Starting phenix.real_space_refine on Fri Mar 15 11:40:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c7g_16457/03_2024/8c7g_16457.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c7g_16457/03_2024/8c7g_16457.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c7g_16457/03_2024/8c7g_16457.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c7g_16457/03_2024/8c7g_16457.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c7g_16457/03_2024/8c7g_16457.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8c7g_16457/03_2024/8c7g_16457.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.023 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 57 5.16 5 C 7410 2.51 5 N 1963 2.21 5 O 2095 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 9": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 127": "OE1" <-> "OE2" Residue "A PHE 161": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 204": "OD1" <-> "OD2" Residue "A GLU 290": "OE1" <-> "OE2" Residue "A PHE 336": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 372": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 313": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 452": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 319": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 328": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 493": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 11525 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 607, 4802 Classifications: {'peptide': 607} Link IDs: {'PTRANS': 25, 'TRANS': 581} Chain breaks: 2 Chain: "B" Number of atoms: 3311 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 402, 3301 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 6 Conformer: "B" Number of residues, atoms: 402, 3301 Classifications: {'peptide': 402} Link IDs: {'PTRANS': 17, 'TRANS': 384} Chain breaks: 6 bond proxies already assigned to first conformer: 3359 Chain: "C" Number of atoms: 3412 Number of conformers: 1 Conformer: "" Number of residues, atoms: 420, 3412 Classifications: {'peptide': 420} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 13, 'TRANS': 406} Chain breaks: 1 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AHIS B 392 " occ=0.50 ... (18 atoms not shown) pdb=" NE2BHIS B 392 " occ=0.50 Time building chain proxies: 7.33, per 1000 atoms: 0.64 Number of scatterers: 11525 At special positions: 0 Unit cell: (74.844, 103.488, 194.964, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 57 16.00 O 2095 8.00 N 1963 7.00 C 7410 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: 3.65 Conformation dependent library (CDL) restraints added in 2.3 seconds 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2746 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 15 sheets defined 41.0% alpha, 19.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.17 Creating SS restraints... Processing helix chain 'A' and resid 358 through 363 Processing helix chain 'A' and resid 365 through 374 Processing helix chain 'A' and resid 379 through 393 Processing helix chain 'A' and resid 399 through 423 removed outlier: 3.650A pdb=" N LYS A 412 " --> pdb=" O SER A 408 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N ILE A 413 " --> pdb=" O ARG A 409 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N GLN A 423 " --> pdb=" O GLN A 419 " (cutoff:3.500A) Processing helix chain 'A' and resid 448 through 458 removed outlier: 3.687A pdb=" N GLN A 454 " --> pdb=" O LEU A 450 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ILE A 455 " --> pdb=" O ASP A 451 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N ARG A 458 " --> pdb=" O GLN A 454 " (cutoff:3.500A) Processing helix chain 'A' and resid 465 through 479 removed outlier: 3.502A pdb=" N LEU A 471 " --> pdb=" O SER A 467 " (cutoff:3.500A) removed outlier: 3.923A pdb=" N PHE A 479 " --> pdb=" O SER A 475 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 498 Processing helix chain 'A' and resid 500 through 511 removed outlier: 3.824A pdb=" N LEU A 504 " --> pdb=" O SER A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 516 through 526 removed outlier: 3.595A pdb=" N HIS A 526 " --> pdb=" O PHE A 522 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 544 removed outlier: 4.032A pdb=" N SER A 534 " --> pdb=" O ASP A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 546 through 558 removed outlier: 3.853A pdb=" N ILE A 550 " --> pdb=" O ALA A 546 " (cutoff:3.500A) Processing helix chain 'A' and resid 559 through 571 removed outlier: 3.629A pdb=" N ASN A 569 " --> pdb=" O ARG A 565 " (cutoff:3.500A) Processing helix chain 'A' and resid 578 through 589 removed outlier: 3.779A pdb=" N LYS A 589 " --> pdb=" O ALA A 585 " (cutoff:3.500A) Processing helix chain 'A' and resid 590 through 610 removed outlier: 3.603A pdb=" N PHE A 594 " --> pdb=" O ASP A 590 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 619 removed outlier: 3.598A pdb=" N GLN A 619 " --> pdb=" O LYS A 616 " (cutoff:3.500A) Processing helix chain 'A' and resid 620 through 631 removed outlier: 3.821A pdb=" N ILE A 624 " --> pdb=" O CYS A 620 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N GLN A 625 " --> pdb=" O THR A 621 " (cutoff:3.500A) Processing helix chain 'B' and resid 28 through 31 removed outlier: 3.505A pdb=" N LYS B 31 " --> pdb=" O GLU B 28 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 28 through 31' Processing helix chain 'B' and resid 42 through 61 removed outlier: 3.788A pdb=" N ASP B 49 " --> pdb=" O THR B 45 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N VAL B 50 " --> pdb=" O LYS B 46 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 removed outlier: 3.592A pdb=" N CYS B 69 " --> pdb=" O GLU B 66 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 116 removed outlier: 3.530A pdb=" N ILE B 116 " --> pdb=" O GLY B 113 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 113 through 116' Processing helix chain 'B' and resid 117 through 137 removed outlier: 4.100A pdb=" N TYR B 121 " --> pdb=" O SER B 117 " (cutoff:3.500A) removed outlier: 3.747A pdb=" N TYR B 129 " --> pdb=" O LEU B 125 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N GLN B 135 " --> pdb=" O MET B 131 " (cutoff:3.500A) Processing helix chain 'B' and resid 138 through 142 removed outlier: 3.857A pdb=" N CYS B 142 " --> pdb=" O PHE B 139 " (cutoff:3.500A) Processing helix chain 'B' and resid 151 through 168 removed outlier: 3.932A pdb=" N LEU B 155 " --> pdb=" O LYS B 151 " (cutoff:3.500A) removed outlier: 3.563A pdb=" N LEU B 156 " --> pdb=" O ARG B 152 " (cutoff:3.500A) removed outlier: 4.243A pdb=" N GLN B 166 " --> pdb=" O GLN B 162 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) Processing helix chain 'B' and resid 178 through 184 Processing helix chain 'B' and resid 192 through 201 removed outlier: 3.533A pdb=" N PHE B 196 " --> pdb=" O ASP B 192 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 209 removed outlier: 3.996A pdb=" N THR B 208 " --> pdb=" O THR B 204 " (cutoff:3.500A) Processing helix chain 'B' and resid 230 through 245 Processing helix chain 'B' and resid 332 through 361 removed outlier: 3.813A pdb=" N TYR B 336 " --> pdb=" O LYS B 332 " (cutoff:3.500A) Proline residue: B 345 - end of helix removed outlier: 3.657A pdb=" N THR B 348 " --> pdb=" O ALA B 344 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 404 through 415 removed outlier: 3.504A pdb=" N LEU B 408 " --> pdb=" O PRO B 404 " (cutoff:3.500A) Processing helix chain 'B' and resid 461 through 477 removed outlier: 3.695A pdb=" N VAL B 465 " --> pdb=" O THR B 461 " (cutoff:3.500A) removed outlier: 4.402A pdb=" N THR B 466 " --> pdb=" O LEU B 462 " (cutoff:3.500A) removed outlier: 4.490A pdb=" N GLN B 467 " --> pdb=" O LEU B 463 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ILE B 472 " --> pdb=" O GLU B 468 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LEU B 477 " --> pdb=" O PHE B 473 " (cutoff:3.500A) Processing helix chain 'C' and resid 105 through 108 Processing helix chain 'C' and resid 109 through 114 Processing helix chain 'C' and resid 140 through 155 Processing helix chain 'C' and resid 189 through 208 removed outlier: 3.607A pdb=" N LEU C 193 " --> pdb=" O SER C 189 " (cutoff:3.500A) Processing helix chain 'C' and resid 209 through 220 removed outlier: 3.608A pdb=" N ARG C 220 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing helix chain 'C' and resid 232 through 240 removed outlier: 3.945A pdb=" N PHE C 236 " --> pdb=" O SER C 232 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N LEU C 239 " --> pdb=" O LEU C 235 " (cutoff:3.500A) Processing helix chain 'C' and resid 252 through 259 Processing helix chain 'C' and resid 267 through 282 Processing helix chain 'C' and resid 311 through 325 Processing helix chain 'C' and resid 326 through 330 removed outlier: 4.152A pdb=" N LYS C 329 " --> pdb=" O GLU C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 372 through 390 Processing helix chain 'C' and resid 392 through 402 removed outlier: 3.602A pdb=" N ILE C 396 " --> pdb=" O CYS C 392 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLN C 402 " --> pdb=" O GLU C 398 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 414 Processing helix chain 'C' and resid 437 through 441 Processing helix chain 'C' and resid 442 through 462 removed outlier: 4.068A pdb=" N ARG C 448 " --> pdb=" O THR C 444 " (cutoff:3.500A) Processing helix chain 'C' and resid 498 through 521 removed outlier: 3.723A pdb=" N VAL C 502 " --> pdb=" O ASP C 498 " (cutoff:3.500A) removed outlier: 3.721A pdb=" N ILE C 503 " --> pdb=" O LYS C 499 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LYS C 504 " --> pdb=" O ALA C 500 " (cutoff:3.500A) removed outlier: 6.078A pdb=" N ASP C 518 " --> pdb=" O GLU C 514 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL C 519 " --> pdb=" O LYS C 515 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N TYR C 520 " --> pdb=" O GLU C 516 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 10 through 12 Processing sheet with id=AA2, first strand: chain 'A' and resid 17 through 18 removed outlier: 3.935A pdb=" N CYS A 348 " --> pdb=" O ASP A 343 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 28 through 31 Processing sheet with id=AA4, first strand: chain 'A' and resid 74 through 77 removed outlier: 4.043A pdb=" N SER A 74 " --> pdb=" O GLN A 87 