_start: 0.7591 (mm-40) cc_final: 0.7306 (mt0) REVERT: H 672 ASP cc_start: 0.3556 (p0) cc_final: 0.3272 (m-30) REVERT: G 620 GLN cc_start: 0.8348 (OUTLIER) cc_final: 0.7168 (mt0) REVERT: G 674 LEU cc_start: 0.7515 (tp) cc_final: 0.6949 (tt) REVERT: G 685 PHE cc_start: 0.8289 (t80) cc_final: 0.7986 (t80) REVERT: G 724 ASP cc_start: 0.8007 (m-30) cc_final: 0.7572 (m-30) REVERT: G 731 ASP cc_start: 0.8026 (m-30) cc_final: 0.7330 (t0) REVERT: G 787 CYS cc_start: 0.6893 (OUTLIER) cc_final: 0.6441 (m) REVERT: G 817 GLU cc_start: 0.6208 (mm-30) cc_final: 0.5880 (pt0) outliers start: 106 outliers final: 86 residues processed: 308 average time/residue: 0.1467 time to fit residues: 72.4266 Evaluate side-chains 314 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 102 poor density : 212 time to evaluate : 0.763 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 314 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 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 75 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 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 284 LEU Chi-restraints excluded: chain B residue 295 LEU Chi-restraints excluded: chain B residue 298 VAL Chi-restraints excluded: chain B residue 329 ASP Chi-restraints excluded: chain B residue 383 LEU 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 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 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 533 ILE Chi-restraints excluded: chain D residue 66 LEU 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 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 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 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS 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 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 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 787 CYS Chi-restraints excluded: chain G residue 815 GLU 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 203 optimal weight: 3.9990 chunk 273 optimal weight: 1.9990 chunk 229 optimal weight: 1.9990 chunk 198 optimal weight: 2.9990 chunk 213 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 86 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 208 optimal weight: 0.7980 chunk 264 optimal weight: 4.9990 chunk 94 optimal weight: 0.0050 overall best weight: 1.1598 ------------------------------------------------------------------------------- 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 ** B 268 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 272 HIS ** H 478 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 754 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 493 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 558 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4104 r_free = 0.4104 target = 0.183165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3579 r_free = 0.3579 target = 0.132400 restraints weight = 26560.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.127990 restraints weight = 25315.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.130856 restraints weight = 22638.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.130881 restraints weight = 13800.796| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.131546 restraints weight = 12800.566| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7790 moved from start: 0.2588 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= 0.138 Angle : 0.550 9.220 31358 Z= 0.271 Chirality : 0.039 0.180 3725 Planarity : 0.004 0.078 3926 Dihedral : 5.212 59.245 3127 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.73 % Favored : 94.20 % Rotamer: Outliers : 3.97 % Allowed : 28.49 % Favored : 67.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.16 (0.17), residues: 2845 helix: 1.30 (0.14), residues: 1588 sheet: -1.75 (0.31), residues: 276 loop : -1.98 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 224 TYR 0.014 0.001 TYR H 171 PHE 0.038 0.001 PHE H 391 TRP 0.018 0.001 TRP G 487 HIS 0.009 0.001 HIS D 272 Details of bonding type rmsd covalent geometry : bond 0.00339 (23108) covalent geometry : angle 0.55018 (31358) hydrogen bonds : bond 0.03382 ( 1055) hydrogen bonds : angle 3.75517 ( 3102) ********************** 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 316 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 101 poor density : 215 time to evaluate : 0.902 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 5 MET cc_start: 0.7999 (tpp) cc_final: 0.7284 (tpp) REVERT: A 24 GLU cc_start: 0.7586 (mt-10) cc_final: 0.7183 (mt-10) REVERT: A 60 ASN cc_start: 0.8753 (m-40) cc_final: 0.8317 (m110) REVERT: B 227 GLU cc_start: 0.8233 (OUTLIER) cc_final: 0.7838 (mt-10) REVERT: B 252 GLU cc_start: 0.8192 (OUTLIER) cc_final: 0.7177 (mt-10) REVERT: B 258 GLU cc_start: 0.7982 (OUTLIER) cc_final: 0.5795 (tm-30) REVERT: C 137 GLN cc_start: 0.6997 (OUTLIER) cc_final: 0.6382 (mp10) REVERT: C 149 GLU cc_start: 0.6513 (tp30) cc_final: 0.6214 (tp30) REVERT: C 180 LEU cc_start: 0.7502 (OUTLIER) cc_final: 0.7132 (mp) REVERT: C 210 CYS cc_start: 0.7089 (t) cc_final: 0.6408 (t) REVERT: C 222 LEU