Starting phenix.real_space_refine on Fri Jul 3 02:39:16 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.cif Found real_map, /net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_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 { restraint_files = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.map" model { file = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7nnl_12478/07_2026/7nnl_12478.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/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: 1.92, per 1000 atoms: 0.17 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: 0.71 Conformation dependent library (CDL) restraints added in 581.2 milliseconds 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: 0.21 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: 1.52 Time building geometry restraints manager: 0.95 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: 6257 22.67 - 45.34: 386 45.34 - 68.00: 79 68.00 - 90.67: 12 90.67 - 113.34: 1 Dihedral angle restraints: 6735 sinusoidal: 2611 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 6732 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: 0.000 Normalize map: mean=0, sd=1: 1.180 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: 0.170 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 9.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 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 : 15.460 113.340 4085 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 6.00 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. 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 ARG 0.017 0.001 ARG B 293 TYR 0.028 0.001 TYR A 381 PHE 0.037 0.002 PHE A 471 TRP 0.022 0.002 TRP B 245 HIS 0.001 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00596 / 0.34 (11289) covalent geometry : angle 0.90900 / 0.47 (15322) hydrogen bonds : bond 0.10694 / 7.80 ( 623) hydrogen bonds : angle 5.37222 / 3.88 ( 1830) *********************** 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 : 0.299 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: 0.0800 time to fit residues: 16.6249 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 : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 98 optimal weight: 1.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 130 optimal weight: 5.9990 chunk 124 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 77 optimal weight: 0.0170 chunk 122 optimal weight: 2.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 5.9990 overall best weight: 0.6820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3668 r_free = 0.3668 target = 0.140559 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3131 r_free = 0.3131 target = 0.099489 restraints weight = 13718.752| |-----------------------------------------------------------------------------| r_work (start): 0.3050 rms_B_bonded: 1.90 r_work: 0.2910 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.0902 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= 0.116 Angle : 0.510 6.998 15322 Z= 0.263 Chirality : 0.039 0.157 1822 Planarity : 0.004 0.055 1918 Dihedral : 10.735 87.919 1686 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 0.96 % Allowed : 5.35 % Favored : 93.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.19 (0.22), residues: 1445 helix: 0.77 (0.18), residues: 844 sheet: -1.25 (0.55), residues: 92 loop : -1.38 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 293 TYR 0.020 0.001 TYR A 381 PHE 0.014 0.001 PHE A 471 TRP 0.010 0.001 TRP B 71 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00264 / 0.12 (11289) covalent geometry : angle 0.50956 / 0.26 (15322) hydrogen bonds : bond 0.03559 / 2.44 ( 623) hydrogen bonds : angle 4.36604 / 3.18 ( 1830) *********************** 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 150 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 139 time to evaluate : 0.403 Fit side-chains REVERT: A 54 ASP cc_start: 0.7543 (t0) cc_final: 0.7318 (t0) REVERT: B 77 LEU cc_start: 0.8170 (OUTLIER) cc_final: 0.7936 (tp) REVERT: B 131 ILE cc_start: 0.7713 (pt) cc_final: 0.7421 (pt) REVERT: B 374 PHE cc_start: 0.5051 (p90) cc_final: 0.4742 (p90) outliers start: 11 outliers final: 6 residues processed: 145 average time/residue: 0.0795 time to fit residues: 17.4893 Evaluate side-chains 131 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 124 time to evaluate : 0.260 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 118 optimal weight: 10.0000 chunk 3 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 67 optimal weight: 5.9990 chunk 54 optimal weight: 0.2980 chunk 98 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 22 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3645 r_free = 0.3645 target = 0.138745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.097297 restraints weight = 13843.345| |-----------------------------------------------------------------------------| r_work (start): 0.3025 rms_B_bonded: 1.85 r_work: 0.2906 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2788 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2788 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8592 moved from start: 0.1162 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= 0.120 