Starting phenix.real_space_refine on Sun Apr 7 09:06:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raf_4773/04_2024/6raf_4773_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raf_4773/04_2024/6raf_4773.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raf_4773/04_2024/6raf_4773.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raf_4773/04_2024/6raf_4773.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raf_4773/04_2024/6raf_4773_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6raf_4773/04_2024/6raf_4773_updated.pdb" } resolution = 3.8 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= 0.003 sd= 0.066 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: 6 Type Number sf(0) Gaussians P 5 5.49 5 Mg 1 5.21 5 S 25 5.16 5 C 6563 2.51 5 N 1793 2.21 5 O 1787 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A ASP 126": "OD1" <-> "OD2" Residue "A ASP 158": "OD1" <-> "OD2" Residue "A PHE 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 229": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 245": "OD1" <-> "OD2" Residue "A ASP 269": "OD1" <-> "OD2" Residue "A TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 278": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 325": "OE1" <-> "OE2" Residue "A ASP 332": "OD1" <-> "OD2" Residue "A GLU 336": "OE1" <-> "OE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A GLU 341": "OE1" <-> "OE2" Residue "A GLU 352": "OE1" <-> "OE2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A TYR 362": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 368": "OE1" <-> "OE2" Residue "A GLU 371": "OE1" <-> "OE2" Residue "A PHE 381": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 410": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 420": "OD1" <-> "OD2" Residue "A ASP 423": "OD1" <-> "OD2" Residue "A GLU 430": "OE1" <-> "OE2" Residue "A GLU 431": "OE1" <-> "OE2" Residue "A PHE 444": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 446": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 467": "OE1" <-> "OE2" Residue "A GLU 477": "OE1" <-> "OE2" Residue "A TYR 486": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ASP 529": "OD1" <-> "OD2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A GLU 545": "OE1" <-> "OE2" Residue "A PHE 568": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 575": "OE1" <-> "OE2" Residue "A GLU 576": "OE1" <-> "OE2" Residue "B ASP 50": "OD1" <-> "OD2" Residue "B GLU 91": "OE1" <-> "OE2" Residue "B TYR 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 106": "OD1" <-> "OD2" Residue "B ASP 108": "OD1" <-> "OD2" Residue "B PHE 109": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 110": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 125": "OD1" <-> "OD2" Residue "B ASP 184": "OD1" <-> "OD2" Residue "B GLU 189": "OE1" <-> "OE2" Residue "B GLU 192": "OE1" <-> "OE2" Residue "B PHE 281": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 317": "OD1" <-> "OD2" Residue "B GLU 318": "OE1" <-> "OE2" Residue "B ASP 324": "OD1" <-> "OD2" Residue "B GLU 325": "OE1" <-> "OE2" Residue "B ASP 326": "OD1" <-> "OD2" Residue "B GLU 333": "OE1" <-> "OE2" Residue "B PHE 422": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 455": "OE1" <-> "OE2" Residue "B GLU 470": "OE1" <-> "OE2" Residue "B ASP 500": "OD1" <-> "OD2" Residue "B ASP 506": "OD1" <-> "OD2" Residue "B GLU 508": "OE1" <-> "OE2" Residue "B ASP 546": "OD1" <-> "OD2" Residue "B GLU 557": "OE1" <-> "OE2" Residue "B ASP 570": "OD1" <-> "OD2" Residue "C ASP 30": "OD1" <-> "OD2" Residue "C TYR 31": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 62": "OD1" <-> "OD2" Residue "C GLU 89": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 10174 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 588, 4710 Classifications: {'peptide': 588} Link IDs: {'PTRANS': 24, 'TRANS': 563} Chain: "B" Number of atoms: 4508 Number of conformers: 1 Conformer: "" Number of residues, atoms: 571, 4508 Classifications: {'peptide': 571} Link IDs: {'PTRANS': 18, 'TRANS': 552} Chain: "C" Number of atoms: 897 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 897 Classifications: {'peptide': 121} Link IDs: {'PTRANS': 6, 'TRANS': 114} Chain: "A" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.62, per 1000 atoms: 0.55 Number of scatterers: 10174 At special positions: 0 Unit cell: (95.853, 92.622, 157.242, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 25 16.00 P 5 15.00 Mg 1 11.99 O 1787 8.00 N 1793 7.00 C 6563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 50 " - pdb=" SG CYS C 108 " distance=2.06 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: 4.06 Conformation dependent library (CDL) restraints added in 1.8 seconds 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2342 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 9 sheets defined 60.3% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.31 Creating SS restraints... Processing helix chain 'A' and resid 12 through 21 removed outlier: 3.917A pdb=" N TYR A 21 " --> pdb=" O ARG A 17 " (cutoff:3.500A) Processing helix chain 'A' and resid 23 through 44 removed outlier: 5.663A pdb=" N LEU A 27 " --> pdb=" O PRO A 24 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N THR A 40 " --> pdb=" O LEU A 37 " (cutoff:3.500A) removed outlier: 3.783A pdb=" N LEU A 41 " --> pdb=" O VAL A 38 " (cutoff:3.500A) Processing helix chain 'A' and resid 46 through 57 removed outlier: 3.847A pdb=" N PHE A 50 " --> pdb=" O THR A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 71 through 119 Processing helix chain 'A' and resid 122 through 127 Processing helix chain 'A' and resid 130 through 137 Processing helix chain 'A' and resid 139 through 172 