Starting phenix.real_space_refine on Sun Mar 17 08:29:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogp_12885/03_2024/7ogp_12885.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogp_12885/03_2024/7ogp_12885.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogp_12885/03_2024/7ogp_12885.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogp_12885/03_2024/7ogp_12885.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogp_12885/03_2024/7ogp_12885.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ogp_12885/03_2024/7ogp_12885.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians Zn 1 6.06 5 S 87 5.16 5 C 10927 2.51 5 N 2975 2.21 5 O 3181 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 9": "OD1" <-> "OD2" Residue "A GLU 12": "OE1" <-> "OE2" Residue "A GLU 36": "OE1" <-> "OE2" Residue "A TYR 43": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 150": "NH1" <-> "NH2" Residue "A ASP 231": "OD1" <-> "OD2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A ARG 338": "NH1" <-> "NH2" Residue "A ARG 384": "NH1" <-> "NH2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A ASP 419": "OD1" <-> "OD2" Residue "A ASP 421": "OD1" <-> "OD2" Residue "A GLU 438": "OE1" <-> "OE2" Residue "A GLU 460": "OE1" <-> "OE2" Residue "A GLU 482": "OE1" <-> "OE2" Residue "A GLU 483": "OE1" <-> "OE2" Residue "B ASP 436": "OD1" <-> "OD2" Residue "B ASP 439": "OD1" <-> "OD2" Residue "B GLU 491": "OE1" <-> "OE2" Residue "C ARG 7": "NH1" <-> "NH2" Residue "C GLU 8": "OE1" <-> "OE2" Residue "C ASP 20": "OD1" <-> "OD2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C ARG 68": "NH1" <-> "NH2" Residue "C ARG 80": "NH1" <-> "NH2" Residue "C ARG 92": "NH1" <-> "NH2" Residue "C TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 125": "OD1" <-> "OD2" Residue "C GLU 182": "OE1" <-> "OE2" Residue "C ARG 194": "NH1" <-> "NH2" Residue "C ARG 209": "NH1" <-> "NH2" Residue "C ARG 234": "NH1" <-> "NH2" Residue "C ARG 243": "NH1" <-> "NH2" Residue "C ASP 244": "OD1" <-> "OD2" Residue "C ASP 247": "OD1" <-> "OD2" Residue "C ARG 257": "NH1" <-> "NH2" Residue "C ARG 264": "NH1" <-> "NH2" Residue "C ARG 268": "NH1" <-> "NH2" Residue "C ARG 285": "NH1" <-> "NH2" Residue "C ASP 286": "OD1" <-> "OD2" Residue "C ARG 288": "NH1" <-> "NH2" Residue "C ARG 314": "NH1" <-> "NH2" Residue "C GLU 315": "OE1" <-> "OE2" Residue "C ARG 321": "NH1" <-> "NH2" Residue "C ARG 326": "NH1" <-> "NH2" Residue "C ARG 327": "NH1" <-> "NH2" Residue "C ASP 329": "OD1" <-> "OD2" Residue "C GLU 336": "OE1" <-> "OE2" Residue "C ARG 339": "NH1" <-> "NH2" Residue "C ASP 352": "OD1" <-> "OD2" Residue "C ARG 355": "NH1" <-> "NH2" Residue "C ARG 359": "NH1" <-> "NH2" Residue "C ARG 362": "NH1" <-> "NH2" Residue "C ASP 364": "OD1" <-> "OD2" Residue "C ARG 370": "NH1" <-> "NH2" Residue "C ARG 414": "NH1" <-> "NH2" Residue "C ASP 416": "OD1" <-> "OD2" Residue "C ARG 426": "NH1" <-> "NH2" Residue "C ARG 427": "NH1" <-> "NH2" Residue "C ARG 432": "NH1" <-> "NH2" Residue "C ARG 443": "NH1" <-> "NH2" Residue "C ARG 450": "NH1" <-> "NH2" Residue "C ASP 456": "OD1" <-> "OD2" Residue "C ASP 540": "OD1" <-> "OD2" Residue "C ARG 543": "NH1" <-> "NH2" Residue "C ARG 552": "NH1" <-> "NH2" Residue "C GLU 580": "OE1" <-> "OE2" Residue "C ASP 581": "OD1" <-> "OD2" Residue "C GLU 611": "OE1" <-> "OE2" Residue "C GLU 695": "OE1" <-> "OE2" Residue "D ARG 72": "NH1" <-> "NH2" Residue "D ASP 76": "OD1" <-> "OD2" Residue "D ARG 88": "NH1" <-> "NH2" Residue "D ASP 107": "OD1" <-> "OD2" Residue "D ARG 159": "NH1" <-> "NH2" Residue "D ARG 200": "NH1" <-> "NH2" Residue "D GLU 207": "OE1" <-> "OE2" Residue "D ARG 216": "NH1" <-> "NH2" Residue "D ASP 225": "OD1" <-> "OD2" Residue "D ARG 250": "NH1" <-> "NH2" Residue "D GLU 261": "OE1" <-> "OE2" Residue "D ARG 264": "NH1" <-> "NH2" Residue "D ARG 282": "NH1" <-> "NH2" Residue "D ARG 322": "NH1" <-> "NH2" Residue "D ARG 356": "NH1" <-> "NH2" Residue "D ASP 377": "OD1" <-> "OD2" Residue "D GLU 589": "OE1" <-> "OE2" Residue "D ASP 614": "OD1" <-> "OD2" Residue "D ASP 664": "OD1" <-> "OD2" Residue "E GLU 12": "OE1" <-> "OE2" Residue "E GLU 28": "OE1" <-> "OE2" Residue "E ARG 33": "NH1" <-> "NH2" Residue "E ARG 44": "NH1" <-> "NH2" Residue "E ASP 51": "OD1" <-> "OD2" Residue "E ARG 67": "NH1" <-> "NH2" Residue "E ARG 80": "NH1" <-> "NH2" Residue "E ARG 86": "NH1" <-> "NH2" Residue "E ARG 121": "NH1" <-> "NH2" Residue "E ARG 156": "NH1" <-> "NH2" Residue "E GLU 326": "OE1" <-> "OE2" Residue "E GLU 363": "OE1" <-> "OE2" Residue "E GLU 379": "OE1" <-> "OE2" Residue "E GLU 420": "OE1" <-> "OE2" Residue "E ASP 441": "OD1" <-> "OD2" Residue "E GLU 444": "OE1" <-> "OE2" Residue "E ARG 510": "NH1" <-> "NH2" Residue "E ARG 530": "NH1" <-> "NH2" Residue "E GLU 531": "OE1" <-> "OE2" Residue "E ARG 541": "NH1" <-> "NH2" Time to flip residues: 0.06s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 17171 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 2932 Number of conformers: 1 Conformer: "" Number of residues, atoms: 361, 2932 Classifications: {'peptide': 361} Link IDs: {'PTRANS': 17, 'TRANS': 343} Chain breaks: 3 Chain: "B" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 203, 1619 Classifications: {'peptide': 203} Link IDs: {'PTRANS': 9, 'TRANS': 193} Chain breaks: 1 Chain: "C" Number of atoms: 5482 Number of conformers: 1 Conformer: "" Number of residues, atoms: 693, 5482 Classifications: {'peptide': 693} Link IDs: {'PTRANS': 41, 'TRANS': 651} Chain breaks: 1 Chain: "D" Number of atoms: 4110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 510, 4110 Classifications: {'peptide': 510} Link IDs: {'PTRANS': 22, 'TRANS': 487} Chain breaks: 1 Chain: "E" Number of atoms: 3027 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3027 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 16, 'TRANS': 360} Chain breaks: 2 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'HIS:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12397 SG CYS D 288 27.168 82.638 18.330 1.00114.84 S ATOM 12831 SG CYS D 341 26.654 81.151 21.553 1.00112.95 S ATOM 12897 SG CYS D 350 30.298 83.034 19.593 1.00107.75 S ATOM 12918 SG CYS D 353 28.107 83.820 21.262 1.00104.38 S Time building chain proxies: 9.19, per 1000 atoms: 0.54 Number of scatterers: 17171 At special positions: 0 Unit cell: (119.85, 137.7, 114.75, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) Zn 1 29.99 S 87 16.00 O 3181 8.00 N 2975 7.00 C 10927 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 - 3.50 Amino acid : False - 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: 6.29 Conformation dependent library (CDL) restraints added in 3.2 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN D 701 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 341 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 350 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 353 " pdb="ZN ZN D 701 " - pdb=" SG CYS D 288 " Number of angles added : 6 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 4030 Finding SS restraints... Secondary structure from input PDB file: 90 helices and 19 sheets defined 41.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.97 Creating SS restraints... Processing helix chain 'A' and resid 9 through 14 removed outlier: 3.652A pdb=" N HIS A 14 " --> pdb=" O HIS A 10 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 156 removed outlier: 4.375A pdb=" N GLY A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 194 removed outlier: 3.847A pdb=" N ASN A 194 " --> pdb=" O PHE A 190 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 211 removed outlier: 3.559A pdb=" N CYS A 210 " --> pdb=" O SER A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 273 removed outlier: 3.819A pdb=" N ASN A 253 " --> pdb=" O ILE A 249 " (cutoff:3.500A) removed outlier: 3.584A pdb=" N MET A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 321 removed outlier: 3.745A pdb=" N GLN A 319 " --> pdb=" O GLY A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 322 through 333 Processing helix chain 'A' and resid 336 through 347 removed outlier: 3.570A pdb=" N ASN A 347 " --> pdb=" O PHE A 343 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 365 removed outlier: 3.578A pdb=" N ALA A 356 " --> pdb=" O ASN A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 385 No H-bonds generated for 'chain 'A' and resid 383 through 385' Processing helix chain 'A' and resid 408 through 412 removed outlier: 4.131A pdb=" N LYS A 412 " --> pdb=" O LEU A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 430 through 437 Processing helix chain 'A' and resid 438 through 440 No H-bonds generated for 'chain 'A' and resid 438 through 440' Processing helix chain 'A' and resid 456 through 460 removed outlier: 3.520A pdb=" N LEU A 459 " --> pdb=" O SER A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 474 removed outlier: 3.833A pdb=" N THR A 468 " --> pdb=" O PRO A 464 " (cutoff:3.500A) removed outlier: 4.037A pdb=" N ILE A 469 " --> pdb=" O VAL A 465 " (cutoff:3.500A) Processing helix chain 'A' and resid 480 through 485 removed outlier: 3.718A pdb=" N LEU A 485 " --> pdb=" O LEU A 481 " (cutoff:3.500A) Processing helix chain 'B' and resid 313 through 322 removed outlier: 3.831A pdb=" N ALA B 317 " --> pdb=" O GLY B 313 " (cutoff:3.500A) removed outlier: 3.511A pdb=" N TYR B 318 " --> pdb=" O ASP B 314 " (cutoff:3.500A) Processing helix chain 'B' and resid 324 through 331 Processing helix chain 'B' and resid 337 through 346 removed outlier: 3.860A pdb=" N CYS B 344 " --> pdb=" O LEU B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 347 through 354 removed outlier: 3.596A pdb=" N VAL B 350 " --> pdb=" O CYS B 347 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N THR B 351 " --> pdb=" O VAL B 348 " (cutoff:3.500A) removed outlier: 4.197A pdb=" N ALA B 352 " --> pdb=" O ALA B 349 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N THR B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 357 through 367 removed outlier: 3.720A pdb=" N VAL B 367 " --> pdb=" O LEU B 363 " (cutoff:3.500A) Processing helix chain 'B' and resid 374 through 380 removed outlier: 3.960A pdb=" N SER B 378 " --> pdb=" O ARG B 375 " (cutoff:3.500A) removed outlier: 4.131A pdb=" N ILE B 380 " --> pdb=" O PHE B 377 " (cutoff:3.500A) Processing helix chain 'B' and resid 381 through 399 removed outlier: 3.655A pdb=" N HIS B 387 " --> pdb=" O ASN B 383 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 408 removed outlier: 3.813A pdb=" N MET B 408 " --> pdb=" O ALA B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 434 through 442 Processing helix chain 'B' and resid 460 through 474 Processing helix chain 'B' and resid 483 through 490 Processing helix chain 'B' and resid 504 through 521 removed outlier: 3.873A pdb=" N ILE B 509 " --> pdb=" O ILE B 505 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR B 510 " --> pdb=" O LYS B 506 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N ASN B 520 " --> pdb=" O LEU B 516 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 20 removed outlier: 3.639A pdb=" N LEU C 19 " --> pdb=" O HIS C 16 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N ASP C 20 " --> pdb=" O THR C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 16 through 20' Processing helix chain 'C' and resid 27 through 38 removed outlier: 3.520A pdb=" N VAL C 35 " --> pdb=" O GLY C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 56 through 61 removed outlier: 3.658A pdb=" N ALA C 61 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 removed outlier: 3.776A pdb=" N GLU C 138 " --> pdb=" O ARG C 134 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N THR C 139 " --> pdb=" O GLU C 135 " (cutoff:3.500A) Processing helix chain 'C' and resid 189 through 193 removed outlier: 3.619A pdb=" N LYS C 193 " --> pdb=" O LYS C 189 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 189 through 193' Processing helix chain 'C' and resid 249 through 254 Processing helix chain 'C' and resid 299 through 327 removed outlier: 3.938A pdb=" N VAL C 303 " --> pdb=" O ASP C 299 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N TYR C 305 " --> pdb=" O GLN C 301 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N HIS C 308 " --> pdb=" O LYS C 304 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N TYR C 320 " --> pdb=" O LEU C 316 " (cutoff:3.500A) Processing helix chain 'C' and resid 336 through 348 Processing helix chain 'C' and resid 422 through 428 removed outlier: 4.049A pdb=" N ARG C 426 " --> pdb=" O GLY C 422 " (cutoff:3.500A) Processing helix chain 'C' and resid 430 through 453 removed outlier: 3.643A pdb=" N TYR C 434 " --> pdb=" O TYR C 430 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N GLY C 439 " --> pdb=" O GLU C 435 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ALA C 440 " --> pdb=" O HIS C 436 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ASP C 444 " --> pdb=" O ALA C 440 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N LEU C 445 " --> pdb=" O ALA C 441 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N ALA C 453 " --> pdb=" O LEU C 449 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 470 removed outlier: 3.693A pdb=" N SER C 468 " --> pdb=" O GLN C 464 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N MET C 470 " --> pdb=" O LEU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 472 through 491 Processing helix chain 'C' and resid 491 through 498 Processing helix chain 'C' and resid 504 through 515 removed outlier: 3.523A pdb=" N VAL C 508 " --> pdb=" O PRO C 504 " (cutoff:3.500A) removed outlier: 4.351A pdb=" N ASP C 514 " --> pdb=" O THR C 510 " (cutoff:3.500A) Processing helix chain 'C' and resid 528 through 538 Processing helix chain 'C' and resid 618 through 628 Processing helix chain 'C' and resid 632 through 643 removed outlier: 3.935A pdb=" N GLU C 636 " --> pdb=" O GLY C 632 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE C 637 " --> pdb=" O PRO C 633 " (cutoff:3.500A) removed outlier: 4.085A pdb=" N LEU C 638 " --> pdb=" O THR C 634 " (cutoff:3.500A) removed outlier: 3.938A pdb=" N THR C 641 " --> pdb=" O ILE C 637 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASN C 643 " --> pdb=" O ASP C 639 " (cutoff:3.500A) Processing helix chain 'C' and resid 643 through 657 removed outlier: 3.770A pdb=" N ILE C 651 " --> pdb=" O HIS C 647 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N ALA C 657 " --> pdb=" O SER C 653 " (cutoff:3.500A) Processing helix chain 'C' and resid 677 through 689 Processing helix chain 'D' and resid 7 through 13 removed outlier: 4.037A pdb=" N LEU D 11 " --> pdb=" O LYS D 7 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N LEU D 12 " --> pdb=" O ALA D 8 " (cutoff:3.500A) Processing helix chain 'D' and resid 15 through 21 removed outlier: 3.980A pdb=" N TRP D 20 " --> pdb=" O TYR D 16 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N SER D 21 " --> pdb=" O ASP D 17 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 50 removed outlier: 4.090A pdb=" N LEU D 46 " --> pdb=" O ARG D 42 " (cutoff:3.500A) Processing helix chain 'D' and resid 51 through 55 Processing helix chain 'D' and resid 63 through 67 removed outlier: 3.610A pdb=" N HIS D 66 " --> pdb=" O PRO D 63 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N HIS D 67 " --> pdb=" O SER D 64 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 63 through 67' Processing helix chain 'D' and resid 77 through 81 removed outlier: 4.028A pdb=" N ASP D 80 " --> pdb=" O ASN D 77 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N TYR D 81 " --> pdb=" O PRO D 78 " (cutoff:3.500A) No H-bonds generated for 'chain 'D' and resid 77 through 81' Processing helix chain 'D' and resid 90 through 107 removed outlier: 3.982A pdb=" N VAL D 95 " --> pdb=" O SER D 91 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N ILE D 105 " --> pdb=" O ALA D 101 " (cutoff:3.500A) Processing helix chain 'D' and resid 114 through 136 removed outlier: 3.631A pdb=" N LEU D 118 " --> pdb=" O ASP D 114 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ILE D 123 " --> pdb=" O SER D 119 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N VAL D 135 " --> pdb=" O ASN D 131 " (cutoff:3.500A) Processing helix chain 'D' and resid 145 through 154 removed outlier: 3.592A pdb=" N ILE D 149 " --> pdb=" O SER D 145 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N VAL D 152 " --> pdb=" O ASP D 148 " (cutoff:3.500A) Processing helix chain 'D' and resid 155 through 161 removed outlier: 3.705A pdb=" N ALA D 161 " --> pdb=" O LYS D 157 " (cutoff:3.500A) Processing helix chain 'D' and resid 168 through 174 Processing helix chain 'D' and resid 175 through 185 removed outlier: 3.572A pdb=" N LYS D 179 " --> pdb=" O ILE D 175 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N VAL D 180 " --> pdb=" O SER D 176 " (cutoff:3.500A) removed outlier: 4.038A pdb=" N VAL D 183 " --> pdb=" O LYS D 179 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ASN D 185 " --> pdb=" O LYS D 181 " (cutoff:3.500A) Processing helix chain 'D' and resid 193 through 201 Processing helix chain 'D' and resid 241 through 250 removed outlier: 3.652A pdb=" N ARG D 250 " --> pdb=" O MET D 246 " (cutoff:3.500A) Processing helix chain 'D' and resid 259 through 278 removed outlier: 4.147A pdb=" N LEU D 263 " --> pdb=" O ASN D 259 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLU D 267 " --> pdb=" O LEU D 263 " (cutoff:3.500A) removed outlier: 3.576A pdb=" N LEU D 275 " --> pdb=" O ARG D 271 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ILE D 276 " --> pdb=" O LYS D 272 " (cutoff:3.500A) Processing helix chain 'D' and resid 350 through 355 Processing helix chain 'D' and resid 357 through 361 Processing helix chain 'D' and resid 366 through 384 removed outlier: 3.944A pdb=" N VAL D 370 " --> pdb=" O ASN D 366 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N ALA D 371 " --> pdb=" O ILE D 367 " (cutoff:3.500A) removed outlier: 4.167A pdb=" N ALA D 372 " --> pdb=" O GLY D 368 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N LYS D 378 " --> pdb=" O SER D 374 " (cutoff:3.500A) Processing helix chain 'D' and resid 553 through 566 Processing helix chain 'D' and resid 579 through 588 Processing helix chain 'D' and resid 594 through 604 removed outlier: 3.647A pdb=" N CYS D 598 " --> pdb=" O ASN D 594 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N ILE D 600 " --> pdb=" O SER D 596 " (cutoff:3.500A) Processing helix chain 'D' and resid 609 through 613 removed outlier: 3.714A pdb=" N ARG D 613 " --> pdb=" O ALA D 610 " (cutoff:3.500A) Processing helix chain 'D' and resid 628 through 635 Processing helix chain 'D' and