Starting phenix.real_space_refine on Tue Jul 29 20:32:15 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7nnl_12478/07_2025/7nnl_12478.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnl_12478/07_2025/7nnl_12478.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2025/7nnl_12478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2025/7nnl_12478.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2025/7nnl_12478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2025/7nnl_12478.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.008 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 K 10 8.98 5 P 8 5.49 5 S 63 5.16 5 C 7165 2.51 5 N 1838 2.21 5 O 2015 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 11099 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 4155 Number of conformers: 1 Conformer: "" Number of residues, atoms: 557, 4155 Classifications: {'peptide': 557} Link IDs: {'PTRANS': 25, 'TRANS': 531} Chain: "C" Number of atoms: 1431 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1431 Classifications: {'peptide': 190} Link IDs: {'PTRANS': 13, 'TRANS': 176} Chain: "D" Number of atoms: 200 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 200 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 5072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 682, 5072 Classifications: {'peptide': 682} Link IDs: {'PTRANS': 26, 'TRANS': 655} Chain: "A" Number of atoms: 208 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 208 Unusual residues: {' K': 8, 'CDL': 2} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' K': 2, 'ACP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 6.22, per 1000 atoms: 0.56 Number of scatterers: 11099 At special positions: 0 Unit cell: (97.152, 115.368, 145.728, 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) K 10 19.00 S 63 16.00 P 8 15.00 O 2015 8.00 N 1838 7.00 C 7165 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.54 Conformation dependent library (CDL) restraints added in 1.5 seconds 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 9 sheets defined 62.4% alpha, 5.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 1 through 32 removed outlier: 3.842A pdb=" N ARG A 21 " --> pdb=" O MET A 17 " (cutoff:3.500A) Proline residue: A 22 - end of helix removed outlier: 3.619A pdb=" N ARG A 29 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N LEU A 30 " --> pdb=" O GLY A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 51 Processing helix chain 'A' and resid 58 through 83 Processing helix chain 'A' and resid 84 through 87 removed outlier: 3.734A pdb=" N LEU A 87 " --> pdb=" O GLN A 84 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 98 through 111 removed outlier: 3.692A pdb=" N PHE A 109 " --> pdb=" O THR A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 131 Processing helix chain 'A' and resid 134 through 157 removed outlier: 3.582A pdb=" N ALA A 141 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLY A 144 " --> pdb=" O SER A 140 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N VAL A 147 " --> pdb=" O SER A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 177 Processing helix chain 'A' and resid 178 through 193 removed outlier: 3.889A pdb=" N LEU A 184 " --> pdb=" O PRO A 180 " (cutoff:3.500A) Processing helix chain 'A' and resid 218 through 229 removed outlier: 3.949A pdb=" N GLN A 222 " --> pdb=" O PRO A 218 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 248 through 274 removed outlier: 4.521A pdb=" N ILE A 262 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Proline residue: A 263 - end of helix removed outlier: 3.520A pdb=" N CYS A 267 " --> pdb=" O PRO A 263 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N MET A 274 " --> pdb=" O PHE A 270 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 305 removed outlier: 4.197A pdb=" N GLY A 280 " --> pdb=" O ASP A 276 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N ILE A 290 " --> pdb=" O ALA A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 313 removed outlier: 4.347A pdb=" N LEU A 310 " --> pdb=" O ASN A 306 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N ALA A 311 " --> pdb=" O PRO A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 328 through 342 Processing helix chain 'A' and resid 355 through 368 removed outlier: 3.686A pdb=" N VAL A 361 " --> pdb=" O LEU A 357 " (cutoff:3.500A) Proline residue: A 362 - end of helix Processing helix chain 'A' and resid 382 through 399 removed outlier: 3.843A pdb=" N PHE A 386 " --> pdb=" O GLY A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 438 removed outlier: 4.627A pdb=" N THR A 424 " --> pdb=" O ALA A 420 " (cutoff:3.500A) Proline residue: A 425 - end of helix Processing helix chain 'A' and resid 438 through 443 Processing helix chain 'A' and resid 449 through 465 removed outlier: 4.085A pdb=" N PHE A 453 " --> pdb=" O GLY A 449 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 495 Processing helix chain 'A' and resid 496 through 508 Processing helix chain 'A' and resid 523 through 549 removed outlier: 4.039A pdb=" N PHE A 527 " --> pdb=" O HIS A 