removed outlier: 3.502A pdb=" N ILE A 144 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LEU A 152 " --> pdb=" O ILE A 148 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N VAL A 153 " --> pdb=" O THR A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 174 through 182 removed outlier: 3.869A pdb=" N VAL A 179 " --> pdb=" O LYS A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 221 Processing helix chain 'A' and resid 223 through 229 Processing helix chain 'A' and resid 232 through 284 removed outlier: 3.815A pdb=" N LEU A 242 " --> pdb=" O LYS A 238 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N LEU A 259 " --> pdb=" O ARG A 255 " (cutoff:3.500A) removed outlier: 4.269A pdb=" N PHE A 261 " --> pdb=" O PHE A 257 " (cutoff:3.500A) Proline residue: A 262 - end of helix Processing helix chain 'A' and resid 290 through 332 removed outlier: 3.761A pdb=" N GLN A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Proline residue: A 306 - end of helix removed outlier: 4.058A pdb=" N ASP A 309 " --> pdb=" O GLN A 305 " (cutoff:3.500A) removed outlier: 3.856A pdb=" N PHE A 314 " --> pdb=" O LEU A 310 " (cutoff:3.500A) removed outlier: 5.042A pdb=" N ASN A 315 " --> pdb=" O SER A 311 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU A 316 " --> pdb=" O ASP A 312 " (cutoff:3.500A) removed outlier: 4.942A pdb=" N PHE A 317 " --> pdb=" O LYS A 313 " (cutoff:3.500A) removed outlier: 5.640A pdb=" N GLN A 318 " --> pdb=" O PHE A 314 " (cutoff:3.500A) removed outlier: 4.769A pdb=" N GLY A 319 " --> pdb=" O ASN A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 406 removed outlier: 3.759A pdb=" N VAL A 403 " --> pdb=" O LYS A 399 " (cutoff:3.500A) Processing helix chain 'A' and resid 424 through 426 No H-bonds generated for 'chain 'A' and resid 424 through 426' Processing helix chain 'A' and resid 429 through 435 removed outlier: 3.667A pdb=" N ARG A 434 " --> pdb=" O GLU A 430 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N HIS A 435 " --> pdb=" O GLU A 431 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 454 Processing helix chain 'A' and resid 463 through 472 removed outlier: 3.605A pdb=" N GLU A 468 " --> pdb=" O GLU A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 476 through 481 Processing helix chain 'A' and resid 499 through 513 Processing helix chain 'A' and resid 530 through 543 Processing helix chain 'A' and resid 556 through 561 Processing helix chain 'A' and resid 579 through 585 Processing helix chain 'A' and resid 588 through 597 Processing helix chain 'B' and resid 6 through 53 Proline residue: B 15 - end of helix removed outlier: 4.055A pdb=" N ARG B 19 " --> pdb=" O PRO B 15 " (cutoff:3.500A) removed outlier: 4.519A pdb=" N TYR B 20 " --> pdb=" O TYR B 16 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N ARG B 21 " --> pdb=" O VAL B 17 " (cutoff:3.500A) removed outlier: 5.875A pdb=" N TRP B 22 " --> pdb=" O GLY B 18 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N ARG B 23 " --> pdb=" O ARG B 19 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N TYR B 24 " --> pdb=" O TYR B 20 " (cutoff:3.500A) Proline residue: B 42 - end of helix Processing helix chain 'B' and resid 58 through 104 removed outlier: 3.543A pdb=" N VAL B 84 " --> pdb=" O ARG B 80 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N THR B 104 " --> pdb=" O HIS B 100 " (cutoff:3.500A) Processing helix chain 'B' and resid 107 through 110 No H-bonds generated for 'chain 'B' and resid 107 through 110' Processing helix chain 'B' and resid 115 through 132 Processing helix chain 'B' and resid 135 through 157 Processing helix chain 'B' and resid 159 through 206 removed outlier: 4.217A pdb=" N ILE B 168 " --> pdb=" O TYR B 164 " (cutoff:3.500A) removed outlier: 4.790A pdb=" N LEU B 169 " --> pdb=" O LEU B 165 " (cutoff:3.500A) Proline residue: B 170 - end of helix removed outlier: 3.547A pdb=" N LEU B 179 " --> pdb=" O ALA B 175 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N LEU B 182 " --> pdb=" O PHE B 178 " (cutoff:3.500A) Processing helix chain 'B' and resid 208 through 211 No H-bonds generated for 'chain 'B' and resid 208 through 211' Processing helix chain 'B' and resid 217 through 269 removed outlier: 3.896A pdb=" N VAL B 241 " --> pdb=" O ALA B 237 " (cutoff:3.500A) Proline residue: B 244 - end of helix removed outlier: 3.956A pdb=" N ALA B 247 " --> pdb=" O GLY B 243 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N MET B 253 " --> pdb=" O LEU B 249 " (cutoff:3.500A) Processing helix chain 'B' and resid 275 through 316 removed outlier: 4.334A pdb=" N TRP B 290 " --> pdb=" O ALA B 286 " (cutoff:3.500A) Proline residue: B 291 - end of helix removed outlier: 3.621A pdb=" N GLY B 294 " --> pdb=" O TRP B 290 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N TRP B 297 " --> pdb=" O LEU B 293 " (cutoff:3.500A) Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 378 through 384 removed outlier: 4.266A pdb=" N VAL B 384 " --> pdb=" O ALA B 381 " (cutoff:3.500A) Processing helix chain 'B' and resid 402 through 404 No H-bonds generated for 'chain 'B' and resid 402 through 404' Processing helix chain 'B' and resid 407 through 413 Processing helix chain 'B' and resid 428 through 432 Processing helix chain 'B' and resid 441 through 450 Processing helix chain 'B' and resid 454 through 459 Processing helix chain 'B' and resid 463 through 465 No H-bonds generated for 'chain 'B' and resid 463 through 465' Processing helix chain 'B' and resid 477 through 490 Processing helix chain 'B' and resid 507 through 520 Processing helix chain 'B' and resid 533 through 538 removed outlier: 3.652A pdb=" N ARG B 537 " --> pdb=" O ALA B 534 " (cutoff:3.500A) removed