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N ARG A 88 " --> pdb=" O SER A 92 " (cutoff:3.500A) removed outlier: 7.094A pdb=" N SER A 92 " --> pdb=" O ARG A 88 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 117 through 122 removed outlier: 3.656A pdb=" N GLY A 119 " --> pdb=" O ILE A 131 " (cutoff:3.500A) removed outlier: 6.845A pdb=" N VAL A 136 " --> pdb=" O SER A 153 " (cutoff:3.500A) removed outlier: 4.627A pdb=" N SER A 153 " --> pdb=" O VAL A 136 " (cutoff:3.500A) removed outlier: 7.372A pdb=" N VAL A 138 " --> pdb=" O VAL A 151 " (cutoff:3.500A) removed outlier: 3.897A pdb=" N VAL A 142 " --> pdb=" O GLN A 147 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N GLN A 147 " --> pdb=" O VAL A 142 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 161 through 163 Processing sheet with id=AA7, first strand: chain 'A' and resid 210 through 215 removed outlier: 3.725A pdb=" N HIS A 251 " --> pdb=" O VAL A 237 " (cutoff:3.500A) removed outlier: 6.381A pdb=" N LEU A 239 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LYS A 249 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 10.332A pdb=" N THR A 296 " --> pdb=" O ARG A 248 " (cutoff:3.500A) removed outlier: 7.468A pdb=" N CYS A 250 " --> pdb=" O THR A 296 " (cutoff:3.500A) removed outlier: 8.280A pdb=" N HIS A 298 " --> pdb=" O CYS A 250 " (cutoff:3.500A) removed outlier: 7.262A pdb=" N VAL A 252 " --> pdb=" O HIS A 298 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLU A 290 " --> pdb=" O TYR A 297 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 262 through 266 removed outlier: 3.668A pdb=" N ALA A 262 " --> pdb=" O HIS A 273 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 311 through 312 removed outlier: 3.599A pdb=" N LEU A 312 " --> pdb=" O LEU A 324 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N LEU A 324 " --> pdb=" O LEU A 312 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'B' and resid 7 through 8 Processing sheet with id=AB2, first strand: chain 'B' and resid 33 through 36 removed outlier: 5.407A pdb=" N VAL B 33 " --> pdb=" O ASN B 19 " (cutoff:3.500A) removed outlier: 7.201A pdb=" N ASN B 19 " --> pdb=" O VAL B 33 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N LEU B 12 " --> pdb=" O ASN B 95 " (cutoff:3.500A) removed outlier: 6.125A pdb=" N ASN B 95 " --> pdb=" O LEU B 12 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N SER B 14 " --> pdb=" O VAL B 93 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N THR B 78 " --> pdb=" O LEU B 94 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N THR B 77 " --> pdb=" O THR B 74 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N SER C 162 " --> pdb=" O HIS B 73 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N THR C 161 " --> pdb=" O PHE C 172 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N SER C 123 " --> pdb=" O PRO C 128 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 186 through 187 removed outlier: 6.224A pdb=" N ILE B 186 " --> pdb=" O HIS B 391 " (cutoff:3.500A) removed outlier: 8.360A pdb=" N THR B 393 " --> pdb=" O ILE B 186 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N GLN B 390 " --> pdb=" O ASN B 385 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N TYR B 439 " --> pdb=" O THR B 435 " (cutoff:3.500A) removed outlier: 3.823A pdb=" N ARG B 445 " --> pdb=" O GLU B 429 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N GLU B 429 " --> pdb=" O ARG B 445 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N GLU B 430 " --> pdb=" O GLU C 472 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N GLU C 472 " --> pdb=" O GLU B 430 " (cutoff:3.500A) removed outlier: 7.137A pdb=" N GLN B 432 " --> pdb=" O ILE C 470 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N ILE C 470 " --> pdb=" O GLN B 432 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N LYS B 434 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 5.958A pdb=" N LYS C 468 " --> pdb=" O ALA C 483 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N ALA C 483 " --> pdb=" O LYS C 468 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N HIS C 420 " --> pdb=" O ILE C 492 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 222 through 225 removed outlier: 5.105A pdb=" N VAL B 223 " --> pdb=" O TYR B 219 " (cutoff:3.500A) removed outlier: 5.757A pdb=" N TYR B 219 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 3.603A pdb=" N CYS B 225 " --> pdb=" O MET B 217 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N GLU B 214 " --> pdb=" O PHE B 323 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N MET B 295 " --> pdb=" O LEU B 310 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 261 through 262 removed outlier: 6.582A pdb=" N ILE C 261 " --> pdb=" O LEU C 431 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 333 through 337 removed outlier: 3.604A pdb=" N PHE C 290 " --> pdb=" O LEU C 366 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N ALA C 301 " --> pdb=" O LEU C 293 " (cutoff:3.500A) removed outlier: 4.015A pdb=" N ALA C 526 " --> pdb=" O LEU C 302 " (cutoff:3.500A) 541 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.39 Time building geometry restraints manager: 4.