resid 637 through 642 Processing helix chain 'D' and resid 653 through 657 removed outlier: 3.740A pdb=" N PHE D 657 " --> pdb=" O PRO D 654 " (cutoff:3.500A) Processing helix chain 'D' and resid 667 through 672 removed outlier: 3.663A pdb=" N LYS D 672 " --> pdb=" O ASP D 668 " (cutoff:3.500A) Processing helix chain 'E' and resid 3 through 13 Processing helix chain 'E' and resid 18 through 23 Processing helix chain 'E' and resid 24 through 30 removed outlier: 3.625A pdb=" N GLU E 28 " --> pdb=" O GLY E 24 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 51 removed outlier: 3.676A pdb=" N ASP E 51 " --> pdb=" O ASP E 47 " (cutoff:3.500A) Processing helix chain 'E' and resid 52 through 57 removed outlier: 4.034A pdb=" N VAL E 55 " --> pdb=" O ILE E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 70 through 79 removed outlier: 3.594A pdb=" N GLU E 76 " --> pdb=" O LEU E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 322 through 325 removed outlier: 4.054A pdb=" N GLU E 325 " --> pdb=" O GLY E 322 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 322 through 325' Processing helix chain 'E' and resid 326 through 338 removed outlier: 3.605A pdb=" N SER E 334 " --> pdb=" O SER E 330 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N CYS E 336 " --> pdb=" O LEU E 332 " (cutoff:3.500A) removed outlier: 4.251A pdb=" N ASN E 337 " --> pdb=" O HIS E 333 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N SER E 338 " --> pdb=" O SER E 334 " (cutoff:3.500A) Processing helix chain 'E' and resid 341 through 348 Processing helix chain 'E' and resid 356 through 367 removed outlier: 3.521A pdb=" N MET E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 368 through 372 removed outlier: 4.010A pdb=" N LEU E 372 " --> pdb=" O ALA E 369 " (cutoff:3.500A) Processing helix chain 'E' and resid 389 through 394 Processing helix chain 'E' and resid 394 through 410 removed outlier: 3.585A pdb=" N TYR E 399 " --> pdb=" O SER E 395 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N ALA E 400 " --> pdb=" O GLU E 396 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N MET E 407 " --> pdb=" O MET E 403 " (cutoff:3.500A) removed outlier: 4.247A pdb=" N PHE E 408 " --> pdb=" O PHE E 404 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N GLN E 409 " --> pdb=" O GLY E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 417 through 429 removed outlier: 3.558A pdb=" N GLU E 423 " --> pdb=" O GLN E 419 " (cutoff:3.500A) Processing helix chain 'E' and resid 490 through 495 removed outlier: 3.558A pdb=" N VAL E 494 " --> pdb=" O SER E 490 " (cutoff:3.500A) Processing helix chain 'E' and resid 518 through 522 removed outlier: 4.007A pdb=" N GLY E 521 " --> pdb=" O GLY E 518 " (cutoff:3.500A) Processing helix chain 'E' and resid 529 through 538 removed outlier: 3.907A pdb=" N LEU E 538 " --> pdb=" O ASP E 534 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 310 through 312 removed outlier: 7.337A pdb=" N LEU A 310 " --> pdb=" O THR A 393 " (cutoff:3.500A) removed outlier: 6.084A pdb=" N VAL A 395 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ILE A 312 " --> pdb=" O VAL A 395 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N MET A 372 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N ASN A 424 " --> pdb=" O HIS A 377 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 298 through 300 removed outlier: 6.468A pdb=" N THR A 299 " --> pdb=" O MET A 406 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 410 through 412 Processing sheet with id=AA4, first strand: chain 'C' and resid 52 through 53 removed outlier: 6.200A pdb=" N ILE C 519 " --> pdb=" O LEU C 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 67 through 68 Processing sheet with id=AA6, first strand: chain 'C' and resid 111 through 116 removed outlier: 6.185A pdb=" N GLU C 102 " --> pdb=" O VAL C 75 " (cutoff:3.500A) removed outlier: 5.485A pdb=" N VAL C 75 " --> pdb=" O GLU C 102 " (cutoff:3.500A) removed outlier: 4.155A pdb=" N GLU C 144 " --> pdb=" O VAL C 75 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 119 through 120 Processing sheet with id=AA8, first strand: chain 'C' and resid 168 through 174 removed outlier: 3.567A pdb=" N VAL C 186 " --> pdb=" O ILE C 418 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N PHE C 185 " --> pdb=" O CYS C 398 " (cutoff:3.500A) removed outlier: 5.766A pdb=" N VAL C 400 " --> pdb=" O PHE C 185 " (cutoff:3.500A) removed outlier: 6.986A pdb=" N ALA C 187 " --> pdb=" O VAL C 400 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 198 through 206 removed outlier: 6.387A pdb=" N LYS C 376 " --> pdb=" O VAL C 278 " (cutoff:3.500A) removed outlier: 5.607A pdb=" N VAL C 278 " --> pdb=" O LYS C 376 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 211 through 212 Processing sheet with id=AB2, first strand: chain 'C' and resid 357 through 360 Processing sheet with id=AB3, first strand: chain 'C' and resid 408 through 409 Processing sheet with id=AB4, first strand: chain 'D' and resid 5 through 6 removed outlier: 6.806A pdb=" N TYR D 6 " --> pdb=" O GLU D 30 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 295 through 297 Processing sheet with id=AB6, first strand: chain 'D' and resid 310 through 311 Processing sheet with id=AB7, first strand: chain 'E' and resid 61 through 63 Processing sheet with id=AB8, first strand: chain 'E' and resid 96 through 98 Processing sheet with id=AB9, first strand: chain 'E' and resid 125 through 127 Processing sheet with id=AC1, first strand: chain 'E' and resid 144 through 145 535 hydrogen bonds defined for protein. 1500 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: 5.41 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 5572 1.34 - 1.46: 3041 1.46 - 1.58: 8799 1.58 - 1.69: 1 1.69 - 1.81: 153 Bond restraints: 17566 Sorted by residual: bond pdb=" C ASN C 290 " pdb=" N PRO C 291 " ideal model delta sigma weight residual 1.334 1.390 -0.056 2.34e-02 1.83e+03 5.82e+00 bond pdb=" CA GLU C 8 " pdb=" CB GLU C 8 " ideal model delta sigma weight residual 1.527 1.581 -0.054 2.48e-02 1.63e+03 4.67e+00 bond pdb=" N PHE C 240 " pdb=" CA PHE C 240 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.30e+00 bond pdb=" N MET B 368 " pdb=" CA MET B 368 " ideal model delta sigma weight residual 1.457 1.481 -0.023 1.29e-02 6.01e+03 3.23e+00 bond pdb=" C ASN A 379 " pdb=" N PRO A 380 " ideal model delta sigma weight residual 1.334 1.373 -0.040 2.34e-02 1.83e+03 2.85e+00 ... (remaining 17561 not shown) Histogram of bond angle deviations from ideal: 100.14 - 106.96: 594 106.96 - 113.78: 9556 113.78 - 120.60: 7141 120.60 - 127.42: 6291 127.42 - 134.24: 203 Bond angle restraints: 23785 Sorted by residual: angle pdb=" N VAL E 389 " pdb=" CA VAL E 389 " pdb=" C VAL E 389 " ideal model delta sigma weight residual 113.53 107.76 5.77 9.80e-01 1.04e+00 3.47e+01 angle pdb=" CA GLU C 8 " pdb=" CB GLU C 8 " pdb=" CG GLU C 8 " ideal model delta sigma weight residual 114.10 123.12 -9.02 2.00e+00 2.50e-01 2.03e+01 angle pdb=" C PRO E 519 " pdb=" N THR E 520 " pdb=" CA THR E 520 " ideal model delta sigma weight residual 121.54 130.08 -8.54 1.91e+00 2.74e-01 2.00e+01 angle pdb=" N LYS A 224 " pdb=" CA LYS A 224 " pdb=" C LYS A 224 " ideal model delta sigma weight residual 109.81 118.33 -8.52 2.21e+00 2.05e-01 1.49e+01 angle pdb=" C LYS E 162 " pdb=" N GLN E 163 " pdb=" CA GLN E 163 " ideal model delta sigma weight residual 121.54 128.88 -7.34 1.91e+00 2.74e-01 1.48e+01 ... (remaining 23780 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.36: 9210 16.36 - 32.72: 1071 32.72 - 49.08: 241 49.08 - 65.44: 47 65.44 - 81.81: 12 Dihedral angle restraints: 10581 sinusoidal: 4324 harmonic: 6257 Sorted by residual: dihedral pdb=" CA LYS A 277 " pdb=" C LYS A 277 " pdb=" N PRO A 278 " pdb=" CA PRO A 278 " ideal model delta harmonic sigma weight residual 180.00 157.52 22.48 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA ALA A 413 " pdb=" C ALA A 413 " pdb=" N PRO A 414 " pdb=" CA PRO A 414 " ideal model delta harmonic sigma weight residual 180.00 158.47 21.53 0 5.00e+00 4.00e-02 1.85e+01 dihedral pdb=" CA LEU E 116 " pdb=" C LEU E 116 " pdb=" N PRO E 117 " pdb=" CA PRO E 117 " ideal model delta harmonic sigma weight residual -180.00 -158.62 -21.38 0 5.00e+00 4.00e-02 1.83e+01 ... (remaining 10578 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 2165 0.061 - 0.121: 361 0.121 - 0.182: 76 0.182 - 0.242: 2 0.242 - 0.303: 1 Chirality restraints: 2605 Sorted by residual: chirality pdb=" CB ILE D 292 " pdb=" CA ILE D 292 " pdb=" CG1 ILE D 292 " pdb=" CG2 ILE D 292 " both_signs ideal model delta sigma weight residual False 2.64 2.95 -0.30 2.00e-01 2.50e+01 2.30e+00 chirality pdb=" CA ASN C 290 " pdb=" N ASN C 290 " pdb=" C ASN C 290 " pdb=" CB ASN C 290 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.32e+00 chirality pdb=" CA LYS A 224 " pdb=" N LYS A 224 " pdb=" C LYS A 224 " pdb=" CB LYS A 224 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.21 2.00e-01 2.50e+01 1.05e+00 ... (remaining 2602 not shown) Planarity restraints: 3068 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS D 665 " -0.036 5.00e-02 4.00e+02 5.38e-02 4.63e+00 pdb=" N PRO D 666 " 0.093 5.00e-02 4.00e+02 pdb=" CA PRO D 666 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO D 666 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 