cc_start: 0.7587 (OUTLIER) cc_final: 0.7160 (tt) REVERT: C 235 LEU cc_start: 0.7665 (OUTLIER) cc_final: 0.7422 (mt) REVERT: C 374 LEU cc_start: 0.7771 (OUTLIER) cc_final: 0.7352 (mp) REVERT: C 511 ARG cc_start: 0.6463 (tpt90) cc_final: 0.5881 (ttp-170) REVERT: D 99 LEU cc_start: 0.7354 (OUTLIER) cc_final: 0.6808 (mp) REVERT: D 118 GLU cc_start: 0.7407 (mp0) cc_final: 0.7124 (mp0) REVERT: D 379 LEU cc_start: 0.8013 (OUTLIER) cc_final: 0.7769 (tt) REVERT: D 546 ARG cc_start: 0.8175 (OUTLIER) cc_final: 0.7960 (mtm-85) REVERT: D 561 GLN cc_start: 0.7534 (OUTLIER) cc_final: 0.7070 (pp30) REVERT: D 614 LEU cc_start: 0.8531 (OUTLIER) cc_final: 0.8310 (tt) REVERT: H 183 LEU cc_start: 0.7075 (OUTLIER) cc_final: 0.6482 (mt) REVERT: H 396 MET cc_start: 0.5042 (ttt) cc_final: 0.4841 (ttt) REVERT: H 459 MET cc_start: 0.7597 (ptp) cc_final: 0.7198 (ptp) REVERT: H 529 LYS cc_start: 0.8838 (mmtt) cc_final: 0.8428 (ttpt) REVERT: H 544 ARG cc_start: 0.7373 (ptp90) cc_final: 0.5454 (mmt180) REVERT: H 672 ASP cc_start: 0.3531 (p0) cc_final: 0.3267 (m-30) REVERT: G 461 ARG cc_start: 0.4248 (tpt170) cc_final: 0.3811 (tpp-160) REVERT: G 620 GLN cc_start: 0.8578 (OUTLIER) cc_final: 0.7554 (mt0) REVERT: G 674 LEU cc_start: 0.7561 (tp) cc_final: 0.6994 (tt) REVERT: G 685 PHE cc_start: 0.8349 (t80) cc_final: 0.7921 (t80) REVERT: G 724 ASP cc_start: 0.8035 (m-30) cc_final: 0.7578 (m-30) REVERT: G 731 ASP cc_start: 0.8019 (m-30) cc_final: 0.7385 (t0) outliers start: 101 outliers final: 82 residues processed: 302 average time/residue: 0.1688 time to fit residues: 80.6756 Evaluate side-chains 307 residues out of total 2545 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 97 poor density : 210 time to evaluate : 0.903 ------------------------------------------------------------------------------- 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 289 HIS Chi-restraints excluded: chain A residue 292 THR Chi-restraints excluded: chain A residue 314 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 33 THR Chi-restraints excluded: chain B residue 38 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 75 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 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 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 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 307 VAL 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 533 ILE Chi-restraints excluded: chain D residue 66 LEU 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 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 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 753 LEU Chi-restraints excluded: chain H residue 778 VAL Chi-restraints excluded: chain H residue 785 HIS 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 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 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 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 152 optimal weight: 0.6980 chunk 171 optimal weight: 7.9990 chunk 276 optimal weight: 0.7980 chunk 158 optimal weight: 2.9990 chunk 234 optimal weight: 2.9990 chunk 157 optimal weight: 0.8980 chunk 174 optimal weight: 20.0000 chunk 197 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 186 optimal weight: 4.9990 chunk 214 optimal weight: 2.9990 overall best weight: 1.6784 ------------------------------------------------------------------------------- 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 ** 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 754 GLN ** 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 = 0.4102 r_free = 0.4102 target = 0.185520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.133924 restraints weight = 27177.855| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.129409 restraints weight = 23834.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.131976 restraints weight = 25373.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.132192 restraints weight = 15173.661| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.135449 restraints weight = 13450.323| |-----------------------------------------------------------------------------| r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 23108 Z= 0.178 Angle : 0.590 9.115 31358 Z= 0.292 Chirality : 0.041 0.181 3725 Planarity : 0.005 0.078 3926 Dihedral : 5.370 58.928 3127 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.07 % Allowed : 6.15 % Favored : 93.78 % Rotamer: Outliers : 3.97 % Allowed : 28.41 % Favored : 67.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.31 (0.16), residues: 2845 helix: 1.19 (0.14), residues: 1589 sheet: -1.86 (0.31), residues: 275 loop : -2.07 (0.19), residues: 981 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG D 224 TYR 0.017 0.001 TYR B 61 PHE 0.023 0.002 PHE A 330 TRP 0.017 0.001 TRP H 367 HIS 0.008 0.001 HIS A 135 Details of bonding type rmsd covalent geometry : bond 0.00447 (23108) covalent geometry : angle 0.58979 (31358) hydrogen bonds : bond 0.03798 ( 1055) hydrogen bonds : angle 3.88492 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3514.44 seconds wall clock time: 61 minutes 38.05 seconds (3698.05 seconds total)