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3730 1.34 - 1.46: 2125 1.46 - 1.58: 5824 1.58 - 1.69: 0 1.69 - 1.81: 82 Bond restraints: 11761 Sorted by residual: bond pdb=" N SER C 250 " pdb=" CA SER C 250 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.78e+00 bond pdb=" CG1 ILE B 57 " pdb=" CD1 ILE B 57 " ideal model delta sigma weight residual 1.513 1.468 0.045 3.90e-02 6.57e+02 1.34e+00 bond pdb=" CA SER C 250 " pdb=" CB SER C 250 " ideal model delta sigma weight residual 1.530 1.507 0.023 2.00e-02 2.50e+03 1.28e+00 bond pdb=" CB THR B 74 " pdb=" CG2 THR B 74 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.72e-01 bond pdb=" C ILE C 310 " pdb=" N HIS C 311 " ideal model delta sigma weight residual 1.331 1.312 0.019 2.07e-02 2.33e+03 8.66e-01 ... (remaining 11756 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.08: 226 106.08 - 113.10: 6481 113.10 - 120.11: 4057 120.11 - 127.12: 5050 127.12 - 134.14: 110 Bond angle restraints: 15924 Sorted by residual: angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" C ASN C 251 " ideal model delta sigma weight residual 107.60 127.87 -20.27 1.83e+00 2.99e-01 1.23e+02 angle pdb=" N ASN C 251 " pdb=" CA ASN C 251 " pdb=" CB ASN C 251 " ideal model delta sigma weight residual 112.27 100.57 11.70 1.77e+00 3.19e-01 4.37e+01 angle pdb=" C ASN C 251 " pdb=" CA ASN C 251 " pdb=" CB ASN C 251 " ideal model delta sigma weight residual 111.70 104.69 7.01 1.52e+00 4.33e-01 2.13e+01 angle pdb=" N SER C 244 " pdb=" CA SER C 244 " pdb=" C SER C 244 " ideal model delta sigma weight residual 111.00 120.02 -9.02 2.80e+00 1.28e-01 1.04e+01 angle pdb=" OG1 THR A 426 " pdb=" CB THR A 426 " pdb=" CG2 THR A 426 " ideal model delta sigma weight residual 109.30 103.35 5.95 2.00e+00 2.50e-01 8.85e+00 ... (remaining 15919 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 6465 17.62 - 35.24: 527 35.24 - 52.86: 109 52.86 - 70.47: 8 70.47 - 88.09: 8 Dihedral angle restraints: 7117 sinusoidal: 2899 harmonic: 4218 Sorted by residual: dihedral pdb=" CA LEU C 288 " pdb=" C LEU C 288 " pdb=" N VAL C 289 " pdb=" CA VAL C 289 " ideal model delta harmonic sigma weight residual -180.00 -161.86 -18.14 0 5.00e+00 4.00e-02 1.32e+01 dihedral pdb=" CA ASN A 200 " pdb=" C ASN A 200 " pdb=" N PRO A 201 " pdb=" CA PRO A 201 " ideal model delta harmonic sigma weight residual 180.00 162.31 17.69 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA MET B 182 " pdb=" C MET B 182 " pdb=" N LEU B 183 " pdb=" CA LEU B 183 " ideal model delta harmonic sigma weight residual 180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 7114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.071: 1626 0.071 - 0.141: 199 0.141 - 0.212: 4 0.212 - 0.283: 1 0.283 - 0.354: 1 Chirality restraints: 1831 Sorted by residual: chirality pdb=" CA SER C 244 " pdb=" N SER C 244 " pdb=" C SER C 244 " pdb=" CB SER C 244 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA ASN C 252 " pdb=" N ASN C 252 " pdb=" C ASN C 252 " pdb=" CB ASN C 252 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.88e+00 chirality pdb=" CB THR A 426 " pdb=" CA THR A 426 " pdb=" OG1 THR A 426 " pdb=" CG2 THR A 426 " both_signs ideal model delta sigma weight residual False 2.55 2.72 -0.17 2.00e-01 2.50e+01 6.91e-01 ... (remaining 1828 not shown) Planarity restraints: 2019 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 293 " 0.041 5.00e-02 4.00e+02 6.22e-02 6.18e+00 pdb=" N PRO B 294 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 294 " 0.033 5.00e-02 4.00e+02 pdb=" CD PRO B 294 " 0.034 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 246 " -0.038 5.00e-02 4.00e+02 5.78e-02 5.34e+00 pdb=" N PRO A 247 " 0.100 5.00e-02 4.00e+02 pdb=" CA PRO A 247 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO A 247 " -0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 200 " 0.034 5.00e-02 4.00e+02 5.26e-02 4.43e+00 pdb=" N PRO A 201 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 201 " 0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 201 " 0.029 5.00e-02 4.00e+02 ... (remaining 2016 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 93 2.67 - 3.23: 10057 3.23 - 3.78: 15519 3.78 - 4.34: 20747 4.34 - 4.90: 36295 Nonbonded interactions: 82711 Sorted by model distance: nonbonded pdb=" O ASN C 251 " pdb=" OD1 ASN C 251 " model vdw 2.111 3.040 nonbonded pdb=" OG1 THR A 531 " pdb=" OE1 GLN B 387 " model vdw 2.232 2.440 nonbonded pdb=" NH1 ARG A 73 " pdb=" OE1 GLU A 90 " model vdw 2.258 2.520 nonbonded pdb=" ND2 ASN A 227 " pdb=" OE2 GLU A 234 " model vdw 2.258 2.520 nonbonded pdb=" NH1 ARG A 260 " pdb=" OE1 GLN A 275 " model vdw 2.281 2.520 ... (remaining 82706 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=0.50 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: 1.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.810 Check model and map are aligned: 0.140 Set scattering table: 0.080 Process input model: 32.090 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11761 Z= 0.240 Angle : 0.631 20.273 15924 Z= 0.335 Chirality : 0.046 0.354 1831 Planarity : 0.005 0.062 2019 Dihedral : 13.278 88.092 4371 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 4.