303 " 0.034 5.00e-02 4.00e+02 5.14e-02 4.23e+00 pdb=" N PRO A 304 " -0.089 5.00e-02 4.00e+02 pdb=" CA PRO A 304 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 304 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG C 234 " 0.034 5.00e-02 4.00e+02 5.10e-02 4.17e+00 pdb=" N PRO C 235 " -0.088 5.00e-02 4.00e+02 pdb=" CA PRO C 235 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO C 235 " 0.028 5.00e-02 4.00e+02 ... (remaining 3065 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 4747 2.81 - 3.33: 14086 3.33 - 3.85: 27184 3.85 - 4.38: 31212 4.38 - 4.90: 54194 Nonbonded interactions: 131423 Sorted by model distance: nonbonded pdb=" O LEU A 433 " pdb=" OG1 THR A 437 " model vdw 2.287 2.440 nonbonded pdb=" O HIS A 443 " pdb=" OG SER D 119 " model vdw 2.294 2.440 nonbonded pdb=" O PRO B 312 " pdb=" OG SER C 587 " model vdw 2.302 2.440 nonbonded pdb=" O GLU C 652 " pdb=" OG1 THR C 656 " model vdw 2.319 2.440 nonbonded pdb=" OG1 THR B 494 " pdb=" O ASN B 496 " model vdw 2.323 2.440 ... (remaining 131418 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 4.650 Check model and map are aligned: 0.270 Set scattering table: 0.160 Process input model: 48.790 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 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 0.056 17566 Z= 0.192 Angle : 0.685 10.457 23785 Z= 0.381 Chirality : 0.049 0.303 2605 Planarity : 0.005 0.054 3068 Dihedral : 14.591 81.806 6551 Min Nonbonded Distance : 2.287 Molprobity Statistics. All-atom Clashscore : 3.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 0.27 % Allowed : 4.07 % Favored : 95.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.75 (0.13), residues: 2118 helix: -3.73 (0.10), residues: 798 sheet: -1.92 (0.36), residues: 160 loop : -2.96 (0.14), residues: 1160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP D 320 HIS 0.006 0.001 HIS C 436 PHE 0.020 0.001 PHE C 240 TYR 0.014 0.001 TYR D 243 ARG 0.002 0.000 ARG E 510 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 502 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 497 time to evaluate : 2.045 Fit side-chains revert: symmetry clash REVERT: A 227 GLU cc_start: 0.4937 (mm-30) cc_final: 0.4056 (tp30) REVERT: A 256 MET cc_start: 0.6174 (mpp) cc_final: 0.4927 (tpt) REVERT: A 282 ARG cc_start: 0.7241 (mtm180) cc_final: 0.7018 (ttm170) REVERT: A 421 ASP cc_start: 0.7266 (t0) cc_final: 0.5720 (p0) REVERT: B 343 GLU cc_start: 0.8093 (mt-10) cc_final: 0.7821 (mt-10) REVERT: B 410 VAL cc_start: 0.8279 (t) cc_final: 0.8014 (m) REVERT: B 412 LEU cc_start: 0.7505 (tt) cc_final: 0.7212 (tp) REVERT: C 109 LYS cc_start: 0.6207 (mptt) cc_final: 0.5171 (mmmt) REVERT: C 336 GLU cc_start: 0.7673 (tt0) cc_final: 0.7382 (tp30) REVERT: C 478 TYR cc_start: 0.5976 (t80) cc_final: 0.5041 (t80) REVERT: C 562 LYS cc_start: 0.7245 (mmtm) cc_final: 0.6945 (pttp) REVERT: C 615 ARG cc_start: 0.7479 (ttt-90) cc_final: 0.7208 (ttt90) REVERT: C 658 GLU cc_start: 0.7883 (pm20) cc_final: 0.7423 (pm20) REVERT: D 157 LYS cc_start: 0.7957 (mmtm) cc_final: 0.7566 (mttp) REVERT: D 205 LYS cc_start: 0.6944 (mtmt) cc_final: 0.6240 (mptt) REVERT: D 251 SER cc_start: 0.9176 (t) cc_final: 0.8645 (p) REVERT: D 267 GLU cc_start: 0.6714 (tp30) cc_final: 0.6297 (pt0) REVERT: D 268 TYR cc_start: 0.6500 (t80) cc_final: 0.6168 (t80) REVERT: D 321 ILE cc_start: 0.7636 (mt) cc_final: 0.7377 (mt) REVERT: D 325 GLU cc_start: 0.7368 (mp0) cc_final: 0.7142 (mp0) REVERT: D 607 ILE cc_start: 0.6821 (mm) cc_final: 0.6354 (mm) REVERT: D 631 ARG cc_start: 0.7188 (mtt180) cc_final: 0.6870 (mtt-85) REVERT: D 649 GLU cc_start: 0.6633 (mp0) cc_final: 0.6061 (mt-10) REVERT: D 658 LEU cc_start: 0.7064 (pp) cc_final: 0.6642 (pp) REVERT: D 661 MET cc_start: 0.4373 (mmm) cc_final: 0.3288 (mtp) REVERT: E 11 ARG cc_start: 0.7029 (tpm170) cc_final: 0.6240 (ttm170) REVERT: E 51 ASP cc_start: 0.6620 (p0) cc_final: 0.6302 (m-30) REVERT: E 56 LEU cc_start: 0.7596 (mp) cc_final: 0.7183 (tt) REVERT: E 63 TYR cc_start: 0.6713 (t80) cc_final: 0.6328 (t80) REVERT: E 94 ASP cc_start: 0.7467 (m-30) cc_final: 0.7246 (m-30) REVERT: E 342 MET cc_start: 0.3957 (tpt) cc_final: 0.3608 (mmm) REVERT: E 356 THR cc_start: 0.6363 (OUTLIER) cc_final: 0.5964 (p) REVERT: E 409 GLN cc_start: 0.8115 (tm-30) cc_final: 0.7639 (tm-30) REVERT: E 412 ARG cc_start: 0.5047 (ptp90) cc_final: 0.4695 (mmm160) REVERT: E 416 TRP cc_start: 0.6707 (m100) cc_final: 0.6479 (m100) REVERT: E 436 LYS cc_start: 0.7732 (pttm) cc_final: 0.7163 (pttt) REVERT: E 437 ARG cc_start: 0.7187 (mtp85) cc_final: 0.6847 (mmm-85) outliers start: 5 outliers final: 0 residues processed: 499 average time/residue: 0.3389 time to fit residues: 240.6991 Evaluate side-chains 307 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 306 time to evaluate : 1.877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 356 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 179 optimal weight: 0.0980 chunk 161 optimal weight: 0.0370 chunk 89 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 108 optimal weight: 0.0570 chunk 86 optimal weight: 7.9990 chunk 166 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 101 optimal weight: 0.4980 chunk 124 optimal weight: 6.9990 chunk 193 optimal weight: 7.9990 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 HIS A 193 GLN A 291 ASN A 319 GLN A 350 GLN A 389 GLN A 415 ASN A 453 HIS B 386 ASN B 448 GLN ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 3 GLN ** C 154 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN C 538 ASN C 600 ASN D 71 ASN D 189 GLN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 342 ASN D 653 ASN D 663 ASN D 665 HIS E 36 ASN E 371 HIS ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 499 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 22 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7169 moved from start: 0.1935 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.091 17566 Z= 0.121 Angle : 0.475 6.845 23785 Z= 0.246 Chirality : 0.040 0.181 2605 Planarity : 0.004 0.039 3068 Dihedral : 4.009 27.892 2343 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.61 % Allowed : 12.48 % Favored : 85.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.15), residues: 2118 helix: -1.86 (0.15), residues: 801 sheet: -1.40 (0.39), residues: 150 loop : -2.58 (0.15), residues: 1167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 51 HIS 0.003 0.001 HIS A 305 PHE 0.021 0.001 PHE C 34 TYR 0.016 0.001 TYR D 81 ARG 0.005 0.000 ARG E 427 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 325 time to evaluate : 2.074 Fit side-chains REVERT: A 227 GLU cc_start: 0.5078 (mm-30) cc_final: 0.4321 (tp30) REVERT: A 256 MET cc_start: 0.6416 (mpp) cc_final: 0.5107 (tpt) REVERT: A 282 ARG cc_start: 0.7308 (mtm180) cc_final: 0.7077 (ttm170) REVERT: A 421 ASP cc_start: 0.7191 (t0) cc_final: 0.5708 (p0) REVERT: A 423 LEU cc_start: 0.7283 (mp) cc_final: 0.7077 (mp) REVERT: B 319 ASN cc_start: 0.8629 (m-40) cc_final: 0.8298 (m110) REVERT: B 412 LEU cc_start: 0.7641 (tt) cc_final: 0.7402 (tp) REVERT: C 57 GLU cc_start: 0.7771 (mp0) cc_final: 0.7528 (mp0) REVERT: C 80 ARG cc_start: 0.6926 (ptp-110) cc_final: 0.6652 (ptp90) REVERT: C 336 GLU cc_start: 0.8043 (tt0) cc_final: 0.7539 (tp30) REVERT: C 426 ARG cc_start: 0.7876 (mtp180) cc_final: 0.6677 (mtt-85) REVERT: C 478 TYR cc_start: 0.6245 (t80) cc_final: 0.5650 (t80) REVERT: C 615 ARG cc_start: 0.7711 (ttt-90) cc_final: 0.7351 (ttt90) REVERT: D 79 LYS cc_start: 0.7383 (tptt) cc_final: 0.7182 (tptp) REVERT: D 157 LYS cc_start: 0.7963 (mmtm) cc_final: 0.7453 (mtmt) REVERT: D 205 LYS cc_start: 0.7125 (mtmt) cc_final: 0.6342 (mptt) REVERT: D 208 GLN cc_start: 0.7265 (mm110) cc_final: 0.6950 (mt0) REVERT: D 251 SER cc_start: 0.9105 (t) cc_final: 0.8565 (p) REVERT: D 267 GLU cc_start: 0.6677 (tp30) cc_final: 0.6261 (pt0) REVERT: D 268 TYR cc_start: 0.6525 (t80) cc_final: 0.6167 (t80) REVERT: D 574 LYS cc_start: 0.7369 (tmtt) cc_final: 0.6549 (mtpt) REVERT: D 586 MET cc_start: 0.8407 (ttp) cc_final: 0.8162 (ptm) REVERT: D 631 ARG cc_start: 0.7049 (mtt180) cc_final: 0.6815 (mtt-85) REVERT: D 649 GLU cc_start: 0.6624 (mp0) cc_final: 0.6038 (mt-10) REVERT: D 661 MET cc_start: 0.4463 (mmm) cc_final: 0.3310 (mtp) REVERT: E 11 ARG cc_start: 0.6911 (tpm170) cc_final: 0.6236 (ttm110) REVERT: E 51 ASP cc_start: 0.6522 (p0) cc_final: 0.6271 (m-30) REVERT: E 56 LEU cc_start: 0.7289 (mp) cc_final: 0.6941 (tt) REVERT: E 94 ASP cc_start: 0.7462 (m-30) cc_final: 0.7210 (m-30) REVERT: E 342 MET cc_start: 0.3862 (tpt) cc_final: 0.3602 (mmm) REVERT: E 406 TYR cc_start: 0.6121 (OUTLIER) cc_final: 0.5833 (m-80) REVERT: E 409 GLN cc_start: 0.8238 (tm-30) cc_final: 0.7754 (tm-30) REVERT: E 412 ARG cc_start: 0.5311 (ptp90) cc_final: 0.4764 (mmm160) REVERT: E 437 ARG cc_start: 0.7178 (mtp85) cc_final: 0.6875 (mmm-85) outliers start: 30 outliers final: 19 residues processed: 342 average time/residue: 0.3119 time to fit residues: 156.5350 Evaluate side-chains 306 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 286 time to evaluate : 2.