523 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ALA A 540 " --> pdb=" O LEU A 536 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N THR A 542 " --> pdb=" O VAL A 538 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N PHE A 543 " --> pdb=" O GLY A 539 " (cutoff:3.500A) Proline residue: A 545 - end of helix removed outlier: 3.933A pdb=" N LEU A 549 " --> pdb=" O PRO A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 550 through 557 Processing helix chain 'C' and resid 4 through 21 removed outlier: 3.548A pdb=" N VAL C 21 " --> pdb=" O ILE C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 34 Processing helix chain 'C' and resid 34 through 39 Processing helix chain 'C' and resid 91 through 109 removed outlier: 3.605A pdb=" N ASP C 95 " --> pdb=" O ASN C 91 " (cutoff:3.500A) Processing helix chain 'C' and resid 133 through 139 Processing helix chain 'C' and resid 140 through 149 Processing helix chain 'C' and resid 151 through 162 Processing helix chain 'C' and resid 168 through 172 removed outlier: 3.650A pdb=" N ILE C 171 " --> pdb=" O VAL C 168 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N GLY C 172 " --> pdb=" O LYS C 169 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 168 through 172' Processing helix chain 'C' and resid 178 through 190 Processing helix chain 'D' and resid 2 through 25 removed outlier: 3.822A pdb=" N GLY D 8 " --> pdb=" O GLY D 4 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 24 removed outlier: 3.658A pdb=" N GLU B 20 " --> pdb=" O GLN B 16 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N ALA B 21 " --> pdb=" O ALA B 17 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N VAL B 22 " --> pdb=" O LEU B 18 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N LYS B 23 " --> pdb=" O LYS B 19 " (cutoff:3.500A) removed outlier: 4.074A pdb=" N LYS B 24 " --> pdb=" O GLU B 20 " (cutoff:3.500A) Processing helix chain 'B' and resid 29 through 32 removed outlier: 3.979A pdb=" N ARG B 32 " --> pdb=" O ALA B 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 29 through 32' Processing helix chain 'B' and resid 33 through 56 Processing helix chain 'B' and resid 61 through 99 removed outlier: 3.569A pdb=" N SER B 65 " --> pdb=" O ASN B 61 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N LEU B 97 " --> pdb=" O GLN B 93 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N GLY B 99 " --> pdb=" O ASN B 95 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 126 removed outlier: 3.671A pdb=" N LEU B 126 " --> pdb=" O ALA B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 155 through 160 Processing helix chain 'B' and resid 198 through 208 Processing helix chain 'B' and resid 215 through 238 Processing helix chain 'B' and resid 238 through 246 removed outlier: 3.991A pdb=" N TRP B 245 " --> pdb=" O PRO B 241 " (cutoff:3.500A) removed outlier: 4.413A pdb=" N GLY B 246 " --> pdb=" O PHE B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 251 through 263 Processing helix chain 'B' and resid 264 through 285 removed outlier: 3.616A pdb=" N LEU B 270 " --> pdb=" O THR B 266 " (cutoff:3.500A) removed outlier: 4.998A pdb=" N SER B 272 " --> pdb=" O GLY B 268 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N ALA B 273 " --> pdb=" O GLY B 269 " (cutoff:3.500A) removed outlier: 3.961A pdb=" N GLY B 275 " --> pdb=" O LEU B 271 " (cutoff:3.500A) removed outlier: 3.837A pdb=" N VAL B 276 " --> pdb=" O SER B 272 " (cutoff:3.500A) Processing helix chain 'B' and resid 291 through 297 removed outlier: 3.752A pdb=" N VAL B 295 " --> pdb=" O SER B 291 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 334 removed outlier: 4.316A pdb=" N ALA B 334 " --> pdb=" O GLU B 330 " (cutoff:3.500A) Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 346 through 356 Processing helix chain 'B' and resid 399 through 405 Processing helix chain 'B' and resid 413 through 415 No H-bonds generated for 'chain 'B' and resid 413 through 415' Processing helix chain 'B' and resid 416 through 427 removed outlier: 3.798A pdb=" N GLN B 426 " --> pdb=" O GLN B 422 " (cutoff:3.500A) removed outlier: 3.678A pdb=" N GLY B 427 " --> pdb=" O VAL B 423 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 463 Processing helix chain 'B' and resid 474 through 486 Processing helix chain 'B' and resid 495 through 510 removed outlier: 3.925A pdb=" N GLY B 510 " --> pdb=" O TYR B 506 " (cutoff:3.500A) Processing helix chain 'B' and resid 519 through 521 No H-bonds generated for 'chain 'B' and resid 519 through 521' Processing helix chain 'B' and resid 522 through 529 Processing helix chain 'B' and resid 539 through 546 Processing helix chain 'B' and resid 557 through 595 removed outlier: 3.702A pdb=" N LEU B 569 " --> pdb=" O GLY B 565 " (cutoff:3.500A) removed outlier: 3.941A pdb=" N ASP B 583 " --> pdb=" O SER B 579 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N VAL B 584 " --> pdb=" O ILE B 580 " (cutoff:3.500A) removed outlier: 4.499A pdb=" N ALA B 585 " --> pdb=" O ALA B 581 " (cutoff:3.500A) Proline residue: B 592 - end of helix Processing helix chain 'B' and resid 599 