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.22), residues: 1408 helix: 1.38 (0.23), residues: 513 sheet: 0.65 (0.29), residues: 327 loop : -1.54 (0.24), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 160 HIS 0.009 0.001 HIS C 351 PHE 0.016 0.002 PHE C 170 TYR 0.013 0.001 TYR B 16 ARG 0.005 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 1.294 Fit side-chains REVERT: A 127 GLU cc_start: 0.7839 (pm20) cc_final: 0.7526 (pm20) REVERT: A 145 LYS cc_start: 0.8155 (ptpt) cc_final: 0.7944 (ttpp) REVERT: A 197 ASP cc_start: 0.7208 (p0) cc_final: 0.6985 (p0) REVERT: A 236 GLU cc_start: 0.6631 (mt-10) cc_final: 0.6243 (mt-10) REVERT: B 32 LYS cc_start: 0.8144 (ptpt) cc_final: 0.7783 (ptpt) REVERT: B 178 ASP cc_start: 0.6013 (m-30) cc_final: 0.5748 (m-30) REVERT: C 332 GLU cc_start: 0.6972 (tp30) cc_final: 0.6688 (mm-30) outliers start: 0 outliers final: 0 residues processed: 235 average time/residue: 0.3304 time to fit residues: 101.8701 Evaluate side-chains 215 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 215 time to evaluate : 1.164 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.5980 chunk 107 optimal weight: 1.9990 chunk 59 optimal weight: 3.9990 chunk 36 optimal weight: 0.3980 chunk 72 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 128 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 557 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS C 420 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.0794 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11761 Z= 0.268 Angle : 0.573 6.618 15924 Z= 0.298 Chirality : 0.044 0.150 1831 Planarity : 0.005 0.052 2019 Dihedral : 4.225 19.538 1542 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 0.62 % Allowed : 8.58 % Favored : 90.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.22), residues: 1408 helix: 1.50 (0.23), residues: 524 sheet: 0.72 (0.29), residues: 329 loop : -1.52 (0.25), residues: 555 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP C 334 HIS 0.005 0.001 HIS A 124 PHE 0.023 0.002 PHE C 290 TYR 0.017 0.002 TYR A 9 ARG 0.005 0.000 ARG C 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 220 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 18 ARG cc_start: 0.7788 (mmm160) cc_final: 0.7486 (mtp180) REVERT: A 145 LYS cc_start: 0.8164 (ptpt) cc_final: 0.7934 (ptpp) REVERT: A 197 ASP cc_start: 0.7294 (p0) cc_final: 0.6926 (p0) REVERT: B 32 LYS cc_start: 0.8110 (ptpt) cc_final: 0.7802 (ptpt) REVERT: B 98 LYS cc_start: 0.8086 (ttmm) cc_final: 0.7834 (ttpt) REVERT: B 217 MET cc_start: 0.8334 (mtt) cc_final: 0.7949 (mtt) outliers start: 8 outliers final: 7 residues processed: 222 average time/residue: 0.3291 time to fit residues: 95.7193 Evaluate side-chains 222 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 215 time to evaluate : 1.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 490 MET Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 71 optimal weight: 0.9980 chunk 40 optimal weight: 0.6980 chunk 107 optimal weight: 1.9990 chunk 87 optimal weight: 0.0870 chunk 35 optimal weight: 0.0070 chunk 129 optimal weight: 0.8980 chunk 139 optimal weight: 1.9990 chunk 115 optimal weight: 0.6980 chunk 128 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 187 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 11761 Z= 0.180 Angle : 0.503 5.853 15924 Z= 0.263 Chirality : 0.042 0.148 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.026 18.734 1542 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 4.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 1.31 % Allowed : 9.82 % Favored : 88.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.23), residues: 1408 helix: 1.72 (0.23), residues: 524 sheet: 0.54 (0.29), residues: 332 loop : -1.42 (0.25), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 334 HIS 0.004 0.001 HIS A 124 PHE 0.019 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 221 time to evaluate : 1.299 Fit side-chains revert: symmetry clash REVERT: A 11 GLU cc_start: 0.6293 (pm20) cc_final: 0.5975 (pm20) REVERT: A 18 ARG cc_start: 0.7753 (mmm160) cc_final: 0.7510 (mtp180) REVERT: A 145 LYS cc_start: 0.8212 (ptpt) cc_final: 0.7984 (ptpp) REVERT: A 197 ASP cc_start: 0.7243 (p0) cc_final: 0.6883 (p0) REVERT: A 236 GLU cc_start: 0.6663 (mt-10) cc_final: 0.6403 (mt-10) REVERT: B 98 LYS cc_start: 0.8066 (ttmm) cc_final: 0.7834 (ttpt) REVERT: B 217 MET cc_start: 0.8307 (mtt) cc_final: 0.7869 (mtt) outliers start: 17 outliers final: 11 residues processed: 224 average time/residue: 0.3285 time to fit residues: 96.3309 Evaluate side-chains 224 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 213 time to evaluate : 1.347 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 486 GLU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 127 optimal weight: 2.9990 chunk 97 optimal weight: 0.9980 chunk 67 optimal weight: 0.6980 chunk 14 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 86 optimal weight: 0.2980 chunk 129 optimal weight: 0.4980 chunk 137 optimal weight: 0.5980 chunk 122 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 114 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 112 GLN A 187 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6960 moved