Angle : 0.493 7.041 15322 Z= 0.253 Chirality : 0.040 0.133 1822 Planarity : 0.004 0.054 1918 Dihedral : 9.972 88.623 1686 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.23 % Allowed : 8.59 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.12 (0.22), residues: 1445 helix: 1.13 (0.18), residues: 837 sheet: -1.29 (0.57), residues: 82 loop : -1.39 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 438 TYR 0.019 0.001 TYR A 381 PHE 0.012 0.001 PHE A 471 TRP 0.009 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.12 (11289) covalent geometry : angle 0.49335 / 0.25 (15322) hydrogen bonds : bond 0.03475 / 2.37 ( 623) hydrogen bonds : angle 4.24620 / 3.10 ( 1830) *********************** 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 144 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 130 time to evaluate : 0.324 Fit side-chains REVERT: B 77 LEU cc_start: 0.8214 (OUTLIER) cc_final: 0.7980 (tp) REVERT: B 131 ILE cc_start: 0.7713 (pt) cc_final: 0.7453 (pt) REVERT: B 374 PHE cc_start: 0.5113 (p90) cc_final: 0.4811 (p90) outliers start: 14 outliers final: 11 residues processed: 139 average time/residue: 0.0665 time to fit residues: 14.3159 Evaluate side-chains 132 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 120 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 644 LEU 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 72 optimal weight: 3.9990 chunk 140 optimal weight: 0.6980 chunk 133 optimal weight: 0.7980 chunk 120 optimal weight: 6.9990 chunk 49 optimal weight: 0.6980 chunk 109 optimal weight: 10.0000 chunk 74 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3636 r_free = 0.3636 target = 0.137799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.094734 restraints weight = 13886.623| |-----------------------------------------------------------------------------| r_work (start): 0.2962 rms_B_bonded: 1.52 r_work: 0.2869 rms_B_bonded: 2.00 restraints_weight: 0.5000 r_work: 0.2751 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.2751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8619 moved from start: 0.1290 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= 0.131 Angle : 0.498 7.039 15322 Z= 0.255 Chirality : 0.040 0.134 1822 Planarity : 0.004 0.053 1918 Dihedral : 9.690 86.416 1686 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 1.40 % Allowed : 10.17 % Favored : 88.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.22), residues: 1445 helix: 1.22 (0.18), residues: 837 sheet: -1.28 (0.58), residues: 82 loop : -1.37 (0.26), residues: 526 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 438 TYR 0.020 0.001 TYR A 381 PHE 0.010 0.001 PHE A 527 TRP 0.008 0.001 TRP B 71 HIS 0.004 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 (11289) covalent geometry : angle 0.49803 / 0.25 (15322) hydrogen bonds : bond 0.03474 / 2.36 ( 623) hydrogen bonds : angle 4.22538 / 3.08 ( 1830) *********************** 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 143 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 127 time to evaluate : 0.378 Fit side-chains REVERT: A 357 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8718 (mp) REVERT: B 131 ILE cc_start: 0.7686 (pt) cc_final: 0.7425 (pt) outliers start: 16 outliers final: 13 residues processed: 140 average time/residue: 0.0747 time to fit residues: 15.9530 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 : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 443 SER Chi-restraints excluded: chain A residue 508 VAL Chi-restraints excluded: chain C residue 34 PHE 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 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 56 optimal weight: 0.9980 chunk 142 optimal weight: 0.8980 chunk 89 optimal weight: 2.9990 chunk 136 optimal weight: 1.9990 chunk 129 optimal weight: 4.9990 chunk 130 optimal weight: 0.9990 chunk 36 optimal weight: 0.0980 chunk 24 optimal weight: 1.9990 chunk 113 optimal weight: 9.9990 chunk 18 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3642 r_free = 0.3642 target = 0.138367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.096726 restraints weight = 13795.898| |-----------------------------------------------------------------------------| r_work (start): 0.3049 rms_B_bonded: 1.81 r_work: 0.2934 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 11289 Z= 0.105 Angle : 0.484 7.021 15322 Z= 0.247 Chirality : 0.039 0.133 1822 Planarity : 0.004 0.053 1918 Dihedral : 9.211 83.238 1686 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 7.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.84 % Allowed : 11.13 % Favored : 87.