outlier: 4.289A pdb=" N HIS B 538 " --> pdb=" O ALA B 535 " (cutoff:3.500A) Processing helix chain 'B' and resid 556 through 562 removed outlier: 3.578A pdb=" N GLN B 561 " --> pdb=" O GLU B 557 " (cutoff:3.500A) Processing helix chain 'B' and resid 565 through 574 Processing helix chain 'C' and resid 88 through 90 No H-bonds generated for 'chain 'C' and resid 88 through 90' Processing sheet with id= A, first strand: chain 'A' and resid 381 through 383 Processing sheet with id= B, first strand: chain 'A' and resid 572 through 577 removed outlier: 7.063A pdb=" N VAL A 567 " --> pdb=" O VAL A 574 " (cutoff:3.500A) removed outlier: 4.558A pdb=" N GLU A 576 " --> pdb=" O ILE A 565 " (cutoff:3.500A) removed outlier: 6.691A pdb=" N ILE A 565 " --> pdb=" O GLU A 576 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N SER A 549 " --> pdb=" O VAL A 389 " (cutoff:3.500A) removed outlier: 7.467A pdb=" N LEU A 391 " --> pdb=" O SER A 549 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 551 " --> pdb=" O LEU A 391 " (cutoff:3.500A) removed outlier: 8.364A pdb=" N GLY A 393 " --> pdb=" O ILE A 551 " (cutoff:3.500A) removed outlier: 6.321A pdb=" N LEU A 519 " --> pdb=" O LEU A 550 " (cutoff:3.500A) removed outlier: 7.581A pdb=" N ILE A 552 " --> pdb=" O LEU A 519 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N LEU A 521 " --> pdb=" O ILE A 552 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.565A pdb=" N VAL A 358 " --> pdb=" O VAL A 379 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N LEU A 360 " --> pdb=" O LYS A 377 " (cutoff:3.500A) removed outlier: 5.941A pdb=" N LYS A 377 " --> pdb=" O LEU A 360 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 359 through 361 Processing sheet with id= E, first strand: chain 'B' and resid 550 through 554 removed outlier: 6.781A pdb=" N VAL B 544 " --> pdb=" O VAL B 551 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N GLU B 553 " --> pdb=" O ILE B 542 " (cutoff:3.500A) removed outlier: 6.344A pdb=" N ILE B 542 " --> pdb=" O GLU B 553 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N THR B 526 " --> pdb=" O LEU B 367 " (cutoff:3.500A) removed outlier: 7.373A pdb=" N ILE B 369 " --> pdb=" O THR B 526 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N LEU B 528 " --> pdb=" O ILE B 369 " (cutoff:3.500A) removed outlier: 8.650A pdb=" N GLY B 371 " --> pdb=" O LEU B 528 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 346 through 348 removed outlier: 4.077A pdb=" N LEU B 354 " --> pdb=" O LEU B 346 " (cutoff:3.500A) removed outlier: 7.062A pdb=" N ARG B 348 " --> pdb=" O TRP B 352 " (cutoff:3.500A) removed outlier: 5.179A pdb=" N TRP B 352 " --> pdb=" O ARG B 348 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'C' and resid 4 through 7 removed outlier: 3.659A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'C' and resid 118 through 120 removed outlier: 3.530A pdb=" N ALA C 92 " --> pdb=" O VAL C 120 " (cutoff:3.500A) removed outlier: 5.701A pdb=" N ARG C 38 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'C' and resid 101 through 103 removed outlier: 4.026A pdb=" N ALA C 101 " --> pdb=" O VAL C 109 " (cutoff:3.500A) 602 hydrogen bonds defined for protein. 1707 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: 2.95 Time building geometry restraints manager: 4.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1611 1.31 - 1.44: 2811 1.44 - 1.57: 5912 1.57 - 1.70: 9 1.70 - 1.82: 45 Bond restraints: 10388 Sorted by residual: bond pdb=" C4 ATP A 701 " pdb=" C5 ATP A 701 " ideal model delta sigma weight residual 1.388 1.468 -0.080 1.00e-02 1.00e+04 6.37e+01 bond pdb=" C5 ATP A 701 " pdb=" C6 ATP A 701 " ideal model delta sigma weight residual 1.409 1.480 -0.071 1.00e-02 1.00e+04 4.99e+01 bond pdb=" N PRO B 170 " pdb=" CD PRO B 170 " ideal model delta sigma weight residual 1.473 1.556 -0.083 1.40e-02 5.10e+03 3.56e+01 bond pdb=" C4 ADP B 601 " pdb=" C5 ADP B 601 " ideal model delta sigma weight residual 1.490 1.375 0.115 2.00e-02 2.50e+03 3.33e+01 bond pdb=" C5 ATP A 701 " pdb=" N7 ATP A 701 " ideal model delta sigma weight residual 1.387 1.341 0.046 1.00e-02 1.00e+04 2.15e+01 ... (remaining 10383 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.95: 279 105.95 - 113.47: 5369 113.47 - 120.99: 5334 120.99 - 128.51: 3027 128.51 - 136.03: 85 Bond angle restraints: 14094 Sorted by residual: angle pdb=" PB ATP A 701 " pdb=" O3B ATP A 701 " pdb=" PG ATP A 701 " ideal model delta sigma weight residual 139.87 117.34 22.53 1.00e+00 1.00e+00 5.07e+02 angle pdb=" PA ATP A 701 " pdb=" O3A ATP A 701 " pdb=" PB ATP A 701 " ideal model delta sigma weight residual 136.83 118.21 18.62 1.00e+00 1.00e+00 3.47e+02 angle pdb=" N PHE A 260 " pdb=" CA PHE A 260 " pdb=" C PHE A 260 " ideal model delta sigma weight residual 111.02 121.06 -10.04 1.22e+00 6.72e-01 6.78e+01 angle pdb=" C5 ATP A 701 " pdb=" C4 ATP A 701 " pdb=" N3 ATP A 701 " ideal model delta sigma weight residual 126.80 118.73 8.07 1.00e+00 1.00e+00 6.52e+01 angle pdb=" N ILE A 76 " pdb=" CA ILE A 76 " pdb=" CB ILE A 76 " ideal model delta sigma weight residual 110.57 120.13 -9.56 1.28e+00 6.10e-01 5.58e+01 ... (remaining 14089 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.41: 5978 26.41 - 52.82: 153 52.82 - 79.23: 37 79.23 - 105.63: 11 105.63 - 132.04: 2 Dihedral angle restraints: 6181 sinusoidal: 2522 harmonic: 3659 Sorted by residual: dihedral pdb=" O2A ADP B 601 " pdb=" O3A ADP B 601 " pdb=" PA ADP B 601 " pdb=" PB ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 72.04 -132.04 1 2.00e+01 2.50e-03 4.01e+01 dihedral pdb=" C5' ADP B 601 " pdb=" O5' ADP B 601 " pdb=" PA ADP B 601 " pdb=" O2A ADP B 601 " ideal model delta