from start: 0.1112 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11761 Z= 0.208 Angle : 0.513 5.999 15924 Z= 0.269 Chirality : 0.043 0.147 1831 Planarity : 0.004 0.042 2019 Dihedral : 3.999 18.731 1542 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 1.39 % Allowed : 11.52 % Favored : 87.08 % 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: 0.40 (0.23), residues: 1408 helix: 1.76 (0.23), residues: 524 sheet: 0.56 (0.29), residues: 333 loop : -1.43 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 334 HIS 0.004 0.001 HIS C 118 PHE 0.022 0.002 PHE C 290 TYR 0.017 0.001 TYR A 9 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 217 time to evaluate : 1.065 Fit side-chains REVERT: A 11 GLU cc_start: 0.6162 (pm20) cc_final: 0.5856 (pm20) REVERT: A 18 ARG cc_start: 0.7813 (mmm160) cc_final: 0.7565 (mtp180) REVERT: A 145 LYS cc_start: 0.8254 (ptpt) cc_final: 0.8024 (ptpp) REVERT: A 197 ASP cc_start: 0.7205 (p0) cc_final: 0.6821 (p0) REVERT: B 98 LYS cc_start: 0.8082 (ttmm) cc_final: 0.7846 (ttpt) REVERT: C 332 GLU cc_start: 0.6900 (mm-30) cc_final: 0.6692 (mm-30) outliers start: 18 outliers final: 14 residues processed: 222 average time/residue: 0.3184 time to fit residues: 92.5999 Evaluate side-chains 234 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 220 time to evaluate : 1.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 77 optimal weight: 1.9990 chunk 1 optimal weight: 0.3980 chunk 102 optimal weight: 0.7980 chunk 56 optimal weight: 2.9990 chunk 117 optimal weight: 1.9990 chunk 94 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 123 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 46 optimal weight: 0.8980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 11761 Z= 0.319 Angle : 0.584 6.718 15924 Z= 0.303 Chirality : 0.045 0.156 1831 Planarity : 0.004 0.044 2019 Dihedral : 4.251 20.296 1542 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 4.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 1.62 % Allowed : 12.68 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.22), residues: 1408 helix: 1.59 (0.23), residues: 524 sheet: 0.64 (0.28), residues: 333 loop : -1.55 (0.25), residues: 551 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 334 HIS 0.007 0.001 HIS B 238 PHE 0.027 0.002 PHE C 290 TYR 0.026 0.002 TYR A 9 ARG 0.004 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 222 time to evaluate : 0.972 Fit side-chains REVERT: A 11 GLU cc_start: 0.6214 (pm20) cc_final: 0.5964 (pm20) REVERT: A 18 ARG cc_start: 0.7954 (mmm160) cc_final: 0.7630 (mtp180) REVERT: A 145 LYS cc_start: 0.8357 (ptpt) cc_final: 0.8135 (ptpp) REVERT: A 197 ASP cc_start: 0.7172 (p0) cc_final: 0.6821 (p0) REVERT: C 332 GLU cc_start: 0.6868 (mm-30) cc_final: 0.6580 (mm-30) REVERT: C 347 TYR cc_start: 0.8303 (OUTLIER) cc_final: 0.6760 (m-10) outliers start: 21 outliers final: 13 residues processed: 230 average time/residue: 0.3270 time to fit residues: 98.2225 Evaluate side-chains 232 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 218 time to evaluate : 1.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 123 optimal weight: 0.0980 chunk 27 optimal weight: 1.9990 chunk 80 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 137 optimal weight: 1.9990 chunk 114 optimal weight: 1.9990 chunk 63 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 45 optimal weight: 0.9980 chunk 72 optimal weight: 0.9980 chunk 132 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1265 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11761 Z= 0.223 Angle : 0.523 6.553 15924 Z= 0.274 Chirality : 0.043 0.146 1831 Planarity : 0.004 0.042 2019 Dihedral : 4.090 18.987 1542 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.17 % Allowed : 13.07 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.23), residues: 1408 helix: 1.72 (0.23), residues: 524 sheet: 0.56 (0.29), residues: 330 loop : -1.44 (0.25), residues: 554 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 334 HIS 0.004 0.001 HIS B 238 PHE 0.027 0.002 PHE C 290 TYR 0.017 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 250 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 222 time to evaluate : 1.302 Fit side-chains REVERT: A 11 GLU cc_start: 0.6205 (pm20) cc_final: 0.5951 (pm20) REVERT: A 18 ARG cc_start: 0.7886 (mmm160) cc_final: 0.7593 (mtp180) REVERT: A 145 LYS cc_start: 0.8377 (ptpt) cc_final: 0.8149 (ptpp) REVERT: A 197 ASP cc_start: 0.7236 (p0) cc_final: 0.6814 (p0) REVERT: B 98 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7745 (ttpt) REVERT: C 332 GLU cc_start: 0.6811 (mm-30) cc_final: 0.6507 (mm-30) REVERT: C 347 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.6812 (m-10) outliers start: 28 outliers final: 20 residues processed: 233 average time/residue: 0.3108 time to fit residues: 95.6072 Evaluate side-chains 237 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 15 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 100 optimal weight: 2.9990 chunk 77 optimal weight: 0.8980 chunk 115 optimal weight: 0.8980 chunk 76 optimal weight: 0.1980 chunk 136 optimal weight: 1.9990 chunk 85 optimal weight: 0.0970 chunk 83 optimal weight: 1.9990 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.8980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6957 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11761 Z= 0.185 Angle : 0.497 6.531 15924 Z= 0.261 Chirality : 0.042 0.143 1831 Planarity : 0.004 0.041 2019 Dihedral : 3.957 17.930 1542 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.17 % Allowed : 13.23 % Favored : 84.