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 LEU Chi-restraints excluded: chain A residue 363 ILE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 333 ASP Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 367 ASP Chi-restraints excluded: chain C residue 401 MET Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 406 TYR Chi-restraints excluded: chain E residue 413 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 107 optimal weight: 5.9990 chunk 60 optimal weight: 7.9990 chunk 160 optimal weight: 0.9990 chunk 131 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 193 optimal weight: 3.9990 chunk 209 optimal weight: 0.0050 chunk 172 optimal weight: 9.9990 chunk 192 optimal weight: 9.9990 chunk 66 optimal weight: 3.9990 chunk 155 optimal weight: 8.9990 overall best weight: 2.0000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 25 ASN ** A 252 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 291 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 305 HIS A 311 HIS A 324 HIS A 347 ASN A 350 GLN B 369 HIS B 481 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 429 ASN D 127 ASN ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 284 HIS D 663 ASN E 398 ASN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7590 moved from start: 0.4077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.088 17566 Z= 0.219 Angle : 0.587 12.726 23785 Z= 0.301 Chirality : 0.044 0.237 2605 Planarity : 0.004 0.051 3068 Dihedral : 4.567 29.904 2343 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.00 % Favored : 94.00 % Rotamer: Outliers : 2.79 % Allowed : 15.21 % Favored : 82.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.42 (0.16), residues: 2118 helix: -0.79 (0.18), residues: 811 sheet: -1.14 (0.37), residues: 178 loop : -2.37 (0.16), residues: 1129 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP D 26 HIS 0.020 0.001 HIS D 343 PHE 0.021 0.002 PHE C 240 TYR 0.016 0.002 TYR A 477 ARG 0.007 0.001 ARG C 326 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 295 time to evaluate : 1.853 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4105 (OUTLIER) cc_final: 0.3744 (m-70) REVERT: A 224 LYS cc_start: 0.6728 (pttm) cc_final: 0.6372 (tptm) REVERT: A 227 GLU cc_start: 0.4952 (mm-30) cc_final: 0.4678 (pp20) REVERT: A 256 MET cc_start: 0.6257 (mpp) cc_final: 0.4941 (tpt) REVERT: A 412 LYS cc_start: 0.7286 (mmtp) cc_final: 0.7036 (mttp) REVERT: B 308 GLN cc_start: 0.6077 (mp10) cc_final: 0.4464 (tp-100) REVERT: B 412 LEU cc_start: 0.7618 (tt) cc_final: 0.7350 (tp) REVERT: C 107 LYS cc_start: 0.7458 (tttp) cc_final: 0.7011 (tttt) REVERT: C 242 ILE cc_start: 0.8367 (mm) cc_final: 0.8100 (tt) REVERT: C 282 ASP cc_start: 0.8138 (t0) cc_final: 0.7503 (m-30) REVERT: C 336 GLU cc_start: 0.8367 (tt0) cc_final: 0.7989 (tt0) REVERT: C 426 ARG cc_start: 0.7973 (mtp180) cc_final: 0.7711 (mtt-85) REVERT: C 457 ARG cc_start: 0.7057 (OUTLIER) cc_final: 0.6245 (mtp180) REVERT: C 551 TYR cc_start: 0.7731 (p90) cc_final: 0.7057 (p90) REVERT: C 615 ARG cc_start: 0.7839 (ttt-90) cc_final: 0.7508 (ttt90) REVERT: C 621 GLU cc_start: 0.7284 (mp0) cc_final: 0.6878 (mp0) REVERT: D 96 LYS cc_start: 0.7624 (tttm) cc_final: 0.7039 (ttmm) REVERT: D 157 LYS cc_start: 0.8115 (mmtm) cc_final: 0.7786 (mmtp) REVERT: D 174 LYS cc_start: 0.7921 (mmtt) cc_final: 0.7228 (mtmt) REVERT: D 205 LYS cc_start: 0.7126 (mtmt) cc_final: 0.6700 (mptt) REVERT: D 208 GLN cc_start: 0.7511 (mm110) cc_final: 0.7199 (mt0) REVERT: D 251 SER cc_start: 0.9147 (t) cc_final: 0.8567 (p) REVERT: D 267 GLU cc_start: 0.6707 (tp30) cc_final: 0.6256 (pt0) REVERT: D 268 TYR cc_start: 0.6832 (t80) cc_final: 0.6444 (t80) REVERT: D 282 ARG cc_start: 0.7314 (ttp-110) cc_final: 0.7090 (ttp-110) REVERT: D 607 ILE cc_start: 0.6712 (mm) cc_final: 0.6413 (mm) REVERT: D 649 GLU cc_start: 0.6782 (mp0) cc_final: 0.6185 (mt-10) REVERT: D 661 MET cc_start: 0.4986 (mmm) cc_final: 0.3728 (mtp) REVERT: E 11 ARG cc_start: 0.7260 (tpm170) cc_final: 0.6591 (ttm170) REVERT: E 51 ASP cc_start: 0.6869 (p0) cc_final: 0.6593 (m-30) REVERT: E 342 MET cc_start: 0.4123 (tpt) cc_final: 0.3804 (mmm) REVERT: E 359 GLU cc_start: 0.6855 (mp0) cc_final: 0.6044 (tt0) REVERT: E 409 GLN cc_start: 0.8165 (tm-30) cc_final: 0.7698 (tm-30) REVERT: E 412 ARG cc_start: 0.5727 (ptp90) cc_final: 0.5098 (mmm160) outliers start: 52 outliers final: 32 residues processed: 326 average time/residue: 0.3301 time to fit residues: 154.9827 Evaluate side-chains 293 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 259 time to evaluate : 2.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 151 VAL Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 373 VAL Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 467 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 191 optimal weight: 3.9990 chunk 145 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 130 optimal weight: 5.9990 chunk 194 optimal weight: 10.0000 chunk 205 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 184 optimal weight: 0.7980 chunk 55 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 252 GLN A 350 GLN ** A 377 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 379 HIS ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 154 GLN D 66 HIS D 163 HIS ** D 274 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 278 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.4311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.044 17566 Z= 0.131 Angle : 0.478 6.286 23785 Z= 0.246 Chirality : 0.041 0.148 2605 Planarity : 0.003 0.050 3068 Dihedral : 4.140 30.188 2343 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.20 % Favored : 95.80 % Rotamer: Outliers : 2.79 % Allowed : 17.14 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.17), residues: 2118 helix: -0.21 (0.19), residues: 805 sheet: -0.65 (0.41), residues: 161 loop : -2.17 (0.16), residues: 1152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 320 HIS 0.004 0.001 HIS C 436 PHE 0.015 0.001 PHE C 240 TYR 0.015 0.001 TYR A 477 ARG 0.003 0.000 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 271 time to evaluate : 2.017 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 39 ASP cc_start: 0.3329 (OUTLIER) cc_final: 0.2987 (t0) REVERT: A 224 LYS cc_start: 0.6722 (pttm) cc_final: 0.6420 (tptm) REVERT: A 227 GLU cc_start: 0.5052 (mm-30) cc_final: 0.4471 (tp30) REVERT: A 256 MET cc_start: 0.6169 (mpp) cc_final: 0.4921 (tpt) REVERT: A 273 ARG cc_start: 0.5794 (mpt180) cc_final: 0.5336 (mmt180) REVERT: A 303 ASP cc_start: 0.7917 (m-30) cc_final: 0.7644 (m-30) REVERT: A 412 LYS cc_start: 0.7101 (mmtp) cc_final: 0.6796 (mttp) REVERT: B 308 GLN cc_start: 0.5942 (mp10) cc_final: 0.4392 (tp-100) REVERT: B 412 LEU cc_start: 0.7581 (tt) cc_final: 0.7327 (tp) REVERT: C 242 ILE cc_start: 0.8124 (mm) cc_final: 0.7914 (tt) REVERT: C 282 ASP cc_start: 0.7952 (t0) cc_final: 0.7403 (m-30) REVERT: C 426 ARG cc_start: 0.7995 (mtp180) cc_final: 0.7722 (mtt-85) REVERT: C 530 MET cc_start: 0.8266 (mmt) cc_final: 0.7724 (mmm) REVERT: C 551 TYR cc_start: 0.7775 (p90) cc_final: 0.7061 (p90) REVERT: C 615 ARG cc_start: 0.7850 (ttt-90) cc_final: 0.7521 (ttt90) REVERT: C 621 GLU cc_start: 0.7350 (mp0) cc_final: 0.7099 (mp0) REVERT: D 96 LYS cc_start: 0.7666 (tttm) cc_final: 0.7089 (ttmm) REVERT: D 174 LYS cc_start: 0.7941 (mmtt) cc_final: 0.7254 (mtmt) REVERT: D 205 LYS cc_start: 0.7106 (mtmt) cc_final: 0.6689 (mptt) REVERT: D 208 GLN cc_start: 0.7503 (mm110) cc_final: 0.7155 (mt0) REVERT: D 251 SER cc_start: 0.9160 (t) cc_final: 0.8604 (p) REVERT: D 267 GLU cc_start: 0.6768 (tp30) cc_final: 0.6292 (pt0) REVERT: D 282 ARG cc_start: 0.7342 (ttp-110) cc_final: 0.6872 (ttp-110) REVERT: D 649 GLU cc_start: 0.6872 (mp0) cc_final: 0.6169 (mt-10) REVERT: D 661 MET cc_start: 0.5110 (mmm) cc_final: 0.3786 (mtp) REVERT: E 11 ARG cc_start: 0.7242 (tpm170) cc_final: 0.6637 (ttm170) REVERT: E 50 PHE cc_start: 0.6842 (OUTLIER) cc_final: 0.6544 (t80) REVERT: E 51 ASP cc_start: 0.6878 (p0) cc_final: 0.6594 (m-30) REVERT: E 342 MET cc_start: 0.4122 (tpt) cc_final: 0.3832 (mmm) REVERT: E 359 GLU cc_start: 0.6780 (mp0) cc_final: 0.6040 (tt0) REVERT: E 412 ARG cc_start: 0.5590 (ptp90) cc_final: 0.5024 (mmm160) outliers start: 52 outliers final: 37 residues processed: 306 average time/residue: 0.3203 time to fit residues: 142.8971 Evaluate side-chains 295 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 256 time to evaluate : 2.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 39 ASP Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 68 ARG Chi-restraints excluded: chain C residue 79 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 464 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 171 optimal weight: 9.9990 chunk 116 optimal weight: 0.0010 chunk 2 optimal weight: 6.9990 chunk 153 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 175 optimal weight: 3.9990 chunk 142 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 3.9990 chunk 184 optimal weight: 5.9990 chunk 51 optimal weight: 5.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 350 GLN A 388 GLN ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 515 HIS D 274 GLN D 327 HIS D 342 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7692 moved from start: 0.5342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 17566 Z= 0.251 Angle : 0.586 6.435 23785 Z= 0.302 Chirality : 0.044 0.181 2605 Planarity : 0.004 0.043 3068 Dihedral : 4.697 30.956 2343 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.75 % Favored : 93.25 % Rotamer: Outliers : 3.48 % Allowed : 18.32 % Favored : 78.