sinusoidal sigma weight residual -60.00 56.75 -116.74 1 2.00e+01 2.50e-03 3.48e+01 dihedral pdb=" CA ASN A 315 " pdb=" C ASN A 315 " pdb=" N LEU A 316 " pdb=" CA LEU A 316 " ideal model delta harmonic sigma weight residual -180.00 -153.62 -26.38 0 5.00e+00 4.00e-02 2.78e+01 ... (remaining 6178 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1206 0.089 - 0.177: 310 0.177 - 0.266: 64 0.266 - 0.354: 19 0.354 - 0.443: 7 Chirality restraints: 1606 Sorted by residual: chirality pdb=" CA LEU C 104 " pdb=" N LEU C 104 " pdb=" C LEU C 104 " pdb=" CB LEU C 104 " both_signs ideal model delta sigma weight residual False 2.51 2.07 0.44 2.00e-01 2.50e+01 4.90e+00 chirality pdb=" CA VAL C 109 " pdb=" N VAL C 109 " pdb=" C VAL C 109 " pdb=" CB VAL C 109 " both_signs ideal model delta sigma weight residual False 2.44 2.88 -0.44 2.00e-01 2.50e+01 4.88e+00 chirality pdb=" CA THR A 46 " pdb=" N THR A 46 " pdb=" C THR A 46 " pdb=" CB THR A 46 " both_signs ideal model delta sigma weight residual False 2.53 2.11 0.41 2.00e-01 2.50e+01 4.26e+00 ... (remaining 1603 not shown) Planarity restraints: 1782 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL B 384 " 0.093 5.00e-02 4.00e+02 1.41e-01 3.20e+01 pdb=" N PRO B 385 " -0.245 5.00e-02 4.00e+02 pdb=" CA PRO B 385 " 0.080 5.00e-02 4.00e+02 pdb=" CD PRO B 385 " 0.072 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 34 " 0.027 2.00e-02 2.50e+03 5.38e-02 2.89e+01 pdb=" C LEU A 34 " -0.093 2.00e-02 2.50e+03 pdb=" O LEU A 34 " 0.034 2.00e-02 2.50e+03 pdb=" N PHE A 35 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 276 " -0.022 2.00e-02 2.50e+03 4.46e-02 1.99e+01 pdb=" C VAL A 276 " 0.077 2.00e-02 2.50e+03 pdb=" O VAL A 276 " -0.028 2.00e-02 2.50e+03 pdb=" N TYR A 277 " -0.026 2.00e-02 2.50e+03 ... (remaining 1779 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 1673 2.79 - 3.31: 9759 3.31 - 3.84: 16651 3.84 - 4.37: 18356 4.37 - 4.90: 32366 Nonbonded interactions: 78805 Sorted by model distance: nonbonded pdb=" O2B ADP B 601 " pdb="MG MG B 602 " model vdw 2.258 2.170 nonbonded pdb=" OH TYR B 20 " pdb=" OD2 ASP B 93 " model vdw 2.366 2.440 nonbonded pdb=" OG SER B 378 " pdb="MG MG B 602 " model vdw 2.382 2.170 nonbonded pdb=" NH1 ARG C 19 " pdb=" OE1 GLN C 82 " model vdw 2.421 2.520 nonbonded pdb=" O ILE A 438 " pdb=" OH TYR B 214 " model vdw 2.437 2.440 ... (remaining 78800 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 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: 3.900 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 29.580 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7342 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 : 0.008 0.115 10388 Z= 0.519 Angle : 1.584 22.525 14094 Z= 0.996 Chirality : 0.089 0.443 1606 Planarity : 0.012 0.141 1782 Dihedral : 13.654 132.043 3833 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.31 % Allowed : 3.45 % Favored : 96.23 % Rotamer: Outliers : 0.10 % Allowed : 3.24 % Favored : 96.66 % Cbeta Deviations : 0.43 % 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: -0.14 (0.22), residues: 1274 helix: 0.59 (0.18), residues: 780 sheet: 0.33 (0.46), residues: 120 loop : -1.56 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.040 0.003 TRP A 374 HIS 0.004 0.001 HIS B 454 PHE 0.034 0.003 PHE A 304 TYR 0.044 0.005 TYR B 92 ARG 0.033 0.004 ARG A 199 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 232 time to evaluate : 1.198 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8465 (m-40) cc_final: 0.8094 (m-40) REVERT: A 440 LEU cc_start: 0.8892 (mt) cc_final: 0.8516 (mp) REVERT: A 453 ASN cc_start: 0.7109 (t0) cc_final: 0.6657 (t0) REVERT: A 542 LYS cc_start: 0.8538 (mtpp) cc_final: 0.8332 (ttmm) REVERT: B 9 LEU cc_start: 0.7798 (mt) cc_final: 0.7545 (mp) REVERT: B 214 TYR cc_start: 0.8331 (m-80) cc_final: 0.7943 (m-80) REVERT: B 281 PHE cc_start: 0.8837 (m-80) cc_final: 0.8492 (m-80) REVERT: B 303 GLN cc_start: 0.7925 (mm-40) cc_final: 0.7291 (tm-30) REVERT: B 353 LEU cc_start: 0.7580 (mt) cc_final: 0.7306 (mt) REVERT: B 355 ARG cc_start: 0.7675 (tpt-90) cc_final: 0.7170 (mmm-85) REVERT: C 39 GLN cc_start: 0.6922 (tt0) cc_final: 0.6585 (tp40) REVERT: C 45 ARG cc_start: 0.5997 (ttp-170) cc_final: 0.5761 (ttm170) outliers start: 1 outliers final: 1 residues processed: 232 average time/residue: 0.2936 time to fit residues: 89.6450 Evaluate side-chains 142 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 141 time to evaluate : 1.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 107 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 53 optimal weight: 0.4980 chunk 32 optimal weight: 4.9990 chunk 64 optimal weight: 0.7980 chunk 51 optimal weight: 1.9990 chunk 99 optimal weight: 0.0770 chunk 38 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 74 optimal weight: 5.9990 chunk 115 optimal weight: 8.9990 overall best weight: 0.7940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 280 GLN B 556 HIS ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 10388 Z= 0.226 Angle : 0.665 10.810 14094 Z= 0.345 Chirality : 0.042 0.197 1606 Planarity : 0.006 0.067 1782 Dihedral : 7.660 130.990 1481 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.08 % Allowed : 1.02 % Favored : 98.90 % Rotamer: Outliers : 1.91 % Allowed : 9.73 % Favored : 88.36 % 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: 1.13 (0.22), residues: 1274 helix: 1.71 (0.18), residues: 781 sheet: 0.25 (0.43), residues: 123 loop : -1.15 (0.28), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 446 HIS 0.006 0.001 HIS A 561 PHE 0.017 0.002 PHE A 261 TYR 0.018 0.001 TYR B 92 ARG 0.007 0.001 ARG B 394 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 179 time to evaluate : 1.105 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8396 (m-40) cc_final: 0.7930 (m-40) REVERT: A 314 PHE cc_start: 0.4913 (OUTLIER) cc_final: 0.4663 (p90) REVERT: A 317 PHE cc_start: 0.6488 (m-10) cc_final: 0.5323 (t80) REVERT: A 338 LYS cc_start: 0.8165 (OUTLIER) cc_final: 0.7683 (mttp) REVERT: A 440 LEU cc_start: 0.8820 (mt) cc_final: 0.8602 (mp) REVERT: B 288 LEU cc_start: 0.9169 (OUTLIER) cc_final: 0.8852 (tt) REVERT: B 303 GLN cc_start: 0.7938 (mm-40) cc_final: 0.7363 (tm-30) REVERT: B 355 ARG cc_start: 0.7717 (tpt-90) cc_final: 0.7200 (ttp80) REVERT: B 365 MET cc_start: 0.7634 (ttm) cc_final: 0.7430 (ttm) REVERT: C 39 GLN cc_start: 0.7423 (tt0) cc_final: 0.6946 (tp40) REVERT: C 45 ARG cc_start: 0.6378 (ttp-170) cc_final: 0.5751 (ttm-80) REVERT: C 60 TYR cc_start: 0.6950 (m-80) cc_final: 0.6738 (m-80) REVERT: C 112 LYS cc_start: 0.8884 (tppt) cc_final: 0.8651 (tptp) outliers start: 20 outliers final: 12 residues processed: 194 average time/residue: 0.2515 time to fit residues: 66.7341 Evaluate side-chains 161 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 146 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 24 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 64 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 95 optimal weight: 0.9990 chunk 78 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 124 optimal weight: 4.9990 chunk 102 optimal weight: 3.9990 chunk 114 optimal weight: 0.7980 chunk 39 optimal weight: 1.9990 chunk 92 optimal weight: 0.4980 overall best weight: 1.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN A 554 HIS B 479 GLN ** C 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 10388 Z= 0.319 Angle : 0.688 11.223 14094 Z= 0.350 Chirality : 0.044 0.164 1606 Planarity : 0.005 0.047 1782 Dihedral : 7.463 120.020 1479 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.08 % Allowed : 2.12 % Favored : 97.80 % Rotamer: Outliers : 2.77 % Allowed : 13.26 % Favored : 83.97 % 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: 1.19 (0.23), residues: 1274 helix: 1.71 (0.18), residues: 779 sheet: 0.42 (0.45), residues: 122 loop : -1.04 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 193 HIS 0.006 0.001 HIS A 561 PHE 0.018 0.002 PHE A 168 TYR 0.022 0.002 TYR B 92 ARG 0.005 0.001 ARG B 482 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 184 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 155 time to evaluate : 1.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8392 (m-40) cc_final: 0.8001 (m-40) REVERT: A 145 ASN cc_start: 0.8235 (t0) cc_final: 0.7730 (t0) REVERT: A 338 LYS cc_start: 0.8207 (OUTLIER) cc_final: 0.7812 (mttp) REVERT: A 440 LEU cc_start: 0.8907 (mt) cc_final: 0.8639 (mp) REVERT: A 502 LYS cc_start: 0.8148 (mtmm) cc_final: 0.7655 (mtmm) REVERT: B 214 TYR cc_start: 0.8671 (m-80) cc_final: 0.8371 (m-80) REVERT: B 288 LEU cc_start: 0.9190 (OUTLIER) cc_final: 0.8871 (tt) REVERT: B 314 GLU cc_start: 0.8039 (tm-30) cc_final: 0.7641 (tm-30) REVERT: B 355 ARG cc_start: 0.7902 (tpt-90) cc_final: 0.7337 (ttp80) REVERT: B 365 MET cc_start: 0.7911 (ttm) cc_final: 0.7599 (ttm) REVERT: C 39 GLN cc_start: 0.7600 (tt0) cc_final: 0.7076 (tp40) REVERT: C 112 LYS cc_start: 0.8678 (tppt) cc_final: 0.8475 (tptp) outliers start: 29 outliers final: 19 residues processed: 174 average time/residue: 0.2720 time to fit residues: 64.5109 Evaluate side-chains 165 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 144 time to evaluate : 1.235 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 338 LYS Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 532 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 183 ILE Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 322 ILE Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 65 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 114 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 59 optimal weight: 0.0670 chunk 12 optimal weight: 0.0980 chunk 55 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 115 optimal weight: 9.9990 chunk 122 optimal weight: 4.9990 chunk 60 optimal weight: 0.5980 chunk 109 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7443 moved from start: 0.3307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 10388 Z= 0.180 Angle : 0.588 8.739 14094 Z= 0.294 Chirality : 0.040 0.180 1606 Planarity : 0.004 0.043 1782 Dihedral : 6.844 103.396 1479 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 2.77 % Allowed : 14.31 % Favored : 82.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.23), residues: 1274 helix: 2.00 (0.18), residues: 779 sheet: 0.35 (0.45), residues: 122 loop : -0.96 (0.29), residues: 373 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 193 HIS 0.005 0.001 HIS A 561 PHE 0.017 0.001 PHE B 163 TYR 0.015 0.001 TYR B 92 ARG 0.005 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 164 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8236 (m-40) cc_final: 0.7817 (m-40) REVERT: A 145 ASN cc_start: 0.8160 (t0) cc_final: 0.7604 (t0) REVERT: A 440 LEU cc_start: 0.8651 (mt) cc_final: 0.8448 (mp) REVERT: A 502 LYS cc_start: 0.8035 (mtmm) cc_final: 0.7712 (mttm) REVERT: A 512 LEU cc_start: 0.6769 (OUTLIER) cc_final: 0.6368 (mm) REVERT: A 569 ARG cc_start: 0.7280 (ttt90) cc_final: 0.6775 (ttm110) REVERT: B 214 TYR cc_start: 0.8748 (m-80) cc_final: 0.8468 (m-80) REVERT: B 355 ARG cc_start: 0.7775 (tpt-90) cc_final: 0.7305 (mmm-85) REVERT: C 39 GLN cc_start: 0.7618 (tt0) cc_final: 0.7152 (tp40) outliers start: 29 outliers final: 15 residues processed: 176 average time/residue: 0.2676 time to fit residues: 64.8862 Evaluate side-chains 165 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 149 time to evaluate : 1.114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 174 LEU Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 102 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 91 optimal weight: 0.0770 chunk 50 optimal weight: 0.0970 chunk 104 optimal weight: 0.8980 chunk 84 optimal weight: 0.9990 chunk 0 optimal weight: 0.7980 chunk 62 optimal weight: 1.9990 chunk 110 optimal weight: 4.9990 chunk 30 optimal weight: 0.7980 overall best weight: 0.3936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7418 moved from start: 0.3578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10388 Z= 0.162 Angle : 0.565 7.000 14094 Z= 0.280 Chirality : 0.039 0.174 1606 Planarity : 0.004 0.050 1782 Dihedral : 6.332 89.520 1479 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 2.86 % Allowed : 15.17 % Favored : 81.97 % 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: 1.66 (0.23), residues: 1274 helix: 2.15 (0.18), residues: 780 sheet: -0.01 (0.43), residues: 131 loop : -0.81 (0.30), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 446 HIS 0.006 0.001 HIS B 454 PHE 0.015 0.001 PHE B 163 TYR 0.012 0.001 TYR B 92 ARG 0.006 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 156 time to evaluate : 1.130 Fit side-chains revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8169 (m-40) cc_final: 0.7798 (m-40) REVERT: A 145 ASN cc_start: 0.8117 (t0) cc_final: 0.7603 (t0) REVERT: A 168 PHE cc_start: 0.7956 (OUTLIER) cc_final: 0.7618 (m-10) REVERT: A 317 PHE cc_start: 0.6722 (m-10) cc_final: 0.5280 (t80) REVERT: A 502 LYS cc_start: 0.8026 (mtmm) cc_final: 0.7496 (mtmm) REVERT: A 512 LEU cc_start: 0.6722 (OUTLIER) cc_final: 0.6410 (mm) REVERT: A 569 ARG cc_start: 0.7293 (ttt90) cc_final: 0.6764 (ttm110) REVERT: B 214 TYR cc_start: 0.8819 (m-80) cc_final: 0.8578 (m-80) REVERT: B 355 ARG cc_start: 0.7752 (tpt-90) cc_final: 0.7340 (mmm-85) outliers start: 30 outliers final: 18 residues processed: 169 average time/residue: 0.2694 time to fit residues: 62.7627 Evaluate side-chains 166 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 146 time to evaluate : 1.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 41 optimal weight: 5.9990 chunk 110 optimal weight: 4.9990 chunk 24 optimal weight: 1.9990 chunk 72 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 102 optimal weight: 0.8980 chunk 56 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 64 optimal weight: 0.9980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.3776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10388 Z= 0.217 Angle : 0.597 8.112 14094 Z= 0.294 Chirality : 0.040 0.178 1606 Planarity : 0.004 0.042 1782 Dihedral : 6.028 89.774 1479 Min Nonbonded Distance : 1.965 Molprobity Statistics. All-atom Clashscore : 8.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.44 % Allowed : 16.22 % Favored : 80.34 % 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: 1.59 (0.23), residues: 1274 helix: 2.07 (0.18), residues: 780 sheet: -0.10 (0.43), residues: 129 loop : -0.75 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 446 HIS 0.006 0.001 HIS A 561 PHE 0.015 0.001 PHE B 163 TYR 0.015 0.001 TYR B 92 ARG 0.006 0.000 ARG A 560 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 181 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 145 time to evaluate : 1.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8183 (m-40) cc_final: 0.7812 (m-40) REVERT: A 145 ASN cc_start: 0.8189 (t0) cc_final: 0.7651 (t0) REVERT: A 168 PHE cc_start: 0.8005 (OUTLIER) cc_final: 0.7616 (m-10) REVERT: A 317 PHE cc_start: 0.6784 (m-10) cc_final: 0.5360 (t80) REVERT: A 502 LYS cc_start: 0.8019 (mtmm) cc_final: 0.7438 (mttp) REVERT: A 569 ARG cc_start: 0.7356 (ttt90) cc_final: 0.6784 (ttm110) REVERT: B 288 LEU cc_start: 0.9214 (OUTLIER) cc_final: 0.8929 (tt) REVERT: B 355 ARG cc_start: 0.7778 (tpt-90) cc_final: 0.7405 (ttp80) REVERT: B 365 MET cc_start: 0.7779 (ttm) cc_final: 0.7535 (ttm) outliers start: 36 outliers final: 26 residues processed: 166 average time/residue: 0.2397 time to fit residues: 55.0650 Evaluate side-chains 170 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 142 time to evaluate : 1.143 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 358 VAL Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 288 LEU Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Chi-restraints excluded: chain C residue 69 THR Chi-restraints excluded: chain C residue 77 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 118 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 70 optimal weight: 0.7980 chunk 89 optimal weight: 0.7980 chunk 69 optimal weight: 0.6980 chunk 103 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 74 optimal weight: 0.1980 chunk 56 optimal weight: 8.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN B 531 HIS C 82 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7450 moved from start: 0.3929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10388 Z= 0.187 Angle : 0.583 8.611 14094 Z= 0.284 Chirality : 0.039 0.177 1606 Planarity : 0.004 0.040 1782 Dihedral : 5.766 88.779 1479 Min Nonbonded Distance : 2.017 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 3.05 % Allowed : 16.89 % Favored : 80.06 % 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: 1.76 (0.23), residues: 1274 helix: 2.20 (0.18), residues: 776 sheet: -0.14 (0.42), residues: 133 loop : -0.58 (0.31), residues: 365 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 446 HIS 0.004 0.001 HIS A 561 PHE 0.015 0.001 PHE C 68 TYR 0.014 0.001 TYR B 92 ARG 0.008 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 153 time to evaluate : 1.271 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8177 (m-40) cc_final: 0.7792 (m-40) REVERT: A 134 MET cc_start: 0.8369 (tpt) cc_final: 0.8110 (tpt) REVERT: A 145 ASN cc_start: 0.8181 (t0) cc_final: 0.7612 (t0) REVERT: A 168 PHE cc_start: 0.7975 (OUTLIER) cc_final: 0.7575 (m-10) REVERT: A 317 PHE cc_start: 0.6769 (m-10) cc_final: 0.5316 (t80) REVERT: A 502 LYS cc_start: 0.8022 (mtmm) cc_final: 0.7448 (mttp) REVERT: A 512 LEU cc_start: 0.6782 (OUTLIER) cc_final: 0.6444 (mm) REVERT: A 569 ARG cc_start: 0.7280 (ttt90) cc_final: 0.6777 (ttm110) REVERT: B 365 MET cc_start: 0.7905 (ttm) cc_final: 0.7670 (ttm) REVERT: B 475 LEU cc_start: 0.5996 (OUTLIER) cc_final: 0.5777 (mt) outliers start: 32 outliers final: 21 residues processed: 168 average time/residue: 0.2407 time to fit residues: 55.9588 Evaluate side-chains 174 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 150 time to evaluate : 1.194 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 148 ILE Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 75 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 73 optimal weight: 0.0060 chunk 36 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 83 optimal weight: 0.5980 chunk 60 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 96 optimal weight: 0.0370 overall best weight: 0.4874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 10388 Z= 0.174 Angle : 0.580 9.737 14094 Z= 0.282 Chirality : 0.039 0.185 1606 Planarity : 0.004 0.039 1782 Dihedral : 5.621 88.632 1479 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 2.86 % Allowed : 17.75 % Favored : 79.39 % 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: 1.81 (0.23), residues: 1274 helix: 2.25 (0.18), residues: 777 sheet: -0.17 (0.42), residues: 133 loop : -0.58 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.001 TRP B 352 HIS 0.004 0.001 HIS A 561 PHE 0.015 0.001 PHE A 171 TYR 0.021 0.001 TYR C 113 ARG 0.008 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 162 time to evaluate : 1.152 Fit side-chains revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8095 (m-40) cc_final: 0.7702 (m-40) REVERT: A 134 MET cc_start: 0.8364 (tpt) cc_final: 0.8106 (tpt) REVERT: A 145 ASN cc_start: 0.8164 (t0) cc_final: 0.7612 (t0) REVERT: A 168 PHE cc_start: 0.7984 (OUTLIER) cc_final: 0.7682 (m-10) REVERT: A 317 PHE cc_start: 0.6800 (m-10) cc_final: 0.5503 (t80) REVERT: A 502 LYS cc_start: 0.8018 (mtmm) cc_final: 0.7445 (mttp) REVERT: A 512 LEU cc_start: 0.6792 (OUTLIER) cc_final: 0.6490 (mm) REVERT: A 569 ARG cc_start: 0.7289 (ttt90) cc_final: 0.6787 (ttm110) REVERT: B 12 ARG cc_start: 0.7486 (mtp85) cc_final: 0.7124 (mtp85) REVERT: B 240 ARG cc_start: 0.7511 (mtp180) cc_final: 0.6819 (mtm110) REVERT: B 288 LEU cc_start: 0.9189 (tp) cc_final: 0.8927 (tt) REVERT: B 304 ARG cc_start: 0.7557 (ttp80) cc_final: 0.7201 (tmm-80) REVERT: B 319 LYS cc_start: 0.8618 (tppt) cc_final: 0.8366 (mmmt) REVERT: B 365 MET cc_start: 0.7929 (ttm) cc_final: 0.7711 (ttm) REVERT: B 475 LEU cc_start: 0.5986 (OUTLIER) cc_final: 0.5758 (mt) REVERT: C 112 LYS cc_start: 0.8086 (ptmm) cc_final: 0.7299 (tmmt) outliers start: 30 outliers final: 24 residues processed: 175 average time/residue: 0.2600 time to fit residues: 61.9380 Evaluate side-chains 173 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 146 time to evaluate : 1.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 111 HIS Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 184 ASP Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 111 optimal weight: 0.8980 chunk 117 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 114 optimal weight: 2.9990 chunk 68 optimal weight: 0.2980 chunk 49 optimal weight: 0.8980 chunk 89 optimal weight: 0.0060 chunk 35 optimal weight: 0.0010 chunk 103 optimal weight: 0.7980 chunk 107 optimal weight: 0.7980 chunk 113 optimal weight: 0.7980 overall best weight: 0.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 453 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7415 moved from start: 0.4236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10388 Z= 0.166 Angle : 0.593 9.357 14094 Z= 0.286 Chirality : 0.039 0.204 1606 Planarity : 0.004 0.038 1782 Dihedral : 5.518 88.851 1479 Min Nonbonded Distance : 2.025 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.48 % Allowed : 18.70 % Favored : 78.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.86 (0.24), residues: 1274 helix: 2.29 (0.18), residues: 778 sheet: -0.19 (0.43), residues: 132 loop : -0.53 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 114 HIS 0.003 0.001 HIS A 561 PHE 0.021 0.001 PHE C 68 TYR 0.017 0.001 TYR C 113 ARG 0.008 0.000 ARG B 304 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 157 time to evaluate : 1.230 Fit side-chains revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8129 (m-40) cc_final: 0.7782 (m-40) REVERT: A 145 ASN cc_start: 0.8123 (t0) cc_final: 0.7599 (t0) REVERT: A 168 PHE cc_start: 0.7903 (OUTLIER) cc_final: 0.7613 (m-10) REVERT: A 317 PHE cc_start: 0.6870 (m-10) cc_final: 0.5450 (t80) REVERT: A 502 LYS cc_start: 0.8029 (mtmm) cc_final: 0.7482 (mttp) REVERT: A 512 LEU cc_start: 0.6783 (OUTLIER) cc_final: 0.6561 (mm) REVERT: A 569 ARG cc_start: 0.7285 (ttt90) cc_final: 0.6770 (ttm110) REVERT: B 12 ARG cc_start: 0.7453 (mtp85) cc_final: 0.7072 (mtp85) REVERT: B 240 ARG cc_start: 0.7432 (mtp180) cc_final: 0.6651 (mtm110) REVERT: B 288 LEU cc_start: 0.9160 (tp) cc_final: 0.8904 (tt) REVERT: B 304 ARG cc_start: 0.7580 (ttp80) cc_final: 0.7167 (tmm-80) REVERT: B 319 LYS cc_start: 0.8621 (tppt) cc_final: 0.8367 (mmmt) REVERT: B 475 LEU cc_start: 0.5950 (OUTLIER) cc_final: 0.5730 (mt) outliers start: 26 outliers final: 20 residues processed: 167 average time/residue: 0.2673 