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.47 (0.23), residues: 1408 helix: 1.86 (0.23), residues: 524 sheet: 0.58 (0.29), residues: 331 loop : -1.42 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 334 HIS 0.003 0.001 HIS A 238 PHE 0.026 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 217 time to evaluate : 1.362 Fit side-chains REVERT: A 11 GLU cc_start: 0.6210 (pm20) cc_final: 0.5962 (pm20) REVERT: A 18 ARG cc_start: 0.7870 (mmm160) cc_final: 0.7579 (mtp180) REVERT: A 145 LYS cc_start: 0.8367 (ptpt) cc_final: 0.8145 (ptpp) REVERT: A 197 ASP cc_start: 0.7222 (p0) cc_final: 0.6811 (p0) REVERT: B 98 LYS cc_start: 0.8080 (ttmm) cc_final: 0.7744 (ttpt) REVERT: C 332 GLU cc_start: 0.6838 (mm-30) cc_final: 0.6502 (mm-30) REVERT: C 347 TYR cc_start: 0.8294 (OUTLIER) cc_final: 0.6816 (m-10) outliers start: 28 outliers final: 23 residues processed: 231 average time/residue: 0.3154 time to fit residues: 95.8107 Evaluate side-chains 237 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 213 time to evaluate : 1.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 83 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 41 optimal weight: 0.0970 chunk 26 optimal weight: 0.0570 chunk 87 optimal weight: 1.9990 chunk 93 optimal weight: 0.8980 chunk 67 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 107 optimal weight: 0.5980 chunk 124 optimal weight: 2.9990 chunk 131 optimal weight: 0.9980 overall best weight: 0.5296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6959 moved from start: 0.1384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 11761 Z= 0.193 Angle : 0.501 6.709 15924 Z= 0.263 Chirality : 0.042 0.148 1831 Planarity : 0.004 0.041 2019 Dihedral : 3.922 17.657 1542 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.99 % Favored : 97.01 % Rotamer: Outliers : 2.09 % Allowed : 13.61 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.52 (0.23), residues: 1408 helix: 1.93 (0.23), residues: 524 sheet: 0.57 (0.29), residues: 331 loop : -1.41 (0.25), residues: 553 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 334 HIS 0.013 0.001 HIS A 124 PHE 0.025 0.001 PHE C 290 TYR 0.016 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 214 time to evaluate : 1.318 Fit side-chains REVERT: A 11 GLU cc_start: 0.6214 (pm20) cc_final: 0.5963 (pm20) REVERT: A 18 ARG cc_start: 0.7881 (mmm160) cc_final: 0.7586 (mtp180) REVERT: A 145 LYS cc_start: 0.8371 (ptpt) cc_final: 0.8142 (ptpp) REVERT: A 197 ASP cc_start: 0.7213 (p0) cc_final: 0.6797 (p0) REVERT: B 98 LYS cc_start: 0.8083 (ttmm) cc_final: 0.7748 (ttpt) REVERT: C 173 MET cc_start: 0.7993 (ttt) cc_final: 0.7657 (ttt) REVERT: C 255 THR cc_start: 0.7834 (OUTLIER) cc_final: 0.7462 (m) REVERT: C 347 TYR cc_start: 0.8284 (OUTLIER) cc_final: 0.7074 (m-10) outliers start: 27 outliers final: 24 residues processed: 228 average time/residue: 0.3145 time to fit residues: 94.5858 Evaluate side-chains 241 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 215 time to evaluate : 1.024 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 119 optimal weight: 0.6980 chunk 127 optimal weight: 1.9990 chunk 131 optimal weight: 0.9990 chunk 76 optimal weight: 0.1980 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 115 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6969 moved from start: 0.1409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 11761 Z= 0.224 Angle : 0.522 7.039 15924 Z= 0.274 Chirality : 0.043 0.150 1831 Planarity : 0.004 0.042 2019 Dihedral : 3.981 18.112 1542 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 2.32 % Allowed : 13.38 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1408 helix: 1.91 (0.23), residues: 524 sheet: 0.64 (0.29), residues: 336 loop : -1.48 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 334 HIS 0.013 0.001 HIS A 124 PHE 0.028 0.002 PHE C 290 TYR 0.017 0.001 TYR A 9 ARG 0.005 0.000 ARG A 458 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 213 time to evaluate : 1.323 Fit side-chains REVERT: A 11 GLU cc_start: 0.6230 (pm20) cc_final: 0.5959 (pm20) REVERT: A 18 ARG cc_start: 0.7911 (mmm160) cc_final: 0.7600 (mtp180) REVERT: A 197 ASP cc_start: 0.7201 (p0) cc_final: 0.6784 (p0) REVERT: C 255 THR cc_start: 0.7854 (OUTLIER) cc_final: 0.7490 (m) REVERT: C 347 TYR cc_start: 0.8278 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: C 487 TYR cc_start: 0.8217 (p90) cc_final: 0.7968 (p90) outliers start: 30 outliers final: 28 residues processed: 229 average time/residue: 0.3149 time to fit residues: 95.2908 Evaluate side-chains 241 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 377 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain C residue 239 LEU Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 82 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 93 optimal weight: 0.5980 chunk 141 optimal weight: 1.9990 chunk 130 optimal weight: 2.9990 chunk 112 optimal weight: 0.0870 chunk 11 optimal weight: 0.7980 chunk 87 optimal weight: 0.0970 chunk 69 optimal weight: 0.9980 chunk 89 optimal weight: 1.9990 chunk 120 optimal weight: 1.9990 overall best weight: 0.4356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6947 moved from start: 0.1486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 11761 Z= 0.171 Angle : 0.486 6.963 15924 Z= 0.256 Chirality : 0.042 0.152 1831 Planarity : 0.004 0.040 2019 Dihedral : 3.870 17.207 1542 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 2.32 % Allowed : 13.53 % Favored : 84.