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.77 (0.17), residues: 2118 helix: -0.14 (0.19), residues: 798 sheet: -0.53 (0.41), residues: 158 loop : -2.10 (0.16), residues: 1162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 240 HIS 0.005 0.001 HIS D 97 PHE 0.025 0.002 PHE C 240 TYR 0.024 0.002 TYR D 629 ARG 0.005 0.001 ARG C 234 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 309 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 244 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4557 (OUTLIER) cc_final: 0.3893 (m-70) REVERT: A 224 LYS cc_start: 0.6651 (pttm) cc_final: 0.6087 (tptm) REVERT: A 256 MET cc_start: 0.5957 (mpp) cc_final: 0.4790 (tpt) REVERT: A 303 ASP cc_start: 0.7949 (m-30) cc_final: 0.7648 (m-30) REVERT: A 419 ASP cc_start: 0.7241 (t0) cc_final: 0.6931 (t0) REVERT: B 308 GLN cc_start: 0.6207 (mp10) cc_final: 0.4225 (tp-100) REVERT: B 339 GLU cc_start: 0.8154 (pm20) cc_final: 0.7936 (mp0) REVERT: C 242 ILE cc_start: 0.8393 (mm) cc_final: 0.8148 (tt) REVERT: C 282 ASP cc_start: 0.8135 (t0) cc_final: 0.7807 (m-30) REVERT: C 457 ARG cc_start: 0.6990 (OUTLIER) cc_final: 0.5706 (mtp180) REVERT: C 551 TYR cc_start: 0.8021 (p90) cc_final: 0.7435 (p90) REVERT: C 577 LYS cc_start: 0.7309 (OUTLIER) cc_final: 0.7072 (ttmm) REVERT: C 615 ARG cc_start: 0.7798 (ttt-90) cc_final: 0.7466 (ttt90) REVERT: C 621 GLU cc_start: 0.7435 (mp0) cc_final: 0.7040 (mp0) REVERT: C 678 ARG cc_start: 0.5915 (ttt180) cc_final: 0.5679 (mtp180) REVERT: D 163 HIS cc_start: 0.6906 (m90) cc_final: 0.6630 (m170) REVERT: D 174 LYS cc_start: 0.8029 (mmtt) cc_final: 0.7170 (mttp) REVERT: D 205 LYS cc_start: 0.7103 (mtmt) cc_final: 0.6708 (mptt) REVERT: D 208 GLN cc_start: 0.7570 (mm110) cc_final: 0.7140 (mt0) REVERT: D 282 ARG cc_start: 0.7493 (ttp-110) cc_final: 0.6971 (ttp-110) REVERT: D 649 GLU cc_start: 0.6909 (mp0) cc_final: 0.6168 (mt-10) REVERT: D 661 MET cc_start: 0.5226 (mmm) cc_final: 0.3886 (mtp) REVERT: E 11 ARG cc_start: 0.7324 (tpm170) cc_final: 0.6656 (ttm170) REVERT: E 51 ASP cc_start: 0.6994 (OUTLIER) cc_final: 0.6781 (m-30) REVERT: E 82 TYR cc_start: 0.7743 (t80) cc_final: 0.7137 (t80) REVERT: E 342 MET cc_start: 0.4090 (tpt) cc_final: 0.3800 (mmm) REVERT: E 359 GLU cc_start: 0.7029 (mp0) cc_final: 0.6132 (tt0) REVERT: E 412 ARG cc_start: 0.5632 (ptp90) cc_final: 0.5109 (mmm160) REVERT: E 510 ARG cc_start: 0.7418 (OUTLIER) cc_final: 0.6869 (mmp-170) outliers start: 65 outliers final: 49 residues processed: 289 average time/residue: 0.3295 time to fit residues: 138.0441 Evaluate side-chains 282 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 228 time to evaluate : 2.059 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain D residue 635 CYS Chi-restraints excluded: chain D residue 658 LEU Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Chi-restraints excluded: chain E residue 522 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 69 optimal weight: 0.0020 chunk 185 optimal weight: 3.9990 chunk 40 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 50 optimal weight: 8.9990 chunk 206 optimal weight: 1.9990 chunk 171 optimal weight: 0.9990 chunk 95 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 68 optimal weight: 9.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 41 HIS ** B 319 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 450 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7642 moved from start: 0.5345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 17566 Z= 0.137 Angle : 0.501 9.867 23785 Z= 0.256 Chirality : 0.041 0.200 2605 Planarity : 0.003 0.035 3068 Dihedral : 4.274 30.228 2343 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.67 % Favored : 95.33 % Rotamer: Outliers : 2.95 % Allowed : 19.82 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.18), residues: 2118 helix: 0.25 (0.19), residues: 789 sheet: -0.33 (0.43), residues: 149 loop : -1.89 (0.16), residues: 1180 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 320 HIS 0.004 0.001 HIS C 436 PHE 0.018 0.001 PHE E 151 TYR 0.027 0.001 TYR A 477 ARG 0.007 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 294 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 239 time to evaluate : 1.669 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4462 (OUTLIER) cc_final: 0.3881 (m-70) REVERT: A 224 LYS cc_start: 0.6826 (pttm) cc_final: 0.6328 (tptm) REVERT: A 256 MET cc_start: 0.5823 (mpp) cc_final: 0.4658 (tpt) REVERT: A 303 ASP cc_start: 0.7899 (m-30) cc_final: 0.7624 (m-30) REVERT: A 419 ASP cc_start: 0.7187 (t0) cc_final: 0.6901 (t0) REVERT: B 308 GLN cc_start: 0.6031 (mp10) cc_final: 0.4218 (tp-100) REVERT: B 339 GLU cc_start: 0.8157 (pm20) cc_final: 0.7937 (mp0) REVERT: C 242 ILE cc_start: 0.8227 (mm) cc_final: 0.8000 (tt) REVERT: C 282 ASP cc_start: 0.7992 (t0) cc_final: 0.7734 (m-30) REVERT: C 551 TYR cc_start: 0.7974 (p90) cc_final: 0.7378 (p90) REVERT: C 577 LYS cc_start: 0.7266 (OUTLIER) cc_final: 0.7042 (ttmm) REVERT: C 615 ARG cc_start: 0.7819 (ttt-90) cc_final: 0.7479 (ttt90) REVERT: C 678 ARG cc_start: 0.5930 (ttt180) cc_final: 0.5698 (mtp180) REVERT: C 687 LEU cc_start: 0.6894 (OUTLIER) cc_final: 0.6297 (mp) REVERT: D 163 HIS cc_start: 0.6912 (m90) cc_final: 0.6616 (m170) REVERT: D 174 LYS cc_start: 0.8083 (mmtt) cc_final: 0.7324 (mtmt) REVERT: D 205 LYS cc_start: 0.7289 (mtmt) cc_final: 0.6762 (mmtp) REVERT: D 208 GLN cc_start: 0.7596 (mm110) cc_final: 0.7176 (mt0) REVERT: D 282 ARG cc_start: 0.7478 (ttp-110) cc_final: 0.7019 (ttp-110) REVERT: D 574 LYS cc_start: 0.7700 (tttm) cc_final: 0.6889 (mtpt) REVERT: D 607 ILE cc_start: 0.7107 (mm) cc_final: 0.6894 (mm) REVERT: D 649 GLU cc_start: 0.6862 (mp0) cc_final: 0.6092 (mt-10) REVERT: D 661 MET cc_start: 0.5171 (mmm) cc_final: 0.3942 (mtm) REVERT: E 11 ARG cc_start: 0.7368 (tpm170) cc_final: 0.6718 (ttm170) REVERT: E 50 PHE cc_start: 0.7244 (OUTLIER) cc_final: 0.6605 (t80) REVERT: E 51 ASP cc_start: 0.6943 (p0) cc_final: 0.6736 (m-30) REVERT: E 82 TYR cc_start: 0.7662 (t80) cc_final: 0.6971 (t80) REVERT: E 342 MET cc_start: 0.4078 (tpt) cc_final: 0.3807 (mmm) REVERT: E 359 GLU cc_start: 0.7025 (mp0) cc_final: 0.6087 (tt0) REVERT: E 412 ARG cc_start: 0.5597 (ptp90) cc_final: 0.5079 (mmm160) outliers start: 55 outliers final: 46 residues processed: 278 average time/residue: 0.3251 time to fit residues: 132.8351 Evaluate side-chains 282 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 232 time to evaluate : 2.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 663 VAL Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 237 ASP Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain E residue 17 MET Chi-restraints excluded: chain E residue 49 LEU Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 198 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 117 optimal weight: 0.9980 chunk 150 optimal weight: 6.9990 chunk 116 optimal weight: 10.0000 chunk 173 optimal weight: 10.0000 chunk 115 optimal weight: 4.9990 chunk 205 optimal weight: 6.9990 chunk 128 optimal weight: 0.2980 chunk 125 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 overall best weight: 3.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN A 189 GLN ** B 495 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17566 Z= 0.280 Angle : 0.592 9.976 23785 Z= 0.303 Chirality : 0.044 0.221 2605 Planarity : 0.004 0.036 3068 Dihedral : 4.765 33.065 2343 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.99 % Favored : 93.01 % Rotamer: Outliers : 4.02 % Allowed : 19.28 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (0.17), residues: 2118 helix: 0.06 (0.19), residues: 805 sheet: -0.31 (0.42), residues: 157 loop : -1.97 (0.16), residues: 1156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 240 HIS 0.006 0.001 HIS A 324 PHE 0.026 0.002 PHE C 240 TYR 0.022 0.002 TYR A 477 ARG 0.008 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 307 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 75 poor density : 232 time to evaluate : 2.138 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4726 (OUTLIER) cc_final: 0.4074 (m-70) REVERT: A 224 LYS cc_start: 0.6676 (pttm) cc_final: 0.6086 (tptm) REVERT: A 256 MET cc_start: 0.5788 (mpp) cc_final: 0.4465 (tpp) REVERT: A 303 ASP cc_start: 0.7950 (m-30) cc_final: 0.7562 (m-30) REVERT: A 419 ASP cc_start: 0.7411 (t0) cc_final: 0.6935 (t0) REVERT: B 308 GLN cc_start: 0.6440 (mp10) cc_final: 0.4231 (tp-100) REVERT: B 339 GLU cc_start: 0.8115 (pm20) cc_final: 0.7901 (mp0) REVERT: C 242 ILE cc_start: 0.8426 (mm) cc_final: 0.8161 (tt) REVERT: C 244 ASP cc_start: 0.8136 (t70) cc_final: 0.7877 (m-30) REVERT: C 282 ASP cc_start: 0.8083 (t0) cc_final: 0.7711 (m-30) REVERT: C 457 ARG cc_start: 0.6999 (OUTLIER) cc_final: 0.5298 (mtp180) REVERT: C 551 TYR cc_start: 0.8014 (p90) cc_final: 0.7413 (p90) REVERT: C 577 LYS cc_start: 0.7300 (OUTLIER) cc_final: 0.7062 (ttmm) REVERT: C 615 ARG cc_start: 0.7815 (ttt-90) cc_final: 0.7505 (ttt90) REVERT: C 621 GLU cc_start: 0.7469 (mp0) cc_final: 0.7019 (mp0) REVERT: C 678 ARG cc_start: 0.5926 (ttt180) cc_final: 0.5692 (mtp180) REVERT: C 687 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6362 (mp) REVERT: D 96 LYS cc_start: 0.7829 (tttm) cc_final: 0.7257 (ttmm) REVERT: D 163 HIS cc_start: 0.6975 (m90) cc_final: 0.6622 (m170) REVERT: D 174 LYS cc_start: 0.8069 (mmtt) cc_final: 0.7402 (mtmt) REVERT: D 205 LYS cc_start: 0.7333 (mtmt) cc_final: 0.6675 (mmtp) REVERT: D 208 GLN cc_start: 0.7615 (mm110) cc_final: 0.7184 (mt0) REVERT: D 282 ARG cc_start: 0.7323 (ttp-110) cc_final: 0.6759 (ttp-110) REVERT: D 607 ILE cc_start: 0.7062 (mm) cc_final: 0.6511 (mm) REVERT: D 633 MET cc_start: 0.7920 (OUTLIER) cc_final: 0.7561 (tpt) REVERT: D 649 GLU cc_start: 0.6864 (mp0) cc_final: 0.6112 (mt-10) REVERT: D 661 MET cc_start: 0.5366 (mmm) cc_final: 0.3987 (mtp) REVERT: E 11 ARG cc_start: 0.7333 (tpm170) cc_final: 0.6734 (ttm170) REVERT: E 50 PHE cc_start: 0.7330 (OUTLIER) cc_final: 0.6574 (t80) REVERT: E 51 ASP cc_start: 0.7178 (OUTLIER) cc_final: 0.6875 (m-30) REVERT: E 82 TYR cc_start: 0.7879 (t80) cc_final: 0.6580 (t80) REVERT: E 342 MET cc_start: 0.4043 (tpt) cc_final: 0.3803 (mmm) REVERT: E 359 GLU cc_start: 0.7087 (mp0) cc_final: 0.6182 (tt0) REVERT: E 412 ARG cc_start: 0.5648 (ptp90) cc_final: 0.5122 (mmm160) REVERT: E 510 ARG cc_start: 0.7442 (OUTLIER) cc_final: 0.6893 (mmp-170) outliers start: 75 outliers final: 56 residues processed: 286 average time/residue: 0.3284 time to fit residues: 136.2495 Evaluate side-chains 287 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 223 time to evaluate : 1.