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.22), residues: 1445 helix: 1.38 (0.18), residues: 838 sheet: -1.28 (0.58), residues: 82 loop : -1.31 (0.26), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG C 50 TYR 0.018 0.001 TYR A 381 PHE 0.009 0.001 PHE A 260 TRP 0.009 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00240 / 0.10 (11289) covalent geometry : angle 0.48388 / 0.25 (15322) hydrogen bonds : bond 0.03260 / 2.21 ( 623) hydrogen bonds : angle 4.11538 / 3.00 ( 1830) *********************** 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 149 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 128 time to evaluate : 0.385 Fit side-chains REVERT: B 131 ILE cc_start: 0.7696 (pt) cc_final: 0.7448 (pt) outliers start: 21 outliers final: 17 residues processed: 144 average time/residue: 0.0794 time to fit residues: 17.8601 Evaluate side-chains 140 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 123 time to evaluate : 0.392 ------------------------------------------------------------------------------- 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 443 SER 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 332 THR Chi-restraints excluded: chain B residue 398 VAL Chi-restraints excluded: chain B residue 521 ASN 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 126 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 35 optimal weight: 2.9990 chunk 8 optimal weight: 0.2980 chunk 44 optimal weight: 1.9990 chunk 89 optimal weight: 8.9990 chunk 138 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 132 optimal weight: 1.9990 chunk 109 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 30 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.138678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.096866 restraints weight = 13849.026| |-----------------------------------------------------------------------------| r_work (start): 0.2997 rms_B_bonded: 1.87 r_work: 0.2883 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2767 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.1470 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= 0.111 Angle : 0.490 8.794 15322 Z= 0.249 Chirality : 0.039 0.131 1822 Planarity : 0.004 0.053 1918 Dihedral : 8.933 80.963 1686 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 1.93 % Allowed : 11.66 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1445 helix: 1.37 (0.18), residues: 847 sheet: -1.19 (0.58), residues: 81 loop : -1.27 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG C 50 TYR 0.019 0.001 TYR A 381 PHE 0.011 0.001 PHE B 374 TRP 0.008 0.001 TRP B 71 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.11 (11289) covalent geometry : angle 0.48958 / 0.25 (15322) hydrogen bonds : bond 0.03295 / 2.24 ( 623) hydrogen bonds : angle 4.11098 / 3.00 ( 1830) *********************** 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 149 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 127 time to evaluate : 0.384 Fit side-chains REVERT: B 131 ILE cc_start: 0.7635 (pt) cc_final: 0.7372 (pt) REVERT: B 314 LEU cc_start: 0.8884 (OUTLIER) cc_final: 0.8674 (mm) outliers start: 22 outliers final: 18 residues processed: 145 average time/residue: 0.0853 time to fit residues: 19.1717 Evaluate side-chains 142 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 123 time to evaluate : 0.368 ------------------------------------------------------------------------------- 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 SER 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 306 LEU Chi-restraints excluded: chain B residue 314 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 144 random chunks: chunk 51 optimal weight: 5.9990 chunk 109 optimal weight: 3.9990 chunk 107 optimal weight: 8.9990 chunk 99 optimal weight: 0.6980 chunk 45 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 88 optimal weight: 6.9990 chunk 115 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 118 optimal weight: 0.3980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... 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 = 0.3636 r_free = 0.3636 target = 0.137697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.095946 restraints weight = 13703.609| |-----------------------------------------------------------------------------| r_work (start): 0.2984 rms_B_bonded: 1.81 r_work: 0.2867 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2750 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8563 moved from start: 0.1567 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= 0.124 Angle : 0.497 7.608 15322 Z= 0.253 Chirality : 0.040 0.131 1822 Planarity : 0.004 0.052 1918 Dihedral : 8.689 78.278 1686 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.93 % Allowed : 12.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.22), residues: 1445 helix: 1.37 (0.18), residues: 847 sheet: -1.29 (0.58), residues: 81 loop : -1.24 (0.27), residues: 517 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.019 0.001 TYR A 381 PHE 0.011 0.001 PHE B 374 TRP 0.008 0.001 TRP A 115 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.12 (11289) covalent geometry : angle 0.49724 / 0.25 (15322) hydrogen bonds : bond 0.03378 / 2.30 ( 623) hydrogen bonds : angle 4.12852 / 3.00 ( 1830) *********************** 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 145 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 123 time to evaluate : 0.432 Fit side-chains REVERT: B 131 ILE cc_start: 0.7602 (pt) cc_final: 0.7337 (pt) outliers start: 22 outliers final: 20 residues processed: 141 average time/residue: 0.0764 time to fit residues: 16.9661 Evaluate side-chains 140 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 120 time to evaluate : 0.385 ------------------------------------------------------------------------------- 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 