time to fit residues: 61.1781 Evaluate side-chains 167 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 144 time to evaluate : 1.048 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 74 optimal weight: 3.9990 chunk 120 optimal weight: 2.9990 chunk 73 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 83 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 chunk 116 optimal weight: 7.9990 chunk 100 optimal weight: 0.1980 chunk 10 optimal weight: 2.9990 chunk 77 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 overall best weight: 0.8502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.4300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10388 Z= 0.222 Angle : 0.614 9.264 14094 Z= 0.299 Chirality : 0.040 0.169 1606 Planarity : 0.004 0.038 1782 Dihedral : 5.546 89.003 1479 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.58 % Allowed : 18.80 % Favored : 78.63 % 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: 1.80 (0.23), residues: 1274 helix: 2.22 (0.18), residues: 776 sheet: -0.26 (0.43), residues: 135 loop : -0.47 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 352 HIS 0.004 0.001 HIS A 561 PHE 0.018 0.001 PHE A 171 TYR 0.017 0.001 TYR B 92 ARG 0.008 0.000 ARG A 560 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2548 Ramachandran restraints generated. 1274 Oldfield, 0 Emsley, 1274 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 179 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 152 time to evaluate : 1.198 Fit side-chains revert: symmetry clash REVERT: A 128 ASN cc_start: 0.8110 (m-40) cc_final: 0.7751 (m-40) REVERT: A 134 MET cc_start: 0.8271 (tpt) cc_final: 0.8057 (tpt) REVERT: A 145 ASN cc_start: 0.8202 (t0) cc_final: 0.7647 (t0) REVERT: A 168 PHE cc_start: 0.7993 (OUTLIER) cc_final: 0.7669 (m-10) REVERT: A 317 PHE cc_start: 0.6870 (m-10) cc_final: 0.5445 (t80) REVERT: A 502 LYS cc_start: 0.8030 (mtmm) cc_final: 0.7485 (mttp) REVERT: A 512 LEU cc_start: 0.6803 (OUTLIER) cc_final: 0.6461 (mm) REVERT: A 544 MET cc_start: 0.7765 (mmt) cc_final: 0.7502 (mmt) REVERT: A 569 ARG cc_start: 0.7218 (ttt90) cc_final: 0.6835 (ttm110) REVERT: B 240 ARG cc_start: 0.7643 (mtp180) cc_final: 0.6846 (mtm110) REVERT: B 288 LEU cc_start: 0.9187 (tp) cc_final: 0.8930 (tt) REVERT: B 304 ARG cc_start: 0.7607 (ttp80) cc_final: 0.7199 (tmm-80) REVERT: B 319 LYS cc_start: 0.8581 (tppt) cc_final: 0.8306 (mmmt) REVERT: B 475 LEU cc_start: 0.6025 (OUTLIER) cc_final: 0.5804 (mt) outliers start: 27 outliers final: 24 residues processed: 163 average time/residue: 0.2674 time to fit residues: 58.7915 Evaluate side-chains 177 residues out of total 1048 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 22 VAL Chi-restraints excluded: chain A residue 33 LEU Chi-restraints excluded: chain A residue 34 LEU Chi-restraints excluded: chain A residue 59 VAL Chi-restraints excluded: chain A residue 139 SER Chi-restraints excluded: chain A residue 159 LEU Chi-restraints excluded: chain A residue 168 PHE Chi-restraints excluded: chain A residue 314 PHE Chi-restraints excluded: chain A residue 336 GLU Chi-restraints excluded: chain A residue 383 VAL Chi-restraints excluded: chain A residue 430 GLU Chi-restraints excluded: chain A residue 449 THR Chi-restraints excluded: chain A residue 505 LEU Chi-restraints excluded: chain A residue 507 LEU Chi-restraints excluded: chain A residue 512 LEU Chi-restraints excluded: chain A residue 548 THR Chi-restraints excluded: chain A residue 556 LEU Chi-restraints excluded: chain B residue 10 LEU Chi-restraints excluded: chain B residue 40 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 211 VAL Chi-restraints excluded: chain B residue 464 TYR Chi-restraints excluded: chain B residue 475 LEU Chi-restraints excluded: chain C residue 18 LEU Chi-restraints excluded: chain C residue 24 VAL Chi-restraints excluded: chain C residue 30 ASP Chi-restraints excluded: chain C residue 34 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 127 random chunks: chunk 80 optimal weight: 1.9990 chunk 107 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 92 optimal weight: 0.0040 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 100 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 103 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 18 optimal weight: 0.0770 overall best weight: 0.3950 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3952 r_free = 0.3952 target = 0.162087 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.132636 restraints weight = 13658.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.135697 restraints weight = 8947.517| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.137717 restraints weight = 6698.344| |-----------------------------------------------------------------------------| r_work (final): 0.3700 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7604 moved from start: 0.4418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10388 Z= 0.169 Angle : 0.597 8.655 14094 Z= 0.289 Chirality : 0.039 0.175 1606 Planarity : 0.004 0.039 1782 Dihedral : 5.485 87.461 1479 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 8.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 2.48 % Allowed : 19.27 % Favored : 78.24 % 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: 1.86 (0.24), residues: 1274 helix: 2.29 (0.18), residues: 777 sheet: -0.25 (0.43), residues: 133 loop : -0.49 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 114 HIS 0.003 0.001 HIS B 454 PHE 0.020 0.001 PHE A 171 TYR 0.013 0.001 TYR A 593 ARG 0.008 0.000 ARG A 560 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2212.50 seconds wall clock time: 41 minutes 9.55 seconds (2469.55 seconds total)