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 161 ASN Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain A residue 477 TYR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 324 ASP Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 457 ARG Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 527 VAL Chi-restraints excluded: chain C residue 577 LYS Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 645 LEU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 321 ILE Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 565 THR Chi-restraints excluded: chain D residue 586 MET Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 127 optimal weight: 10.0000 chunk 81 optimal weight: 5.9990 chunk 122 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 40 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 chunk 130 optimal weight: 0.4980 chunk 139 optimal weight: 7.9990 chunk 101 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 161 optimal weight: 7.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 663 ASN ** E 18 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7684 moved from start: 0.5873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 17566 Z= 0.181 Angle : 0.532 10.264 23785 Z= 0.271 Chirality : 0.042 0.226 2605 Planarity : 0.003 0.036 3068 Dihedral : 4.500 31.182 2343 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 3.43 % Allowed : 19.50 % Favored : 77.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.32 (0.18), residues: 2118 helix: 0.25 (0.19), residues: 802 sheet: -0.36 (0.42), residues: 159 loop : -1.84 (0.17), residues: 1157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 320 HIS 0.004 0.001 HIS C 436 PHE 0.018 0.001 PHE C 240 TYR 0.026 0.001 TYR A 477 ARG 0.006 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 295 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 231 time to evaluate : 2.140 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4833 (OUTLIER) cc_final: 0.4166 (m-70) REVERT: A 224 LYS cc_start: 0.6644 (pttm) cc_final: 0.6124 (tptm) REVERT: A 256 MET cc_start: 0.5669 (mpp) cc_final: 0.4392 (tpp) REVERT: A 303 ASP cc_start: 0.7941 (m-30) cc_final: 0.7599 (m-30) REVERT: A 419 ASP cc_start: 0.7371 (t0) cc_final: 0.6905 (t0) REVERT: B 308 GLN cc_start: 0.6309 (mp10) cc_final: 0.4071 (tp-100) REVERT: B 408 MET cc_start: 0.6993 (mmt) cc_final: 0.6514 (mmt) REVERT: C 242 ILE cc_start: 0.8324 (mm) cc_final: 0.8077 (tt) REVERT: C 244 ASP cc_start: 0.8082 (t70) cc_final: 0.7857 (m-30) REVERT: C 282 ASP cc_start: 0.7932 (t0) cc_final: 0.7524 (m-30) REVERT: C 551 TYR cc_start: 0.7981 (p90) cc_final: 0.7393 (p90) REVERT: C 615 ARG cc_start: 0.7832 (ttt-90) cc_final: 0.7510 (ttt90) REVERT: C 678 ARG cc_start: 0.5870 (ttt180) cc_final: 0.5645 (mtp180) REVERT: C 686 LEU cc_start: 0.7028 (OUTLIER) cc_final: 0.6784 (mp) REVERT: C 687 LEU cc_start: 0.6887 (OUTLIER) cc_final: 0.6250 (mp) REVERT: D 96 LYS cc_start: 0.7866 (tttm) cc_final: 0.7288 (ttmm) REVERT: D 112 THR cc_start: 0.8842 (OUTLIER) cc_final: 0.8400 (p) REVERT: D 163 HIS cc_start: 0.6938 (m90) cc_final: 0.6578 (m170) REVERT: D 174 LYS cc_start: 0.8052 (mmtt) cc_final: 0.7395 (mtmt) REVERT: D 205 LYS cc_start: 0.7247 (mtmt) cc_final: 0.6648 (mmtp) REVERT: D 208 GLN cc_start: 0.7613 (mm110) cc_final: 0.7190 (mt0) REVERT: D 282 ARG cc_start: 0.7282 (ttp-110) cc_final: 0.6797 (ttp-110) REVERT: D 631 ARG cc_start: 0.6612 (mtt-85) cc_final: 0.6187 (ttm-80) REVERT: D 633 MET cc_start: 0.8000 (OUTLIER) cc_final: 0.7647 (tpt) REVERT: D 642 MET cc_start: 0.7379 (OUTLIER) cc_final: 0.5482 (mpp) REVERT: D 649 GLU cc_start: 0.6803 (mp0) cc_final: 0.6025 (mt-10) REVERT: D 661 MET cc_start: 0.5233 (mmm) cc_final: 0.3930 (mtp) REVERT: E 11 ARG cc_start: 0.7374 (tpm170) cc_final: 0.6722 (ttm170) REVERT: E 50 PHE cc_start: 0.7311 (OUTLIER) cc_final: 0.6596 (t80) REVERT: E 51 ASP cc_start: 0.7142 (OUTLIER) cc_final: 0.6864 (m-30) REVERT: E 359 GLU cc_start: 0.7097 (mp0) cc_final: 0.6199 (tt0) REVERT: E 412 ARG cc_start: 0.5613 (ptp90) cc_final: 0.5117 (mmm160) REVERT: E 510 ARG cc_start: 0.7275 (OUTLIER) cc_final: 0.6773 (mmp-170) outliers start: 64 outliers final: 50 residues processed: 282 average time/residue: 0.3201 time to fit residues: 132.0804 Evaluate side-chains 281 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 59 poor density : 222 time to evaluate : 2.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 306 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 28 SER Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 99 ILE Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 523 VAL Chi-restraints excluded: chain C residue 590 THR Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain C residue 687 LEU Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 138 SER Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 331 THR Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain D residue 633 MET Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain E residue 40 ASN Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 186 optimal weight: 0.0170 chunk 196 optimal weight: 7.9990 chunk 179 optimal weight: 6.9990 chunk 191 optimal weight: 0.2980 chunk 115 optimal weight: 1.9990 chunk 83 optimal weight: 0.8980 chunk 150 optimal weight: 3.9990 chunk 58 optimal weight: 0.0030 chunk 172 optimal weight: 8.9990 chunk 180 optimal weight: 2.9990 chunk 190 optimal weight: 8.9990 overall best weight: 0.6430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN B 319 ASN C 245 HIS D 342 ASN ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 17566 Z= 0.121 Angle : 0.489 10.034 23785 Z= 0.247 Chirality : 0.041 0.212 2605 Planarity : 0.003 0.036 3068 Dihedral : 4.075 28.580 2343 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 3.43 % Allowed : 19.87 % Favored : 76.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.18), residues: 2118 helix: 0.53 (0.19), residues: 797 sheet: -0.25 (0.43), residues: 146 loop : -1.65 (0.17), residues: 1175 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 320 HIS 0.004 0.001 HIS C 436 PHE 0.013 0.001 PHE D 269 TYR 0.030 0.001 TYR A 477 ARG 0.006 0.000 ARG C 426 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 302 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 64 poor density : 238 time to evaluate : 2.353 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4734 (OUTLIER) cc_final: 0.4158 (m-70) REVERT: A 224 LYS cc_start: 0.6617 (pttm) cc_final: 0.6149 (tptm) REVERT: A 256 MET cc_start: 0.5609 (mpp) cc_final: 0.4410 (tpp) REVERT: A 303 ASP cc_start: 0.7928 (m-30) cc_final: 0.7635 (m-30) REVERT: A 419 ASP cc_start: 0.7246 (t0) cc_final: 0.6803 (t0) REVERT: B 308 GLN cc_start: 0.6251 (mp10) cc_final: 0.4203 (tp-100) REVERT: B 485 ARG cc_start: 0.8159 (ttt-90) cc_final: 0.7576 (ttp80) REVERT: C 242 ILE cc_start: 0.8219 (mm) cc_final: 0.7984 (tt) REVERT: C 244 ASP cc_start: 0.8012 (t70) cc_final: 0.7795 (m-30) REVERT: C 282 ASP cc_start: 0.7797 (t0) cc_final: 0.7518 (m-30) REVERT: C 482 GLU cc_start: 0.7946 (mm-30) cc_final: 0.7540 (mt-10) REVERT: C 551 TYR cc_start: 0.7908 (p90) cc_final: 0.7311 (p90) REVERT: C 615 ARG cc_start: 0.7808 (ttt-90) cc_final: 0.7516 (ttt90) REVERT: C 678 ARG cc_start: 0.5783 (ttt180) cc_final: 0.5579 (mtp180) REVERT: C 686 LEU cc_start: 0.7015 (OUTLIER) cc_final: 0.6801 (mp) REVERT: D 96 LYS cc_start: 0.7803 (tttm) cc_final: 0.7265 (ttmm) REVERT: D 112 THR cc_start: 0.8748 (OUTLIER) cc_final: 0.8313 (p) REVERT: D 163 HIS cc_start: 0.6905 (m90) cc_final: 0.6558 (m170) REVERT: D 174 LYS cc_start: 0.8059 (mmtt) cc_final: 0.7393 (mtmt) REVERT: D 205 LYS cc_start: 0.7263 (mtmt) cc_final: 0.6476 (mmtp) REVERT: D 208 GLN cc_start: 0.7544 (mm110) cc_final: 0.7306 (mp10) REVERT: D 351 MET cc_start: 0.8270 (tpp) cc_final: 0.7596 (mmt) REVERT: D 631 ARG cc_start: 0.6597 (mtt-85) cc_final: 0.6224 (ttm-80) REVERT: D 642 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.5183 (mpp) REVERT: D 649 GLU cc_start: 0.6784 (mp0) cc_final: 0.6023 (mp0) REVERT: D 661 MET cc_start: 0.5112 (mmm) cc_final: 0.3831 (mtm) REVERT: E 11 ARG cc_start: 0.7251 (tpm170) cc_final: 0.6727 (ttm110) REVERT: E 50 PHE cc_start: 0.7193 (OUTLIER) cc_final: 0.6584 (t80) REVERT: E 51 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6999 (m-30) REVERT: E 359 GLU cc_start: 0.7074 (mp0) cc_final: 0.6201 (tt0) REVERT: E 412 ARG cc_start: 0.5566 (ptp90) cc_final: 0.5103 (mmm160) REVERT: E 464 VAL cc_start: 0.7717 (OUTLIER) cc_final: 0.7247 (p) REVERT: E 510 ARG cc_start: 0.7170 (OUTLIER) cc_final: 0.6667 (mmt180) outliers start: 64 outliers final: 47 residues processed: 287 average time/residue: 0.3140 time to fit residues: 132.6836 Evaluate side-chains 282 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 227 time to evaluate : 2.