SER 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 D residue 14 LEU 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 644 LEU 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 16 optimal weight: 5.9990 chunk 76 optimal weight: 9.9990 chunk 86 optimal weight: 8.9990 chunk 134 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 2.9990 chunk 116 optimal weight: 20.0000 chunk 126 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 130 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.137365 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.094187 restraints weight = 13794.996| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 1.52 r_work: 0.2859 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.25 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8627 moved from start: 0.1619 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= 0.125 Angle : 0.506 10.588 15322 Z= 0.255 Chirality : 0.040 0.134 1822 Planarity : 0.004 0.052 1918 Dihedral : 8.483 75.895 1686 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Rotamer: Outliers : 1.84 % Allowed : 11.92 % Favored : 86.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.22), residues: 1445 helix: 1.41 (0.18), residues: 844 sheet: -1.15 (0.58), residues: 79 loop : -1.21 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.019 0.001 TYR A 381 PHE 0.012 0.001 PHE B 374 TRP 0.008 0.001 TRP A 115 HIS 0.003 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 (11289) covalent geometry : angle 0.50592 / 0.26 (15322) hydrogen bonds : bond 0.03376 / 2.30 ( 623) hydrogen bonds : angle 4.13780 / 3.01 ( 1830) *********************** 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: 21 poor density : 119 time to evaluate : 0.418 Fit side-chains REVERT: B 131 ILE cc_start: 0.7676 (pt) cc_final: 0.7416 (pt) outliers start: 21 outliers final: 21 residues processed: 135 average time/residue: 0.0701 time to fit residues: 15.0516 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 : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET 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 413 GLU Chi-restraints excluded: chain A residue 424 THR Chi-restraints excluded: chain A residue 443 SER 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 D residue 14 LEU 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 644 LEU 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 77 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 54 optimal weight: 0.6980 chunk 110 optimal weight: 6.9990 chunk 34 optimal weight: 3.9990 chunk 100 optimal weight: 0.4980 chunk 115 optimal weight: 3.9990 chunk 120 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 83 optimal weight: 0.7980 chunk 44 optimal weight: 0.0770 overall best weight: 1.2140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3610 r_free = 0.3610 target = 0.135634 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.092123 restraints weight = 13766.734| |-----------------------------------------------------------------------------| r_work (start): 0.2953 rms_B_bonded: 1.52 r_work: 0.2859 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2743 rms_B_bonded: 3.23 restraints_weight: 0.2500 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.1708 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11289 Z= 0.145 Angle : 0.523 9.981 15322 Z= 0.264 Chirality : 0.040 0.141 1822 Planarity : 0.004 0.052 1918 Dihedral : 8.464 72.624 1686 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.84 % Allowed : 12.09 % Favored : 86.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.39 (0.22), residues: 1445 helix: 1.36 (0.18), residues: 844 sheet: -1.35 (0.57), residues: 81 loop : -1.30 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.020 0.001 TYR A 381 PHE 0.012 0.001 PHE B 374 TRP 0.009 0.001 TRP A 115 HIS 0.003 0.001 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00346 / 0.14 (11289) covalent geometry : angle 0.52327 / 0.26 (15322) hydrogen bonds : bond 0.03551 / 2.42 ( 623) hydrogen bonds : angle 4.21421 / 3.06 ( 1830) *********************** 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 138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.264 Fit side-chains REVERT: A 357 LEU cc_start: 0.9102 (OUTLIER) cc_final: 0.8777 (mp) REVERT: B 131 ILE cc_start: 0.7608 (pt) cc_final: 0.7346 (pt) REVERT: B 211 GLN cc_start: 0.6951 (pm20) cc_final: 0.5815 (mm-40) outliers start: 21 outliers final: 20 residues processed: 134 average time/residue: 0.0668 time to fit residues: 14.0176 Evaluate side-chains 138 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 117 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 161 SER 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 443 SER 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 D residue 14 LEU 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 644 LEU 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 130 optimal weight: 9.9990 chunk 21 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 chunk 115 optimal weight: 20.0000 chunk 63 optimal weight: 1.9990 chunk 134 optimal weight: 0.6980 chunk 64 optimal weight: 0.8980 chunk 75 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 97 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 624 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.137540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3064 r_free = 0.3064 target = 0.094371 restraints weight = 13777.162| |-----------------------------------------------------------------------------| r_work (start): 0.2969 rms_B_bonded: 1.52 r_work: 0.2874 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8625 moved from start: 0.1722 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= 0.116 Angle : 0.502 9.770 15322 Z= 0.254 Chirality : 0.040 0.138 1822 Planarity : 0.004 0.052 1918 Dihedral : 8.265 69.367 1686 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.93 % Allowed : 12.27 % Favored : 85.