through 606 removed outlier: 3.687A pdb=" N ALA B 604 " --> pdb=" O GLN B 601 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 631 removed outlier: 4.095A pdb=" N ILE B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.046A pdb=" N VAL B 629 " --> pdb=" O ALA B 625 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 638 Processing helix chain 'B' and resid 645 through 680 removed outlier: 4.167A pdb=" N LEU B 659 " --> pdb=" O TRP B 655 " (cutoff:3.500A) Proline residue: B 665 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 202 through 205 Processing sheet with id=AA2, first strand: chain 'A' and resid 403 through 404 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 45 removed outlier: 6.346A pdb=" N ILE C 43 " --> pdb=" O ARG C 50 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N THR C 48 " --> pdb=" O GLU C 45 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 131 through 132 Processing sheet with id=AA5, first strand: chain 'B' and resid 131 through 135 removed outlier: 7.150A pdb=" N VAL B 188 " --> pdb=" O ILE B 147 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 165 through 167 Processing sheet with id=AA7, first strand: chain 'B' and resid 287 through 289 removed outlier: 6.115A pdb=" N ALA B 532 " --> pdb=" O MET B 548 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N ASP B 550 " --> pdb=" O ALA B 532 " (cutoff:3.500A) removed outlier: 6.428A pdb=" N ALA B 534 " --> pdb=" O ASP B 550 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N VAL B 513 " --> pdb=" O VAL B 531 " (cutoff:3.500A) removed outlier: 7.840A pdb=" N VAL B 533 " --> pdb=" O VAL B 513 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N MET B 515 " --> pdb=" O VAL B 533 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N VAL B 301 " --> pdb=" O LEU B 512 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N ALA B 514 " --> pdb=" O VAL B 301 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N VAL B 303 " --> pdb=" O ALA B 514 " (cutoff:3.500A) removed outlier: 8.126A pdb=" N THR B 516 " --> pdb=" O VAL B 303 " (cutoff:3.500A) removed outlier: 6.561A pdb=" N LEU B 305 " --> pdb=" O THR B 516 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ASP B 302 " --> pdb=" O LYS B 466 " (cutoff:3.500A) removed outlier: 7.847A pdb=" N VAL B 468 " --> pdb=" O ASP B 302 " (cutoff:3.500A) removed outlier: 6.042A pdb=" N LEU B 304 " --> pdb=" O VAL B 468 " (cutoff:3.500A) removed outlier: 6.929A pdb=" N ILE B 470 " --> pdb=" O LEU B 304 " (cutoff:3.500A) removed outlier: 6.065A pdb=" N LEU B 306 " --> pdb=" O ILE B 470 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N ASP B 489 " --> pdb=" O THR B 467 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 373 through 374 removed outlier: 3.643A pdb=" N THR B 373 " --> pdb=" O ASN B 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 393 through 396 removed outlier: 6.490A pdb=" N LEU B 431 " --> pdb=" O VAL B 442 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N VAL B 442 " --> pdb=" O LEU B 431 " (cutoff:3.500A) removed outlier: 7.008A pdb=" N VAL B 433 " --> pdb=" O LEU B 440 " (cutoff:3.500A) 623 hydrogen bonds defined for protein. 1830 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: 3.33 Time building geometry restraints manager: 3.03 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: 1781 1.31 - 1.44: 2759 1.44 - 1.57: 6618 1.57 - 1.69: 15 1.69 - 1.82: 116 Bond restraints: 11289 Sorted by residual: bond pdb=" CB7 CDL A 610 " pdb=" OB8 CDL A 610 " ideal model delta sigma weight residual 1.334 1.424 -0.090 1.10e-02 8.26e+03 6.76e+01 bond pdb=" CB7 CDL A 609 " pdb=" OB8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.421 -0.087 1.10e-02 8.26e+03 6.23e+01 bond pdb=" CA7 CDL A 610 " pdb=" OA8 CDL A 610 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" CA7 CDL A 609 " pdb=" OA8 CDL A 609 " ideal model delta sigma weight residual 1.334 1.415 -0.081 1.10e-02 8.26e+03 5.41e+01 bond pdb=" OB2 CDL A 609 " pdb=" PB2 CDL A 609 " ideal model delta sigma weight residual 1.579 1.667 -0.088 1.50e-02 4.44e+03 3.42e+01 ... (remaining 11284 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.13: 15031 3.13 - 6.25: 260 6.25 - 9.38: 28 9.38 - 12.50: 1 12.50 - 15.63: 2 Bond angle restraints: 15322 Sorted by residual: angle pdb=" C51 CDL A 609 " pdb=" CB5 CDL A 609 " pdb=" OB6 CDL A 609 " ideal model delta sigma weight residual 111.33 120.17 -8.84 1.32e+00 5.72e-01 4.47e+01 angle pdb=" C11 CDL A 610 " pdb=" CA5 CDL A 610 " pdb=" OA6 CDL A 610 " ideal model delta sigma weight residual 111.33 119.96 -8.63 1.32e+00 5.72e-01 4.26e+01 angle pdb=" C11 CDL A 609 " pdb=" CA5 CDL A 609 " pdb=" OA6 CDL A 609 " ideal model delta sigma weight residual 111.33 119.79 -8.46 1.32e+00 5.72e-01 4.09e+01 angle pdb=" C51 CDL A 610 " pdb=" CB5 CDL A 610 " pdb=" OB6 CDL A 610 " ideal model delta sigma weight residual 111.33 119.45 -8.12 1.32e+00 5.72e-01 3.78e+01 angle pdb=" C71 CDL A 610 " pdb=" CB7 CDL A 610 " pdb=" OB8 CDL A 610 " ideal model delta sigma weight residual 111.64 120.94 -9.30 1.65e+00 3.69e-01 3.19e+01 ... (remaining 15317 