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 28 ASN Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 319 ASN Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 245 HIS Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 125 optimal weight: 8.9990 chunk 202 optimal weight: 4.9990 chunk 123 optimal weight: 5.9990 chunk 95 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 chunk 212 optimal weight: 0.5980 chunk 195 optimal weight: 0.0270 chunk 168 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 130 optimal weight: 0.9990 chunk 103 optimal weight: 1.9990 overall best weight: 0.6842 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 28 ASN ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7626 moved from start: 0.5832 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 17566 Z= 0.199 Angle : 0.779 59.199 23785 Z= 0.448 Chirality : 0.043 0.554 2605 Planarity : 0.006 0.164 3068 Dihedral : 4.138 29.918 2343 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 3.05 % Allowed : 20.19 % Favored : 76.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2118 helix: 0.55 (0.19), residues: 797 sheet: -0.30 (0.43), residues: 149 loop : -1.63 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 320 HIS 0.090 0.001 HIS C 245 PHE 0.013 0.001 PHE C 240 TYR 0.028 0.001 TYR A 477 ARG 0.005 0.000 ARG D 282 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 4236 Ramachandran restraints generated. 2118 Oldfield, 0 Emsley, 2118 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 285 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 228 time to evaluate : 2.211 Fit side-chains revert: symmetry clash REVERT: A 14 HIS cc_start: 0.4728 (OUTLIER) cc_final: 0.4158 (m-70) REVERT: A 224 LYS cc_start: 0.6623 (pttm) cc_final: 0.6126 (tptm) REVERT: A 256 MET cc_start: 0.5608 (mpp) cc_final: 0.4410 (tpp) REVERT: A 303 ASP cc_start: 0.7929 (m-30) cc_final: 0.7635 (m-30) REVERT: A 419 ASP cc_start: 0.7246 (t0) cc_final: 0.6804 (t0) REVERT: B 308 GLN cc_start: 0.6260 (mp10) cc_final: 0.4203 (tp-100) REVERT: B 485 ARG cc_start: 0.8090 (ttt-90) cc_final: 0.7576 (ttp80) REVERT: C 242 ILE cc_start: 0.8213 (mm) cc_final: 0.7988 (tt) REVERT: C 244 ASP cc_start: 0.8022 (t70) cc_final: 0.7801 (m-30) REVERT: C 282 ASP cc_start: 0.7797 (t0) cc_final: 0.7518 (m-30) REVERT: C 482 GLU cc_start: 0.7945 (mm-30) cc_final: 0.7537 (mt-10) REVERT: C 551 TYR cc_start: 0.7908 (p90) cc_final: 0.7310 (p90) REVERT: C 615 ARG cc_start: 0.7817 (ttt-90) cc_final: 0.7510 (ttt90) REVERT: C 678 ARG cc_start: 0.5783 (ttt180) cc_final: 0.5580 (mtp180) REVERT: C 686 LEU cc_start: 0.7014 (OUTLIER) cc_final: 0.6801 (mp) REVERT: D 96 LYS cc_start: 0.7803 (tttm) cc_final: 0.7265 (ttmm) REVERT: D 112 THR cc_start: 0.8746 (OUTLIER) cc_final: 0.8313 (p) REVERT: D 163 HIS cc_start: 0.6906 (m90) cc_final: 0.6561 (m170) REVERT: D 174 LYS cc_start: 0.8046 (mmtt) cc_final: 0.7393 (mtmt) REVERT: D 205 LYS cc_start: 0.7263 (mtmt) cc_final: 0.6476 (mmtp) REVERT: D 208 GLN cc_start: 0.7543 (mm110) cc_final: 0.7305 (mp10) REVERT: D 342 ASN cc_start: 0.8191 (OUTLIER) cc_final: 0.7980 (p0) REVERT: D 351 MET cc_start: 0.8267 (tpp) cc_final: 0.7585 (mmt) REVERT: D 631 ARG cc_start: 0.6595 (mtt-85) cc_final: 0.6201 (ttm-80) REVERT: D 642 MET cc_start: 0.7084 (OUTLIER) cc_final: 0.5180 (mpp) REVERT: D 649 GLU cc_start: 0.6781 (mp0) cc_final: 0.6019 (mp0) REVERT: D 661 MET cc_start: 0.5111 (mmm) cc_final: 0.3829 (mtm) REVERT: E 11 ARG cc_start: 0.7295 (tpm170) cc_final: 0.6727 (ttm110) REVERT: E 50 PHE cc_start: 0.7196 (OUTLIER) cc_final: 0.6585 (t80) REVERT: E 51 ASP cc_start: 0.7317 (OUTLIER) cc_final: 0.6999 (m-30) REVERT: E 359 GLU cc_start: 0.7075 (mp0) cc_final: 0.6201 (tt0) REVERT: E 412 ARG cc_start: 0.5564 (ptp90) cc_final: 0.5102 (mmm160) REVERT: E 464 VAL cc_start: 0.7715 (OUTLIER) cc_final: 0.7247 (p) REVERT: E 510 ARG cc_start: 0.7169 (OUTLIER) cc_final: 0.6666 (mmt180) outliers start: 57 outliers final: 45 residues processed: 272 average time/residue: 0.3317 time to fit residues: 132.9882 Evaluate side-chains 281 residues out of total 1869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 227 time to evaluate : 2.052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 HIS Chi-restraints excluded: chain A residue 17 PHE Chi-restraints excluded: chain A residue 179 ILE Chi-restraints excluded: chain A residue 262 TYR Chi-restraints excluded: chain A residue 376 PHE Chi-restraints excluded: chain A residue 381 THR Chi-restraints excluded: chain B residue 311 THR Chi-restraints excluded: chain B residue 410 VAL Chi-restraints excluded: chain B residue 412 LEU Chi-restraints excluded: chain B residue 494 THR Chi-restraints excluded: chain B residue 500 VAL Chi-restraints excluded: chain B residue 512 LEU Chi-restraints excluded: chain B residue 519 LEU Chi-restraints excluded: chain C residue 13 LEU Chi-restraints excluded: chain C residue 91 ILE Chi-restraints excluded: chain C residue 96 VAL Chi-restraints excluded: chain C residue 121 SER Chi-restraints excluded: chain C residue 135 GLU Chi-restraints excluded: chain C residue 147 SER Chi-restraints excluded: chain C residue 152 ILE Chi-restraints excluded: chain C residue 161 ASP Chi-restraints excluded: chain C residue 163 THR Chi-restraints excluded: chain C residue 180 THR Chi-restraints excluded: chain C residue 236 ASP Chi-restraints excluded: chain C residue 247 ASP Chi-restraints excluded: chain C residue 366 LEU Chi-restraints excluded: chain C residue 619 GLU Chi-restraints excluded: chain C residue 665 VAL Chi-restraints excluded: chain C residue 667 VAL Chi-restraints excluded: chain C residue 686 LEU Chi-restraints excluded: chain D residue 91 SER Chi-restraints excluded: chain D residue 112 THR Chi-restraints excluded: chain D residue 223 ASN Chi-restraints excluded: chain D residue 231 VAL Chi-restraints excluded: chain D residue 283 LEU Chi-restraints excluded: chain D residue 307 LYS Chi-restraints excluded: chain D residue 318 LEU Chi-restraints excluded: chain D residue 342 ASN Chi-restraints excluded: chain D residue 375 MET Chi-restraints excluded: chain D residue 562 VAL Chi-restraints excluded: chain D residue 619 LYS Chi-restraints excluded: chain D residue 642 MET Chi-restraints excluded: chain E residue 41 MET Chi-restraints excluded: chain E residue 50 PHE Chi-restraints excluded: chain E residue 51 ASP Chi-restraints excluded: chain E residue 126 THR Chi-restraints excluded: chain E residue 150 ILE Chi-restraints excluded: chain E residue 356 THR Chi-restraints excluded: chain E residue 440 VAL Chi-restraints excluded: chain E residue 447 THR Chi-restraints excluded: chain E residue 464 VAL Chi-restraints excluded: chain E residue 484 SER Chi-restraints excluded: chain E residue 494 VAL Chi-restraints excluded: chain E residue 510 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 213 random chunks: chunk 134 optimal weight: 9.9990 chunk 180 optimal weight: 3.9990 chunk 51 optimal weight: 9.9990 chunk 155 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 46 optimal weight: 3.9990 chunk 169 optimal weight: 0.0470 chunk 70 optimal weight: 0.9980 chunk 173 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 319 ASN D 281 GLN ** E 466 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 496 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 = 0.3678 r_free = 0.3678 target = 0.147217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.124982 restraints weight = 24867.641| |-----------------------------------------------------------------------------| r_work (start): 0.3385 rms_B_bonded: 1.64 r_work: 0.3305 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3201 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3201 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.5834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.158 17566 Z= 0.199 Angle : 0.779 59.199 23785 Z= 0.448 Chirality : 0.043 0.554 2605 Planarity : 0.006 0.164 3068 Dihedral : 4.138 29.918 2343 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.05 % Allowed : 5.05 % Favored : 94.90 % Rotamer: Outliers : 2.89 % Allowed : 20.35 % Favored : 76.75 % Cbeta Deviations : 0.10 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.18), residues: 2118 helix: 0.55 (0.19), residues: 797 sheet: -0.30 (0.43), residues: 149 loop : -1.63 (0.17), residues: 1172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP D 320 HIS 0.090 0.001 HIS C 245 PHE 0.013 0.001 PHE C 240 TYR 0.028 0.001 TYR A 477 ARG 0.005 0.000 ARG D 282 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4031.82 seconds wall clock time: 73 minutes 7.74 seconds (4387.74 seconds total)