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.53 (0.22), residues: 1445 helix: 1.45 (0.18), residues: 844 sheet: -1.27 (0.60), residues: 74 loop : -1.22 (0.26), residues: 527 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG C 50 TYR 0.019 0.001 TYR A 381 PHE 0.011 0.001 PHE B 374 TRP 0.010 0.001 TRP A 115 HIS 0.002 0.000 HIS A 451 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.12 (11289) covalent geometry : angle 0.50204 / 0.25 (15322) hydrogen bonds : bond 0.03356 / 2.28 ( 623) hydrogen bonds : angle 4.12927 / 3.01 ( 1830) ********************** 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 142 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 120 time to evaluate : 0.374 Fit side-chains REVERT: A 357 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8756 (mp) REVERT: B 131 ILE cc_start: 0.7609 (pt) cc_final: 0.7342 (pt) REVERT: B 380 GLN cc_start: 0.7502 (mm-40) cc_final: 0.6868 (mm-40) outliers start: 22 outliers final: 21 residues processed: 137 average time/residue: 0.0719 time to fit residues: 15.5094 Evaluate side-chains 139 residues out of total 1141 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 117 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 MET 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 443 SER 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 D residue 14 LEU 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 644 LEU Chi-restraints excluded: chain B residue 664 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/iotbx/cli_parser.py", line 987, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( ^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( ^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( ^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1602, in energies_sites pair_proxies = self.pair_proxies( ^^^^^^^^^^^^^^^^^^ File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1505, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/cctbx/geometry_restraints/manager.py", line 1386, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 55.0796 > 50: distance: 74 - 89: 15.104 distance: 78 - 100: 27.427 distance: 83 - 106: 19.259 distance: 87 - 89: 17.167 distance: 88 - 114: 7.557 distance: 89 - 90: 18.639 distance: 90 - 91: 24.584 distance: 90 - 93: 12.449 distance: 91 - 92: 3.667 distance: 91 - 100: 19.578 distance: 92 - 121: 32.695 distance: 93 - 94: 4.980 distance: 94 - 95: 8.571 distance: 95 - 96: 8.315 distance: 96 - 97: 13.354 distance: 97 - 98: 9.323 distance: 97 - 99: 7.241 distance: 100 - 101: 32.376 distance: 101 - 102: 14.097 distance: 101 - 104: 23.912 distance: 102 - 103: 27.378 distance: 102 - 106: 24.795 distance: 103 - 129: 4.509 distance: 104 - 105: 45.603 distance: 106 - 107: 20.460 distance: 107 - 108: 32.178 distance: 107 - 110: 29.985 distance: 108 - 109: 24.780 distance: 108 - 114: 19.412 distance: 109 - 137: 44.225 distance: 110 - 111: 31.977 distance: 110 - 112: 29.693 distance: 111 - 113: 30.431 distance: 114 - 115: 14.504 distance: 115 - 116: 30.128 distance: 115 - 118: 22.589 distance: 116 - 117: 25.879 distance: 116 - 121: 32.521 distance: 118 - 119: 35.111 distance: 118 - 120: 7.774 distance: 121 - 122: 27.876 distance: 122 - 123: 44.362 distance: 122 - 125: 9.801 distance: 123 - 124: 8.842 distance: 123 - 129: 23.914 distance: 125 - 126: 27.427 distance: 125 - 127: 33.797 distance: 126 - 128: 31.528 distance: 129 - 130: 6.084 distance: 130 - 131: 28.634 distance: 130 - 133: 39.311 distance: 131 - 132: 22.794 distance: 131 - 137: 9.167 distance: 133 - 134: 7.232 distance: 134 - 135: 3.911 distance: 134 - 136: 27.996 distance: 137 - 138: 24.823 distance: 138 - 139: 23.723 distance: 138 - 141: 50.859 distance: 139 - 140: 30.699 distance: 139 - 142: 30.952 distance: 142 - 143: 25.827 distance: 143 - 144: 16.726 distance: 143 - 146: 22.644 distance: 144 - 145: 13.419 distance: 144 - 151: 9.656 distance: 146 - 147: 20.467 distance: 147 - 148: 9.189 distance: 148 - 149: 16.582 distance: 149 - 150: 11.424 distance: 151 - 152: 13.896 distance: 152 - 153: 25.136 distance: 152 - 155: 32.810 distance: 153 - 154: 10.981 distance: 153 - 160: 35.930 distance: 155 - 156: 37.306 distance: 156 - 157: 31.067 distance: 157 - 158: 16.849 distance: 157 - 159: 14.259 distance: 160 - 161: 12.255 distance: 161 - 162: 20.850 distance: 161 - 164: 27.330 distance: 162 - 163: 13.525 distance: 162 - 171: 8.208 distance: 164 - 165: 34.434 distance: 165 - 166: 41.958 distance: 166 - 167: 5.271 distance: 167 - 168: 30.313 distance: 168 - 169: 37.828 distance: 168 - 170: 28.013