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.67: 6274 22.67 - 45.34: 408 45.34 - 68.00: 99 68.00 - 90.67: 21 90.67 - 113.34: 1 Dihedral angle restraints: 6803 sinusoidal: 2679 harmonic: 4124 Sorted by residual: dihedral pdb=" CA GLN B 28 " pdb=" C GLN B 28 " pdb=" N ALA B 29 " pdb=" CA ALA B 29 " ideal model delta harmonic sigma weight residual 180.00 152.50 27.50 0 5.00e+00 4.00e-02 3.02e+01 dihedral pdb=" CA ALA A 470 " pdb=" C ALA A 470 " pdb=" N PHE A 471 " pdb=" CA PHE A 471 " ideal model delta harmonic sigma weight residual 180.00 157.30 22.70 0 5.00e+00 4.00e-02 2.06e+01 dihedral pdb=" CA MET A 397 " pdb=" C MET A 397 " pdb=" N ILE A 398 " pdb=" CA ILE A 398 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 ... (remaining 6800 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 1477 0.059 - 0.117: 312 0.117 - 0.175: 29 0.175 - 0.234: 3 0.234 - 0.292: 1 Chirality restraints: 1822 Sorted by residual: chirality pdb=" CB VAL B 664 " pdb=" CA VAL B 664 " pdb=" CG1 VAL B 664 " pdb=" CG2 VAL B 664 " both_signs ideal model delta sigma weight residual False -2.63 -2.34 -0.29 2.00e-01 2.50e+01 2.14e+00 chirality pdb=" CB ILE B 388 " pdb=" CA ILE B 388 " pdb=" CG1 ILE B 388 " pdb=" CG2 ILE B 388 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.36e+00 chirality pdb=" CA THR A 424 " pdb=" N THR A 424 " pdb=" C THR A 424 " pdb=" CB THR A 424 " both_signs ideal model delta sigma weight residual False 2.53 2.31 0.21 2.00e-01 2.50e+01 1.13e+00 ... (remaining 1819 not shown) Planarity restraints: 1918 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR B 495 " -0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 496 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 496 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 496 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE A 262 " 0.038 5.00e-02 4.00e+02 5.63e-02 5.07e+00 pdb=" N PRO A 263 " -0.097 5.00e-02 4.00e+02 pdb=" CA PRO A 263 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 263 " 0.032 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 471 " -0.019 2.00e-02 2.50e+03 1.62e-02 4.60e+00 pdb=" CG PHE A 471 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE A 471 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 471 " -0.005 2.00e-02 2.50e+03 pdb=" CE1 PHE A 471 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 471 " -0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 471 " -0.004 2.00e-02 2.50e+03 ... (remaining 1915 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.81: 3035 2.81 - 3.39: 12359 3.39 - 3.98: 21822 3.98 - 4.56: 31303 4.56 - 5.14: 45662 Nonbonded interactions: 114181 Sorted by model distance: nonbonded pdb=" OG SER B 90 " pdb=" O VAL B 207 " model vdw 2.230 3.040 nonbonded pdb=" OE2 GLU A 321 " pdb=" OG SER C 85 " model vdw 2.249 3.040 nonbonded pdb=" O VAL A 107 " pdb=" OG1 THR A 111 " model vdw 2.274 3.040 nonbonded pdb=" OG1 THR B 47 " pdb=" OG SER B 69 " model vdw 2.290 3.040 nonbonded pdb=" OG1 THR A 401 " pdb=" OD2 ASP B 300 " model vdw 2.300 3.040 ... (remaining 114176 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 0.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.380 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 26.760 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 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 : 0.006 0.090 11289 Z= 0.342 Angle : 0.909 15.629 15322 Z= 0.474 Chirality : 0.046 0.292 1822 Planarity : 0.006 0.063 1918 Dihedral : 16.458 113.340 4153 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 0.00 % Allowed : 0.09 % Favored : 99.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.21), residues: 1445 helix: -0.08 (0.17), residues: 855 sheet: -1.21 (0.58), residues: 79 loop : -1.53 (0.26), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 245 HIS 0.001 0.000 HIS A 451 PHE 0.037 0.002 PHE A 471 TYR 0.028 0.001 TYR A 381 ARG 0.017 0.001 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.10694 ( 623) hydrogen bonds : angle 5.37222 ( 1830) covalent geometry : bond 0.00596 (11289) covalent geometry : angle 0.90900 (15322) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 139 time to evaluate : 1.230 Fit side-chains REVERT: B 186 TRP cc_start: 0.7531 (p-90) cc_final: 0.6664 (p-90) REVERT: B 374 PHE cc_start: 0.4949 (p90) cc_final: 0.4645 (p90) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2162 time to fit residues: 44.4154 Evaluate side-chains 123 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 123 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 121 optimal weight: 7.9990 chunk 109 optimal weight: 8.9990 chunk 60 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 58 optimal weight: 0.4980 chunk 112 optimal weight: 5.9990 chunk 43 optimal weight: 1.9990 chunk 68 optimal weight: 0.9990 chunk 84 optimal weight: 3.9990 chunk 130 optimal weight: 5.9990 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 114 ASN B 30 GLN B 624 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.135789 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3065 r_free = 0.3065 target = 0.094033 restraints weight = 