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.23), residues: 1408 helix: 1.99 (0.23), residues: 527 sheet: 0.58 (0.29), residues: 332 loop : -1.38 (0.25), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 334 HIS 0.012 0.001 HIS A 124 PHE 0.037 0.001 PHE C 290 TYR 0.015 0.001 TYR B 240 ARG 0.005 0.000 ARG A 458 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2816 Ramachandran restraints generated. 1408 Oldfield, 0 Emsley, 1408 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 215 time to evaluate : 1.358 Fit side-chains REVERT: A 11 GLU cc_start: 0.6223 (pm20) cc_final: 0.5982 (pm20) REVERT: A 18 ARG cc_start: 0.7873 (mmm160) cc_final: 0.7578 (mtp180) REVERT: A 145 LYS cc_start: 0.8402 (ptpt) cc_final: 0.8168 (ptpp) REVERT: A 197 ASP cc_start: 0.7204 (p0) cc_final: 0.6795 (p0) REVERT: B 32 LYS cc_start: 0.8063 (ptpt) cc_final: 0.7759 (ptpt) REVERT: C 173 MET cc_start: 0.7981 (ttt) cc_final: 0.7610 (ttt) REVERT: C 255 THR cc_start: 0.7841 (OUTLIER) cc_final: 0.7462 (m) REVERT: C 332 GLU cc_start: 0.6887 (mm-30) cc_final: 0.6668 (mt-10) REVERT: C 347 TYR cc_start: 0.8260 (OUTLIER) cc_final: 0.7007 (m-10) REVERT: C 487 TYR cc_start: 0.8204 (p90) cc_final: 0.7951 (p90) outliers start: 30 outliers final: 27 residues processed: 232 average time/residue: 0.3156 time to fit residues: 96.3786 Evaluate side-chains 240 residues out of total 1291 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 211 time to evaluate : 1.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 ASP Chi-restraints excluded: chain A residue 72 ILE Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 123 VAL Chi-restraints excluded: chain A residue 136 VAL Chi-restraints excluded: chain A residue 184 LEU Chi-restraints excluded: chain A residue 219 LEU Chi-restraints excluded: chain A residue 306 SER Chi-restraints excluded: chain A residue 453 VAL Chi-restraints excluded: chain A residue 465 THR Chi-restraints excluded: chain A residue 471 LEU Chi-restraints excluded: chain A residue 478 LYS Chi-restraints excluded: chain A residue 499 ARG Chi-restraints excluded: chain A residue 561 ILE Chi-restraints excluded: chain B residue 12 LEU Chi-restraints excluded: chain B residue 165 ASP Chi-restraints excluded: chain B residue 176 GLN Chi-restraints excluded: chain B residue 204 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 243 GLN Chi-restraints excluded: chain B residue 306 LYS Chi-restraints excluded: chain B residue 464 ASP Chi-restraints excluded: chain C residue 209 THR Chi-restraints excluded: chain C residue 253 ILE Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 347 TYR Chi-restraints excluded: chain C residue 352 VAL Chi-restraints excluded: chain C residue 480 LEU Chi-restraints excluded: chain C residue 484 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 142 random chunks: chunk 34 optimal weight: 0.0570 chunk 103 optimal weight: 1.9990 chunk 16 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 112 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 115 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 6 optimal weight: 0.0020 overall best weight: 0.7308 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 390 GLN ** B 437 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3931 r_free = 0.3931 target = 0.151970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.129506 restraints weight = 31506.980| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 3.05 r_work: 0.3466 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3478 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3478 r_free = 0.3478 target_work(ls_wunit_k1) = 0.117 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3478 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7247 moved from start: 0.1436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 11761 Z= 0.250 Angle : 0.539 7.499 15924 Z= 0.282 Chirality : 0.043 0.149 1831 Planarity : 0.004 0.070 2019 Dihedral : 4.022 18.256 1542 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.24 % Allowed : 13.92 % Favored : 83.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.51 (0.23), residues: 1408 helix: 1.92 (0.23), residues: 524 sheet: 0.65 (0.29), residues: 336 loop : -1.50 (0.25), residues: 548 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP C 334 HIS 0.012 0.001 HIS A 124 PHE 0.018 0.002 PHE C 170 TYR 0.018 0.002 TYR A 9 ARG 0.005 0.000 ARG A 458 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2933.44 seconds wall clock time: 53 minutes 16.70 seconds (3196.70 seconds total)