13563.746| |-----------------------------------------------------------------------------| r_work (start): 0.2989 rms_B_bonded: 1.72 r_work: 0.2873 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.2755 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2755 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.1042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 11289 Z= 0.169 Angle : 0.552 7.051 15322 Z= 0.283 Chirality : 0.041 0.147 1822 Planarity : 0.004 0.054 1918 Dihedral : 13.037 89.197 1754 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 0.88 % Allowed : 5.78 % Favored : 93.34 % 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: -0.34 (0.22), residues: 1445 helix: 0.70 (0.18), residues: 839 sheet: -1.36 (0.54), residues: 93 loop : -1.49 (0.26), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.018 0.001 PHE A 471 TYR 0.021 0.001 TYR A 381 ARG 0.006 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03902 ( 623) hydrogen bonds : angle 4.48921 ( 1830) covalent geometry : bond 0.00403 (11289) covalent geometry : angle 0.55206 (15322) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 131 time to evaluate : 1.097 Fit side-chains REVERT: A 357 LEU cc_start: 0.9175 (OUTLIER) cc_final: 0.8788 (mp) REVERT: B 77 LEU cc_start: 0.8220 (OUTLIER) cc_final: 0.7991 (tp) REVERT: B 131 ILE cc_start: 0.7664 (pt) cc_final: 0.7387 (pt) REVERT: B 374 PHE cc_start: 0.5109 (p90) cc_final: 0.4806 (p90) outliers start: 10 outliers final: 6 residues processed: 137 average time/residue: 0.1910 time to fit residues: 40.0235 Evaluate side-chains 129 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 121 time to evaluate : 1.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 206 MET Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 55 optimal weight: 4.9990 chunk 26 optimal weight: 2.9990 chunk 67 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 chunk 12 optimal weight: 0.0770 chunk 23 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 0 optimal weight: 5.9990 chunk 96 optimal weight: 0.7980 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.138148 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.096313 restraints weight = 13848.704| |-----------------------------------------------------------------------------| r_work (start): 0.3012 rms_B_bonded: 1.76 r_work: 0.2895 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2778 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2778 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 moved from start: 0.1198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11289 Z= 0.114 Angle : 0.495 7.044 15322 Z= 0.254 Chirality : 0.039 0.175 1822 Planarity : 0.004 0.055 1918 Dihedral : 11.954 89.850 1754 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.31 % Allowed : 9.29 % Favored : 89.40 % 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: 0.08 (0.22), residues: 1445 helix: 1.09 (0.18), residues: 837 sheet: -1.30 (0.57), residues: 82 loop : -1.40 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.013 0.001 PHE A 260 TYR 0.019 0.001 TYR A 381 ARG 0.004 0.000 ARG B 293 Details of bonding type rmsd hydrogen bonds : bond 0.03467 ( 623) hydrogen bonds : angle 4.26811 ( 1830) covalent geometry : bond 0.00263 (11289) covalent geometry : angle 0.49537 (15322) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 133 time to evaluate : 1.237 Fit side-chains REVERT: A 445 MET cc_start: 0.8221 (ttm) cc_final: 0.8016 (mtt) REVERT: B 374 PHE cc_start: 0.5120 (p90) cc_final: 0.4812 (p90) outliers start: 15 outliers final: 14 residues processed: 145 average time/residue: 0.2015 time to fit residues: 44.2052 Evaluate side-chains 133 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 119 time to evaluate : 1.189 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 77 LEU Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 10 optimal weight: 1.9990 chunk 141 optimal weight: 0.6980 chunk 31 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 76 optimal weight: 9.9990 chunk 120 optimal weight: 9.9990 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 4.9990 chunk 98 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 112 optimal weight: 6.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.136640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3051 r_free = 0.3051 target = 0.093516 restraints weight = 13742.250| |-----------------------------------------------------------------------------| r_work (start): 0.2940 rms_B_bonded: 1.51 r_work: 0.2842 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2727 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11289 Z= 0.148 Angle : 0.513 7.041 15322 Z= 0.262 Chirality : 0.041 0.142 1822 Planarity : 0.004 0.053 1918 Dihedral : 11.693 88.098 1754 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.40 % Allowed : 10.96 % Favored : 87.64 % 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: 0.13 (0.22), residues: 1445 helix: 1.14 (0.18), residues: 838 sheet: -1.30 (0.58), residues: 82 loop : -1.39 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE A 471 TYR 0.020 0.001 TYR A 381 ARG 0.003 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 623) hydrogen bonds : angle 4.28483 ( 1830) covalent geometry : bond 0.00356 (11289) covalent geometry : angle 0.51264 (15322) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 123 time to evaluate : 1.125 Fit side-chains REVERT: A 357 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8718 (mp) REVERT: B 131 ILE cc_start: 0.7715 (pt) cc_final: 0.7459 (pt) outliers start: 16 outliers final: 13 residues processed: 135 average time/residue: 0.2482 time to fit residues: 52.5383 Evaluate side-chains 134 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 120 time to evaluate : 1.843 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 5 optimal weight: 1.9990 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 96 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 17 optimal weight: 2.9990 chunk 116 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.135681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.091962 restraints weight = 13763.137| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 1.52 r_work: 0.2848 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2731 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2731 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11289 Z= 0.154 Angle : 0.517 7.040 15322 Z= 0.264 Chirality : 0.041 0.154 1822 Planarity : 0.004 0.052 1918 Dihedral : 11.333 86.346 1754 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 7.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.10 % Allowed : 11.22 % Favored : 86.68 % 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: 0.20 (0.22), residues: 1445 helix: 1.20 (0.18), residues: 836 sheet: -1.30 (0.58), residues: 82 loop : -1.37 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 71 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE B 374 TYR 0.020 0.001 TYR A 381 ARG 0.002 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03656 ( 623) hydrogen bonds : angle 4.29934 ( 1830) covalent geometry : bond 0.00370 (11289) covalent geometry : angle 0.51746 (15322) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 122 time to evaluate : 1.272 Fit side-chains REVERT: A 357 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8770 (mp) REVERT: B 131 ILE cc_start: 0.7715 (pt) cc_final: 0.7470 (pt) outliers start: 24 outliers final: 17 residues processed: 138 average time/residue: 0.2474 time to fit residues: 52.4137 Evaluate side-chains 137 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.500 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 348 ILE Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 397 MET Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 77 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 126 optimal weight: 0.8980 chunk 132 optimal weight: 0.9990 chunk 88 optimal weight: 0.1980 chunk 11 optimal weight: 0.3980 chunk 34 optimal weight: 4.9990 chunk 99 optimal weight: 0.1980 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.5980 chunk 64 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.138957 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.096108 restraints weight = 13788.315| |-----------------------------------------------------------------------------| r_work (start): 0.2974 rms_B_bonded: 1.51 r_work: 0.2879 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2765 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8299 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11289 Z= 0.097 Angle : 0.476 7.020 15322 Z= 0.245 Chirality : 0.039 0.131 1822 Planarity : 0.004 0.053 1918 Dihedral : 10.798 86.217 1754 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 2.10 % Allowed : 11.74 % Favored : 86.15 % 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: 0.52 (0.23), residues: 1445 helix: 1.48 (0.18), residues: 837 sheet: -1.23 (0.58), residues: 82 loop : -1.25 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.013 0.001 PHE B 374 TYR 0.018 0.001 TYR A 381 ARG 0.003 0.000 ARG B 438 Details of bonding type rmsd hydrogen bonds : bond 0.03230 ( 623) hydrogen bonds : angle 4.10210 ( 1830) covalent geometry : bond 0.00213 (11289) covalent geometry : angle 0.47576 (15322) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 129 time to evaluate : 1.094 Fit side-chains REVERT: B 131 ILE cc_start: 0.7713 (pt) cc_final: 0.7453 (pt) outliers start: 24 outliers final: 16 residues processed: 145 average time/residue: 0.1946 time to fit residues: 42.8713 Evaluate side-chains 138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 122 time to evaluate : 1.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 644 LEU Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 76 optimal weight: 9.9990 chunk 103 optimal weight: 1.9990 chunk 85 optimal weight: 2.9990 chunk 87 optimal weight: 5.9990 chunk 39 optimal weight: 0.7980 chunk 50 optimal weight: 0.0070 chunk 116 optimal weight: 20.0000 chunk 106 optimal weight: 6.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 115 optimal weight: 2.9990 overall best weight: 1.7604 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.135274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.091386 restraints weight = 13963.100| |-----------------------------------------------------------------------------| r_work (start): 0.2931 rms_B_bonded: 1.52 r_work: 0.2838 rms_B_bonded: 1.98 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 3.20 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 11289 Z= 0.185 Angle : 0.546 7.064 15322 Z= 0.278 Chirality : 0.042 0.135 1822 Planarity : 0.004 0.051 1918 Dihedral : 10.857 84.084 1754 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.84 % Allowed : 12.45 % Favored : 85.71 % 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: 1445 helix: 1.29 (0.18), residues: 837 sheet: -1.38 (0.58), residues: 82 loop : -1.37 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 PHE 0.012 0.001 PHE A 471 TYR 0.020 0.001 TYR A 381 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03794 ( 623) hydrogen bonds : angle 4.31287 ( 1830) covalent geometry : bond 0.00449 (11289) covalent geometry : angle 0.54615 (15322) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 119 time to evaluate : 1.566 Fit side-chains REVERT: A 357 LEU cc_start: 0.9089 (OUTLIER) cc_final: 0.8755 (mp) REVERT: B 131 ILE cc_start: 0.7715 (pt) cc_final: 0.7459 (pt) outliers start: 21 outliers final: 17 residues processed: 136 average time/residue: 0.2242 time to fit residues: 47.3250 Evaluate side-chains 136 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 118 time to evaluate : 1.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 318 ILE Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 69 optimal weight: 0.7980 chunk 54 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 109 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 77 optimal weight: 0.0070 chunk 34 optimal weight: 0.5980 chunk 112 optimal weight: 0.0030 chunk 44 optimal weight: 2.9990 overall best weight: 0.4208 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.138671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3083 r_free = 0.3083 target = 0.095528 restraints weight = 13737.122| |-----------------------------------------------------------------------------| r_work (start): 0.3017 rms_B_bonded: 1.51 r_work: 0.2923 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.2808 rms_B_bonded: 3.26 restraints_weight: 0.2500 r_work (final): 0.2808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8350 moved from start: 0.1657 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 11289 Z= 0.100 Angle : 0.489 7.028 15322 Z= 0.249 Chirality : 0.039 0.132 1822 Planarity : 0.004 0.053 1918 Dihedral : 10.379 84.036 1754 Min Nonbonded Distance : 2.396 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.58 % Allowed : 12.45 % Favored : 85.98 % 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: 0.55 (0.23), residues: 1445 helix: 1.52 (0.18), residues: 841 sheet: -1.41 (0.57), residues: 82 loop : -1.24 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 PHE 0.013 0.001 PHE B 374 TYR 0.018 0.001 TYR A 381 ARG 0.005 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03240 ( 623) hydrogen bonds : angle 4.09415 ( 1830) covalent geometry : bond 0.00226 (11289) covalent geometry : angle 0.48880 (15322) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 122 time to evaluate : 1.439 Fit side-chains REVERT: A 246 ASN cc_start: 0.8853 (t0) cc_final: 0.8538 (t0) REVERT: A 413 GLU cc_start: 0.8587 (OUTLIER) cc_final: 0.8243 (pm20) REVERT: B 131 ILE cc_start: 0.7667 (pt) cc_final: 0.7404 (pt) outliers start: 18 outliers final: 17 residues processed: 138 average time/residue: 0.1987 time to fit residues: 42.1098 Evaluate side-chains 137 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 119 time to evaluate : 1.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 124 optimal weight: 9.9990 chunk 39 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 chunk 119 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 137 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.3636 r_free = 0.3636 target = 0.137856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.095834 restraints weight = 13774.606| |-----------------------------------------------------------------------------| r_work (start): 0.3014 rms_B_bonded: 1.87 r_work: 0.2898 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.2780 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8328 moved from start: 0.1690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11289 Z= 0.119 Angle : 0.497 7.030 15322 Z= 0.253 Chirality : 0.040 0.130 1822 Planarity : 0.004 0.052 1918 Dihedral : 10.286 83.246 1754 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.58 % Allowed : 12.53 % Favored : 85.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1445 helix: 1.50 (0.18), residues: 839 sheet: -1.48 (0.56), residues: 82 loop : -1.23 (0.27), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 PHE 0.013 0.001 PHE B 374 TYR 0.019 0.001 TYR A 381 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03350 ( 623) hydrogen bonds : angle 4.12057 ( 1830) covalent geometry : bond 0.00278 (11289) covalent geometry : angle 0.49683 (15322) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 121 time to evaluate : 1.245 Fit side-chains REVERT: B 131 ILE cc_start: 0.7615 (pt) cc_final: 0.7351 (pt) outliers start: 18 outliers final: 18 residues processed: 137 average time/residue: 0.1941 time to fit residues: 41.5786 Evaluate side-chains 138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 120 time to evaluate : 1.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 54 optimal weight: 0.5980 chunk 115 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 120 optimal weight: 10.0000 chunk 109 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 93 optimal weight: 3.9990 chunk 71 optimal weight: 0.0040 chunk 67 optimal weight: 5.9990 chunk 128 optimal weight: 7.9990 chunk 5 optimal weight: 0.7980 overall best weight: 1.2594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 30 GLN B 624 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.136058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.092419 restraints weight = 13798.200| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.51 r_work: 0.2834 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2719 rms_B_bonded: 3.21 restraints_weight: 0.2500 r_work (final): 0.2719 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8360 moved from start: 0.1770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11289 Z= 0.146 Angle : 0.521 7.043 15322 Z= 0.264 Chirality : 0.041 0.130 1822 Planarity : 0.004 0.051 1918 Dihedral : 10.314 81.498 1754 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 1.84 % Allowed : 12.45 % Favored : 85.71 % 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: 0.41 (0.22), residues: 1445 helix: 1.40 (0.18), residues: 838 sheet: -1.53 (0.56), residues: 82 loop : -1.28 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 PHE 0.011 0.001 PHE B 374 TYR 0.020 0.001 TYR A 381 ARG 0.003 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03584 ( 623) hydrogen bonds : angle 4.21591 ( 1830) covalent geometry : bond 0.00350 (11289) covalent geometry : angle 0.52083 (15322) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2890 Ramachandran restraints generated. 1445 Oldfield, 0 Emsley, 1445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 118 time to evaluate : 1.171 Fit side-chains REVERT: A 357 LEU cc_start: 0.9077 (OUTLIER) cc_final: 0.8738 (mp) REVERT: B 131 ILE cc_start: 0.7712 (pt) cc_final: 0.7458 (pt) REVERT: B 211 GLN cc_start: 0.6932 (pm20) cc_final: 0.5801 (mm-40) outliers start: 21 outliers final: 19 residues processed: 137 average time/residue: 0.1885 time to fit residues: 40.1373 Evaluate side-chains 138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 118 time to evaluate : 1.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 161 SER Chi-restraints excluded: chain A residue 205 ASN Chi-restraints excluded: chain A residue 329 VAL Chi-restraints excluded: chain A residue 357 LEU Chi-restraints excluded: chain A residue 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE Chi-restraints excluded: chain C residue 168 VAL Chi-restraints excluded: chain C residue 189 ASP Chi-restraints excluded: chain B residue 14 VAL Chi-restraints excluded: chain B residue 30 GLN Chi-restraints excluded: chain B residue 147 ILE Chi-restraints excluded: chain B residue 165 VAL Chi-restraints excluded: chain B residue 215 THR Chi-restraints excluded: chain B residue 253 THR Chi-restraints excluded: chain B residue 306 LEU Chi-restraints excluded: chain B residue 332 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 64 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 chunk 137 optimal weight: 0.9980 chunk 56 optimal weight: 0.8980 chunk 90 optimal weight: 10.0000 chunk 111 optimal weight: 3.9990 overall best weight: 0.7338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3629 r_free = 0.3629 target = 0.137152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3057 r_free = 0.3057 target = 0.093862 restraints weight = 13688.633| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 1.50 r_work: 0.2900 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2785 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2785 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1758 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 11289 Z= 0.114 Angle : 0.500 7.020 15322 Z= 0.255 Chirality : 0.040 0.128 1822 Planarity : 0.004 0.052 1918 Dihedral : 10.192 81.197 1754 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.67 % Allowed : 12.62 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.23), residues: 1445 helix: 1.50 (0.18), residues: 838 sheet: -1.40 (0.57), residues: 80 loop : -1.24 (0.27), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 PHE 0.011 0.001 PHE B 374 TYR 0.018 0.001 TYR A 381 ARG 0.004 0.000 ARG C 50 Details of bonding type rmsd hydrogen bonds : bond 0.03389 ( 623) hydrogen bonds : angle 4.14184 ( 1830) covalent geometry : bond 0.00264 (11289) covalent geometry : angle 0.50039 (15322) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6658.57 seconds wall clock time: 118 minutes 5.40 seconds (7085.40 seconds total)